From ebeea43264c1b07ed78f7444abf6e1af406dd989 Mon Sep 17 00:00:00 2001 From: dsokus Date: Wed, 2 Mar 2011 21:52:14 -0500 Subject: [PATCH 001/187] test --- gtfold-mfe/README | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 34a28f1..ee48a23 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -1,3 +1,5 @@ +test + GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction (C) 2007-2010, David A. Bader From 06a3802a3458dce7411246b4c164dad57d02b443 Mon Sep 17 00:00:00 2001 From: dsokus Date: Wed, 2 Mar 2011 21:52:45 -0500 Subject: [PATCH 002/187] test text removed --- gtfold-mfe/README | 2 -- 1 file changed, 2 deletions(-) diff --git a/gtfold-mfe/README b/gtfold-mfe/README index ee48a23..34a28f1 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -1,5 +1,3 @@ -test - GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction (C) 2007-2010, David A. Bader From b76b9c12cbcf32f7e022de58268db1358b4c8149 Mon Sep 17 00:00:00 2001 From: dsokus Date: Wed, 2 Mar 2011 22:42:11 -0500 Subject: [PATCH 003/187] committing a small text file to test if my Github setup works. Signed-off-by: dsokus --- gtfold-mfe/test.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 gtfold-mfe/test.txt diff --git a/gtfold-mfe/test.txt b/gtfold-mfe/test.txt new file mode 100644 index 0000000..229c9b9 --- /dev/null +++ b/gtfold-mfe/test.txt @@ -0,0 +1 @@ +this is to test how my Git setup works - Zs \ No newline at end of file From c4bbb863a303aabb19be14947dbd228f56d72384 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 2 Mar 2011 06:41:16 +0800 Subject: [PATCH 004/187] fixed constraint handling issue - forbid adjacent bp pairing --- gtfold-mfe/src/traceback.c | 3 +++ 1 file changed, 3 insertions(+) diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index dff6ae9..fe408dc 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -37,6 +37,7 @@ #include "algorithms.h" #include "traceback.h" +#define TURN 3 int total_en = 0; void trace(int len) { @@ -68,6 +69,7 @@ void traceW(int j) { if (j == 0 || j == 1) return; for (i = 1; i < j && !done; i++) { + if (j-i < TURN) continue; wim1 = MIN ( 0, W[i-1] ); flag = 1; if (wim1 != W[i-1]) flag = 0; @@ -140,6 +142,7 @@ void traceW(int j) { /* Trace the structure inside V[i][j]. This function traces "which type of loop (i,j) base pair is closing" */ int traceV(int i, int j) { int a, b, c, d, Vij; + if (j-i < TURN) return INFINITY_; a = eH(i, j); b = eS(i, j) + V[indx[i + 1] + j - 1]; From 290afc1e3a9c3351484340715151db83d9ca1eb2 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 2 Mar 2011 06:42:18 +0800 Subject: [PATCH 005/187] place ct file in current working dir --- gtfold-mfe/src/main.cc | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 609e373..b6f3f0f 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -538,10 +538,15 @@ int main(int argc, char** argv) { t1 = get_seconds() - t1; fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1); + size_t pos = 0; std::string suboptfile; suboptfile += argv[fileIndex]; + + if ((pos=suboptfile.find_last_of('/')) > 0) { + suboptfile = suboptfile.substr(pos+1); + } - // if an extension exists, replace it with ct + // if an extension exists, replace it with struct if(suboptfile.find(".") != string::npos) suboptfile.erase(suboptfile.rfind(".")); suboptfile += ".struct"; @@ -594,7 +599,12 @@ int main(int argc, char** argv) { // or build off the input file else { + size_t pos; outputfile += argv[fileIndex]; + + if ((pos=outputfile.find_last_of('/')) > 0) { + outputfile = outputfile.substr(pos+1); + } // if an extension exists, replace it with ct if(outputfile.find(".") != string::npos) From c4401f55b7a349e51ba37de11d9828d230d8d9f2 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 2 Mar 2011 06:42:35 +0800 Subject: [PATCH 006/187] minor code cleanup --- gtfold-mfe/src/algorithms.c | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 83f94d6..3006431 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -205,7 +205,6 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr #endif #endif - //printf("starting.......\n"); /* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/ @@ -266,19 +265,9 @@ int calculate(int len, int **forceList, int **prohibitList, int forcelen, int pr } } -/* - for(j=2; j<=len; j++){ - for (i=j-1; i>0; i--){ - printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]); - } - } -*/ - for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/ calcW(j); - //printV(len); - return W[len]; } /* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP @@ -1218,10 +1207,6 @@ void calcW(int j) { W[j] = Wj; - //printf(",W%dset: %d\n", j, W[j]); - - // if(j==11 || j==35 || j==36) - // printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]); return; } From 1acf3aa83bd980ea5b42f58403c42fa1781fe205 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 13 Apr 2011 12:30:47 -0400 Subject: [PATCH 007/187] fixed bug on reading of sequence --- gtfold-mfe/src/main.cc | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index f9ca8a2..e976d49 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -85,16 +85,14 @@ int read_sequence_file(const char* filename, std::string& seq) { ifstream fs; fs.open(filename, ios::in); - if (fs == NULL) - return FAILURE; + if (!fs.good()) return FAILURE; string line; - getline(fs, line); - while(line.length() > 0) { + while(fs.good()) { + getline(fs, line); // exclude lines starting with FASTA comment characters - if(line[0] != ';' && line[0] != '>') + if(line[0] != ';' && line[0] != '>' && line.length() > 0) seq += line; - getline(fs, line); } fs.close(); From 51abea3dc8f59d4532431010563d279720681178 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 14 Apr 2011 14:15:24 -0400 Subject: [PATCH 008/187] program crashed when run with unambiguous bases sequence, fixed this --- gtfold-mfe/src/energy.c | 46 ++++++++++++++++++++--------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 80f37c3..afed6ec 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -16,8 +16,9 @@ int *VM; int **WM; int *indx; -void create_tables(int len) -{ +int alloc_flag = 0; + +void create_tables(int len) { V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); if (V == NULL) { perror("Cannot allocate variable 'V'"); @@ -74,12 +75,13 @@ void create_tables(int len) exit(-1); } + alloc_flag = 1; + init_tables(len); } -void init_tables(int len) -{ +void init_tables(int len) { int i, j, LLL; for (i = 0; i <= len; i++) { @@ -105,21 +107,21 @@ void init_tables(int len) return; } -void free_tables(int len) -{ - free(indx); - - int i; - for (i = 0; i <= len; i++) - free(WM[i]); - free(WM); - - free(VM); - free(VBI); - free(V); - free(VV); - free(VV1); - free(W); +void free_tables(int len) { + if (alloc_flag == 1) { + free(indx); + + int i; + for (i = 0; i <= len; i++) free(WM[i]); + free(WM); + + free(VM); + free(VBI); + free(V); + free(VV); + free(VV1); + free(W); + } } @@ -215,8 +217,7 @@ inline int eL(int i, int j, int ip, int jp) { return energy; } -inline int eH(int i, int j) -{ +inline int eH(int i, int j) { /* Hairpin loop for all the bases between i and j */ /* size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */ int size; @@ -321,8 +322,7 @@ inline int eH(int i, int j) return energy; } -inline int eS(int i, int j) -{ +inline int eS(int i, int j) { int energy; /* not sure about eparam[1], come from MFold.. = 0 */ energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1]; From 3f0046e514507988c31737738b014003b72b4abd Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 22 Apr 2011 13:43:35 -0400 Subject: [PATCH 009/187] removed printing of seq contents --- gtfold-mfe/src/options.cc | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 06c28c9..1bc103c 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -172,7 +172,6 @@ void printRunConfiguration(string seq) { printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); printf("- input file: %s\n", seqfile.c_str()); - printf(" - sequence length: %d\n", (int)seq.length()); - printf(" - sequence contents: %s\n", seq.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); printf("- output file: %s\n", outputFile.c_str()); } From 27383c24901a8087145b80c1bb62f6f7295f6c7a Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 28 Apr 2011 09:59:48 -0400 Subject: [PATCH 010/187] adding data files in new format --- gtfold-mfe/data/Turner99/dangle.DAT | 8 + gtfold-mfe/data/Turner99/int11.DAT | 24 + gtfold-mfe/data/Turner99/int21.DAT | 96 ++++ gtfold-mfe/data/Turner99/int22.DAT | 648 ++++++++++++++++++++++++++ gtfold-mfe/data/Turner99/loop.DAT | 30 ++ gtfold-mfe/data/Turner99/miscloop.DAT | 12 + gtfold-mfe/data/Turner99/sint2.DAT | 24 + gtfold-mfe/data/Turner99/sint4.DAT | 576 +++++++++++++++++++++++ gtfold-mfe/data/Turner99/stack.DAT | 16 + gtfold-mfe/data/Turner99/tloop.DAT | 30 ++ gtfold-mfe/data/Turner99/tstackh.DAT | 16 + gtfold-mfe/data/Turner99/tstacki.DAT | 16 + gtfold-mfe/data/Turner99/tstackm.DAT | 16 + 13 files changed, 1512 insertions(+) create mode 100644 gtfold-mfe/data/Turner99/dangle.DAT create mode 100644 gtfold-mfe/data/Turner99/int11.DAT create mode 100644 gtfold-mfe/data/Turner99/int21.DAT create mode 100644 gtfold-mfe/data/Turner99/int22.DAT create mode 100644 gtfold-mfe/data/Turner99/loop.DAT create mode 100644 gtfold-mfe/data/Turner99/miscloop.DAT create mode 100644 gtfold-mfe/data/Turner99/sint2.DAT create mode 100644 gtfold-mfe/data/Turner99/sint4.DAT create mode 100644 gtfold-mfe/data/Turner99/stack.DAT create mode 100644 gtfold-mfe/data/Turner99/tloop.DAT create mode 100644 gtfold-mfe/data/Turner99/tstackh.DAT create mode 100644 gtfold-mfe/data/Turner99/tstacki.DAT create mode 100644 gtfold-mfe/data/Turner99/tstackm.DAT diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT new file mode 100644 index 0000000..9fb7c28 --- /dev/null +++ b/gtfold-mfe/data/Turner99/dangle.DAT @@ -0,0 +1,8 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -0.50 -0.80 -0.60 +inf inf inf inf inf inf inf inf -1.70 -0.80 -1.70 -1.20 inf inf inf inf +inf inf inf inf -1.10 -0.40 -1.30 -0.60 inf inf inf inf -0.80 -0.50 -0.80 -0.60 +-0.70 -0.10 -0.70 -0.10 inf inf inf inf -0.70 -0.10 -0.70 -0.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.10 -0.20 -0.20 +inf inf inf inf inf inf inf inf -0.20 -0.30 -0.0 -0.0 inf inf inf inf +inf inf inf inf -0.50 -0.30 -0.20 -0.10 inf inf inf inf -0.30 -0.10 -0.20 -0.20 +-0.30 -0.30 -0.40 -0.20 inf inf inf inf -0.30 -0.30 -0.40 -0.20 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/int11.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 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.50 .50 +3.40 .00 .40 +10.10 -0.30 -0.30 +0.50 +-2.20 +0.30 +1.60 +1.40 +4.10 +1 diff --git a/gtfold-mfe/data/Turner99/sint2.DAT b/gtfold-mfe/data/Turner99/sint2.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/sint2.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 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inf inf inf -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf inf inf -2.20 inf +inf inf inf inf inf inf inf inf inf inf inf inf inf -2.10 inf -0.60 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 inf -1.40 inf +inf inf inf inf inf inf inf inf inf inf inf -2.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf -3.30 inf inf inf inf inf +inf inf inf inf inf inf inf inf inf -2.40 inf -1.40 inf inf inf inf +inf inf inf inf inf inf inf inf -2.10 inf -2.10 inf inf inf inf inf +inf inf inf inf inf inf inf -2.40 inf inf inf inf inf inf inf -1.30 +inf inf inf inf inf inf -3.40 inf inf inf inf inf inf inf -2.50 inf +inf inf inf inf inf -3.30 inf -1.50 inf inf inf inf inf -2.10 inf -0.50 +inf inf inf inf -2.20 inf -2.50 inf inf inf inf inf -1.40 inf 1.30 inf +inf inf inf -1.30 inf inf inf inf inf inf inf -1.00 inf inf inf inf +inf inf -2.40 inf inf inf inf inf inf inf -1.50 inf inf inf inf inf +inf -2.10 inf -1.00 inf inf inf inf inf -1.40 inf 0.30 inf inf inf inf +-0.90 inf -1.30 inf inf inf inf inf -0.60 inf -0.50 inf inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tloop.DAT b/gtfold-mfe/data/Turner99/tloop.DAT new file mode 100644 index 0000000..dda2750 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tloop.DAT @@ -0,0 +1,30 @@ +GGGGAC -3.00 +GGUGAC -3.00 +CGAAAG -3.00 +GGAGAC -3.00 +CGCAAG -3.00 +GGAAAC -3.00 +CGGAAG -3.00 +CUUCGG -3.00 +CGUGAG -3.00 +CGAAGG -2.50 +CUACGG -2.50 +GGCAAC -2.50 +CGCGAG -2.50 +UGAGAG -2.50 +CGAGAG -2.00 +AGAAAU -2.00 +CGUAAG -2.00 +CUAACG -2.00 +UGAAAG -2.00 +GGAAGC -1.50 +GGGAAC -1.50 +UGAAAA -1.50 +AGCAAU -1.50 +AGUAAU -1.50 +CGGGAG -1.50 +AGUGAU -1.50 +GGCGAC -1.50 +GGGAGC -1.50 +GUGAAC -1.50 +UGGAAA -1.50 diff --git a/gtfold-mfe/data/Turner99/tstackh.DAT b/gtfold-mfe/data/Turner99/tstackh.DAT new file mode 100644 index 0000000..7648650 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstackh.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.50 -0.30 -0.30 +inf inf inf inf inf inf inf inf inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -1.20 -0.20 0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.30 -0.60 -1.10 +inf inf inf inf inf inf inf inf -1.50 -1.50 -1.40 -1.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -0.90 -2.90 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -2.20 -2.00 -1.60 -1.10 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -1.40 -1.80 -2.00 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -2.10 inf inf inf inf 0.20 -0.50 -0.30 -0.30 +inf inf inf inf -1.10 -0.70 -2.40 -0.50 inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf -2.40 -2.90 -1.40 -1.20 inf inf inf inf -0.90 -1.10 -0.30 0.00 +inf inf inf inf -1.90 -1.00 -2.20 -1.50 inf inf inf inf -0.30 -0.30 -0.40 -1.10 +-0.50 -0.30 -0.60 -0.50 inf inf inf inf -0.50 -0.30 -0.60 -0.50 inf inf inf inf +-0.20 -0.10 -1.20 -0.00 inf inf inf inf -0.20 -0.10 -1.70 0.00 inf inf inf inf +-1.40 -1.20 -0.70 -0.20 inf inf inf inf -0.80 -1.20 -0.30 -0.70 inf inf inf inf +-0.30 -0.10 -0.50 -0.80 inf inf inf inf -0.60 -0.10 -0.60 -0.80 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tstacki.DAT b/gtfold-mfe/data/Turner99/tstacki.DAT new file mode 100644 index 0000000..dd7b5da --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstacki.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.00 +inf inf inf inf inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf +inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf 0.70 0.70 0.70 0.00 +0.70 0.70 -0.40 0.70 inf inf inf inf 0.70 0.70 -0.40 0.70 inf inf inf inf +0.70 0.70 0.70 0.70 inf inf inf inf 0.70 0.70 0.70 0.70 inf inf inf inf +-0.40 0.70 0.70 0.70 inf inf inf inf -0.40 0.70 0.70 0.70 inf inf inf inf +0.70 0.70 0.70 0.00 inf inf inf inf 0.70 0.70 0.70 0.00 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tstackm.DAT b/gtfold-mfe/data/Turner99/tstackm.DAT new file mode 100644 index 0000000..b850f80 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf -1.00 inf inf inf -1.00 inf inf inf -2.20 -0.80 -1.00 -0.80 -0.90 +inf inf -1.50 inf inf inf -1.50 inf inf inf -2.70 inf -0.60 -0.70 -2.20 -0.70 +inf -1.50 inf -1.00 inf -1.50 inf -1.00 inf -2.70 inf -2.20 -0.80 -2.10 -0.80 -0.80 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -2.20 inf -2.70 inf -1.10 -0.80 -1.10 -0.80 +inf inf inf -1.00 inf inf inf -1.00 -1.70 -1.70 -1.70 -1.70 inf inf inf -1.00 +inf inf -1.50 inf inf inf -1.50 inf -1.00 -1.10 -3.30 -0.80 inf inf -1.50 inf +inf -1.50 inf -1.00 inf -1.50 inf -1.00 -1.70 -2.40 -1.70 -1.70 inf -1.50 inf -1.00 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -1.60 -1.40 -1.60 -1.20 -1.00 inf -1.50 inf +inf inf inf -2.20 -1.10 -1.50 -1.30 -1.90 inf inf inf -1.00 -0.80 -1.00 -0.80 -1.30 +inf inf -2.70 inf -1.10 -0.70 -3.40 -0.50 inf inf -1.50 inf -0.60 -0.70 -2.50 -0.70 +inf -2.70 inf -2.20 -1.60 -3.30 -1.40 -1.30 inf -1.50 inf -1.00 -0.80 -2.10 -0.80 -0.80 +-2.20 inf -2.70 inf -1.70 -1.00 -2.00 -0.70 -1.00 inf -1.50 inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf -1.00 -1.00 -0.80 -1.10 -1.00 inf inf inf -2.00 +-0.70 -0.60 -2.40 -0.50 inf inf -1.50 inf -0.70 -0.60 -1.50 -0.50 inf inf -2.50 inf +-1.10 -2.10 -1.20 -1.00 inf -1.50 inf -1.00 -0.70 -1.40 -0.80 0.30 inf -2.50 inf -2.00 +-0.90 -0.60 -1.40 -0.50 -1.00 inf -1.50 inf -0.50 -0.60 -0.50 -0.50 -2.00 inf -2.50 inf From ef501b8378b297f0669e2925bc85945ad202ee97 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 28 Apr 2011 10:27:01 -0400 Subject: [PATCH 011/187] adding script to covert data to newer format --- gtfold-mfe/scripts/dats2DATs.py | 53 +++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100755 gtfold-mfe/scripts/dats2DATs.py diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py new file mode 100755 index 0000000..e488b84 --- /dev/null +++ b/gtfold-mfe/scripts/dats2DATs.py @@ -0,0 +1,53 @@ +import os, sys, re + +# read in arguments from command line +if len(sys.argv) != 3: + print "need directory names" + print "Usage: dats2DATs.py " +source_dir_name = sys.argv[1] +target_dir_name = sys.argv[2] + +# this function opens a .dat formatted file and returns a string with .DAT file format +def dat2DAT(file_name, num_cols, num_rows): + num_data_rows_seen = 0 + DAT_content = "" + file = open(file_name,'r') + + for line in file.readlines() : + if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line + + return DAT_content + +for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]: + file_name = source_dir_name+"/"+file_prefix+".dat" + output_file_path = target_dir_name+"/"+file_prefix+".DAT" + output_file = open(output_file_path, 'w') + output_file.write(dat2DAT(file_name, 16, 16)) + #print dat2DAT(file_name, 16, 16) + +file_name = source_dir_name+"/tloop.dat" +output_file_path = target_dir_name+"/tloop.DAT" +DAT_content = "" +file = open(file_name,'r') + +for line in file.readlines() : + if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space or ACGU + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line +output_file = open(output_file_path, 'w') +output_file.write(DAT_content) + From fead43c2bb1f5d9e08e6bee13ab87189c53709cf Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 28 Apr 2011 12:36:34 -0400 Subject: [PATCH 012/187] support for new data format --- gtfold-mfe/data/Turner99/Makefile.am | 15 ++++++ gtfold-mfe/data/Turner99/Makefile.in | 13 +++++ gtfold-mfe/data/Turner99/int22.DAT | 72 ---------------------------- 3 files changed, 28 insertions(+), 72 deletions(-) diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index 4cf8fa7..cb09a05 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -3,6 +3,19 @@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + sint2.DAT\ + sint4.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstackm.DAT\ stack.dat\ miscloop.dat\ dangle.dat\ @@ -23,6 +36,8 @@ gtfold_data_DATA = \ tstacki.dat\ tstackm.dat + + EXTRA_DIST = $(gtfold_data_DATA) CLEANFILES = *~ diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index d9a1eb3..d042a79 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -176,6 +176,19 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + sint2.DAT\ + sint4.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstackm.DAT\ stack.dat\ miscloop.dat\ dangle.dat\ diff --git a/gtfold-mfe/data/Turner99/int22.DAT b/gtfold-mfe/data/Turner99/int22.DAT index 4f17932..9691143 100644 --- a/gtfold-mfe/data/Turner99/int22.DAT +++ b/gtfold-mfe/data/Turner99/int22.DAT @@ -1,5 +1,3 @@ - A \/ \_/ A - U /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 @@ -16,8 +14,6 @@ 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - A \/ \_/ C - U /\ | G 2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 2.00 1.70 0.00 2.00 1.70 1.70 2.00 0.70 0.60 2.00 1.60 -1.20 2.00 1.80 -0.80 1.00 0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 @@ -34,8 +30,6 @@ 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 0.70 -0.50 -0.50 2.00 -0.60 0.50 2.00 -0.50 0.10 2.00 0.40 -3.50 2.00 0.50 -3.10 0.50 2.00 0.80 0.80 2.00 0.70 0.80 2.00 -0.20 1.50 2.00 1.70 -0.30 2.00 0.80 0.10 0.00 - A \/ \_/ G - U /\ | C 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 1.90 1.80 0.90 2.00 2.20 2.10 2.00 1.90 0.90 2.00 1.60 -0.80 2.00 1.90 0.70 1.00 0.80 0.70 -0.20 2.00 1.10 2.00 2.00 1.80 -0.20 2.00 0.50 -0.10 2.00 1.80 1.40 1.80 @@ -52,8 +46,6 @@ 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 0.60 -0.50 0.40 2.00 0.00 0.80 2.00 0.70 0.40 2.00 0.40 -3.10 2.00 0.70 -1.60 0.60 1.90 0.80 1.80 2.00 1.30 1.10 2.00 1.00 1.80 2.00 1.70 0.00 2.00 1.00 1.60 0.10 - A \/ \_/ U - U /\ | A 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 @@ -70,8 +62,6 @@ 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - A \/ \_/ G - U /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 @@ -88,8 +78,6 @@ 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - A \/ \_/ U - U /\ | G 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 @@ -106,8 +94,6 @@ 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - C \/ \_/ A - G /\ | U 2.00 1.60 1.00 2.00 2.00 2.60 2.00 2.60 1.00 2.00 1.40 0.20 2.00 2.30 1.50 2.20 2.40 1.90 1.30 2.00 2.40 2.40 2.00 2.40 1.30 2.00 1.70 -0.40 2.00 2.10 0.80 1.50 1.00 0.60 0.00 2.00 1.00 2.00 2.00 2.00 0.00 2.00 0.40 0.00 2.00 1.70 1.30 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0.80 0.30 0.20 -0.70 2.00 0.60 1.50 2.00 1.30 -0.70 2.00 0.00 -0.60 2.00 1.30 0.90 1.30 @@ -160,8 +142,6 @@ 1.90 1.20 1.30 2.00 1.70 1.50 2.00 1.40 1.30 2.00 1.70 -0.40 2.00 1.40 1.10 0.50 -0.40 -1.50 -0.60 2.00 -1.10 -0.20 2.00 -0.40 -0.60 2.00 -0.70 -4.20 2.00 -0.40 -2.60 -0.50 1.40 0.30 1.30 2.00 0.80 0.60 2.00 0.50 1.30 2.00 1.20 -0.50 2.00 0.50 1.10 -0.40 - C \/ \_/ U - G /\ | A 2.00 1.80 0.80 2.00 1.90 2.30 2.00 2.30 0.80 2.00 1.30 0.60 2.00 2.30 1.60 1.90 2.40 2.10 1.10 2.00 2.20 2.10 2.00 2.10 1.10 2.00 1.70 0.00 2.00 2.10 0.90 1.30 1.00 0.80 -0.20 2.00 0.90 1.70 2.00 1.70 -0.20 2.00 0.30 0.40 2.00 1.70 1.40 1.80 @@ -178,8 +158,6 @@ 2.70 1.80 1.80 2.00 1.90 1.80 2.00 1.80 1.80 2.00 2.00 0.70 2.00 1.80 1.60 1.00 0.30 -0.90 -0.10 2.00 -0.80 0.00 2.00 0.00 -0.10 2.00 -0.40 -3.10 2.00 0.00 -2.10 0.00 2.20 0.90 1.80 2.00 1.00 0.90 2.00 0.90 1.80 2.00 1.50 0.60 2.00 0.90 1.60 0.10 - C \/ \_/ G - G /\ | U 2.00 1.60 1.00 2.00 2.00 2.60 2.00 2.60 1.00 2.00 1.40 0.20 2.00 2.30 1.50 2.20 2.40 1.90 1.30 2.00 2.40 2.40 2.00 2.40 1.30 2.00 1.70 -0.40 2.00 2.10 0.80 1.50 1.00 0.60 0.00 2.00 1.00 2.00 2.00 2.00 0.00 2.00 0.40 0.00 2.00 1.70 1.30 2.00 @@ -196,8 +174,6 @@ 2.70 1.60 2.00 2.00 2.10 2.10 2.00 2.10 2.00 2.00 2.00 0.30 2.00 1.80 1.50 1.20 0.30 -1.10 0.10 2.00 -0.70 0.30 2.00 0.30 0.10 2.00 -0.30 -3.50 2.00 0.00 -2.20 0.30 2.20 0.70 1.90 2.00 1.20 1.20 2.00 1.20 1.90 2.00 1.50 0.20 2.00 0.90 1.50 0.30 - C \/ \_/ U - G /\ | G 2.00 1.80 0.80 2.00 1.90 2.30 2.00 2.30 0.80 2.00 1.30 0.60 2.00 2.30 1.60 1.90 2.40 2.10 1.10 2.00 2.20 2.10 2.00 2.10 1.10 2.00 1.70 0.00 2.00 2.10 0.90 1.30 1.00 0.80 -0.20 2.00 0.90 1.70 2.00 1.70 -0.20 2.00 0.30 0.40 2.00 1.70 1.40 1.80 @@ -214,8 +190,6 @@ 2.70 1.80 1.80 2.00 1.90 1.80 2.00 1.80 1.80 2.00 2.00 0.70 2.00 1.80 1.60 1.00 0.30 -0.90 -0.10 2.00 -0.80 0.00 2.00 0.00 -0.10 2.00 -0.40 -3.10 2.00 0.00 -2.10 0.00 2.20 0.90 1.80 2.00 1.00 0.90 2.00 0.90 1.80 2.00 1.50 0.60 2.00 0.90 1.60 0.10 - G \/ \_/ A - C /\ | U 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 1.80 1.40 0.80 2.00 1.80 1.80 2.00 1.80 0.80 2.00 1.20 -1.00 2.00 1.50 0.30 1.00 0.70 0.30 -0.30 2.00 0.70 1.70 2.00 1.70 -0.30 2.00 0.10 -0.30 2.00 1.40 1.00 1.70 @@ -232,8 +206,6 @@ 1.50 0.40 0.90 2.00 0.90 0.90 2.00 0.90 0.90 2.00 0.80 -0.90 2.00 0.60 0.40 0.00 0.00 -1.50 -0.30 2.00 -1.00 0.00 2.00 0.00 -0.30 2.00 -0.70 -3.90 2.00 -0.30 -2.60 -0.10 2.10 0.70 1.90 2.00 1.10 1.10 2.00 1.10 1.90 2.00 1.50 0.10 2.00 0.80 1.40 0.30 - G \/ \_/ C - C /\ | G 1.50 1.20 -0.50 2.00 1.20 1.80 2.00 0.80 0.10 2.00 1.10 -0.70 2.00 1.90 -0.30 1.50 1.20 0.90 -0.80 2.00 0.90 0.90 2.00 0.00 -0.20 2.00 0.80 -2.00 2.00 1.00 -1.60 0.20 0.10 -0.10 -1.90 2.00 -0.20 0.90 2.00 -0.10 -1.30 2.00 -0.20 -1.30 2.00 0.90 -0.90 0.90 @@ -250,8 +222,6 @@ 0.80 0.00 -0.80 2.00 0.00 0.00 2.00 -1.00 -0.10 2.00 0.50 -1.90 2.00 0.00 -1.50 -0.70 -0.70 -1.90 -1.90 2.00 -2.00 -0.90 2.00 -1.90 -1.30 2.00 -1.00 -4.90 2.00 -0.90 -4.50 -0.90 1.50 0.20 0.30 2.00 0.20 0.20 2.00 -0.70 0.90 2.00 1.10 -0.90 2.00 0.30 -0.50 -0.50 - G \/ \_/ G - C /\ | C 0.50 1.30 -0.20 2.00 0.60 2.20 2.00 2.00 0.00 2.00 1.10 -0.10 2.00 2.00 0.90 1.40 1.10 1.00 0.70 2.00 1.10 1.90 2.00 1.10 -1.00 2.00 0.80 -1.60 2.00 1.10 -0.10 0.30 0.40 0.70 -0.50 2.00 0.50 0.70 2.00 0.50 -0.70 2.00 -0.20 -0.60 2.00 1.00 0.60 1.40 @@ -268,8 +238,6 @@ 0.70 0.00 0.20 2.00 0.50 0.30 2.00 0.20 0.20 2.00 0.50 -1.60 2.00 1.70 0.00 0.10 0.10 -1.90 -0.90 2.00 -0.70 -0.30 2.00 -0.70 -0.80 2.00 -1.00 -4.40 2.00 -0.70 -3.00 -1.00 1.50 -0.20 0.90 2.00 0.00 -0.10 2.00 0.40 0.90 2.00 1.10 -1.00 2.00 0.20 0.60 0.60 - G \/ \_/ U - C /\ | A 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 1.80 1.60 0.60 2.00 1.70 1.50 2.00 1.50 0.60 2.00 1.10 -0.60 2.00 1.50 0.40 0.70 0.70 0.50 -0.50 2.00 0.60 1.40 2.00 1.40 -0.50 2.00 0.00 0.10 2.00 1.40 1.10 1.50 @@ -286,8 +254,6 @@ 1.50 0.60 0.70 2.00 0.70 0.60 2.00 0.60 0.70 2.00 0.80 -0.50 2.00 0.60 0.50 -0.20 0.00 -1.30 -0.50 2.00 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1.30 1.70 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 @@ -394,8 +350,6 @@ 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 - U \/ \_/ G - A /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 @@ -412,8 +366,6 @@ 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - U \/ \_/ U - A /\ | G 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 @@ -430,8 +382,6 @@ 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 - G \/ \_/ A - U /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 @@ -448,8 +398,6 @@ 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - G \/ \_/ C - U /\ | G 2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 2.00 1.70 0.00 2.00 1.70 1.70 2.00 0.70 0.60 2.00 1.60 -1.20 2.00 1.80 -0.80 1.00 0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 @@ -466,8 +414,6 @@ 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 0.70 -0.50 -0.50 2.00 -0.60 0.50 2.00 -0.50 0.10 2.00 0.40 -3.50 2.00 0.50 -3.10 0.50 2.00 0.80 0.80 2.00 0.70 0.80 2.00 -0.20 1.50 2.00 1.70 -0.30 2.00 0.80 0.10 0.00 - G \/ \_/ G - U /\ | C 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 1.90 1.80 0.90 2.00 2.20 2.10 2.00 1.90 0.90 2.00 1.60 -0.80 2.00 1.90 0.70 1.00 0.80 0.70 -0.20 2.00 1.10 2.00 2.00 1.80 -0.20 2.00 0.50 -0.10 2.00 1.80 1.40 1.80 @@ -484,8 +430,6 @@ 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 0.60 -0.50 0.40 2.00 0.00 0.80 2.00 0.70 0.40 2.00 0.40 -3.10 2.00 0.70 -1.60 0.60 1.90 0.80 1.80 2.00 1.30 1.10 2.00 1.00 1.80 2.00 1.70 0.00 2.00 1.00 1.60 0.10 - G \/ \_/ U - U /\ | A 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 @@ -502,8 +446,6 @@ 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - G \/ \_/ G - U /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 @@ -520,8 +462,6 @@ 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - G \/ \_/ U - U /\ | G 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 @@ -538,8 +478,6 @@ 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - U \/ \_/ A - G /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 @@ -556,8 +494,6 @@ 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - U \/ \_/ C - G /\ | G 2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 2.10 1.90 0.10 2.00 1.80 1.90 2.00 0.90 0.70 2.00 1.80 -1.00 2.00 1.90 -0.60 1.10 1.10 0.80 -0.90 2.00 0.80 1.80 2.00 0.90 -0.30 2.00 0.70 -0.30 2.00 1.90 0.10 1.90 @@ -574,8 +510,6 @@ 2.70 1.90 1.10 2.00 1.80 1.90 2.00 0.90 1.70 2.00 2.40 0.00 2.00 1.90 0.40 1.10 0.30 -0.90 -0.90 2.00 -1.00 0.10 2.00 -0.90 -0.30 2.00 0.00 -3.90 2.00 0.10 -3.50 0.10 2.30 1.00 1.10 2.00 1.00 1.00 2.00 0.00 1.70 2.00 1.90 -0.10 2.00 1.10 0.30 0.30 - U \/ \_/ G - G /\ | C 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 2.00 1.90 1.00 2.00 2.40 2.20 2.00 2.10 1.00 2.00 1.80 -0.70 2.00 2.10 0.80 1.20 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 @@ -592,8 +526,6 @@ 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 0.20 -0.90 0.00 2.00 -0.40 0.40 2.00 0.30 0.00 2.00 0.00 -3.50 2.00 0.30 -2.00 0.20 2.20 1.10 2.00 2.00 1.50 1.40 2.00 1.20 2.00 2.00 1.90 0.30 2.00 1.20 1.80 0.30 - U \/ \_/ U - G /\ | A 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 @@ -610,8 +542,6 @@ 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 - U \/ \_/ G - G /\ | U 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 @@ -628,8 +558,6 @@ 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - U \/ \_/ U - G /\ | G 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 From 270f6947a43bb67cd269a69bd4022daef9131ee1 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 28 Apr 2011 12:38:08 -0400 Subject: [PATCH 013/187] changes to parse datafiles compatible with UNAfold format --- gtfold-mfe/include/loader.h | 20 +- gtfold-mfe/src/loader.cc | 944 ++++++++++-------------------------- 2 files changed, 261 insertions(+), 703 deletions(-) diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index 20a0708..f8fdc78 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -27,16 +27,16 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic); -int initStackValues(std::string fileName); -int initMiscloopValues(std::string fileName); -int initDangleValues(std::string fileName); -int initLoopValues(std::string fileName); -int initTstkhValues(std::string fileName); -int initTstkiValues(std::string fileName); -int initTloopValues(std::string fileName); -int initInt21Values(std::string fileName); -int initInt22Values(std::string fileName); -int initInt11Values(std::string fileName); +int initStackValues(const std::string& fileName, const std::string& dirPath); +int initMiscloopValues(const std::string& fileName, const std::string& dirPath); +int initDangleValues(const std::string& fileName, const std::string& dirPath); +int initLoopValues(const std::string& fileName, const std::string& dirPath); +int initTstkhValues(const std::string& fileName, const std::string& dirPath); +int initTstkiValues(const std::string& fileName, const std::string& dirPath); +int initTloopValues(const std::string& fileName, const std::string& dirPath); +int initInt21Values(const std::string& fileName, const std::string& dirPath); +int initInt22Values(const std::string& fileName, const std::string& dirPath); +int initInt11Values(const std::string& fileName, const std::string& dirPath); extern std::string EN_DATADIR; diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index f916f3c..18066c6 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -20,6 +20,7 @@ #include #include #include +#include #include #include @@ -77,13 +78,11 @@ float prelog; void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { #ifndef GENBIN - if (!userdatalogic) - { + if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; EN_DATADIR += userdatadir; - } else - { + } else { EN_DATADIR.assign(userdatadir); } #else @@ -95,178 +94,89 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { EN_DATADIR += "/"; } - initMiscloopValues("miscloop.dat"); - // miscloop.dat - Miscellaneous loop file - initStackValues("stack.dat"); - // stack.dat - free energies for base pair stacking - initDangleValues("dangle.dat"); - // dangle.dat - single base stacking free energies - initLoopValues("loop.dat"); - // loop.dat - entropic component for internal, bulge and hairpin loops. - initTstkhValues("tstackh.dat"); - // tstackh.dat - free energies for terminal mismatch stacking in hairpin loops - initTstkiValues("tstacki.dat"); - // tstacki.dat - free energies for terminal mismatch stacking in internal loops - initTloopValues("tloop.dat"); - // tloop.dat - free energies for distinguished tetraloops - initInt21Values("int21.dat"); - // int21.dat - free energies for 2 x 1 interior loops - initInt22Values("int22.dat"); - // int22.dat - free energies for 2 x 2 interior loops - initInt11Values("int11.dat"); - // int11.dat - free energies for 1 x 1 interior loops + initMiscloopValues("miscloop.DAT", EN_DATADIR); + initDangleValues("dangle.DAT", EN_DATADIR); + initStackValues("stack.DAT", EN_DATADIR); + initLoopValues("loop.DAT", EN_DATADIR); + initTstkhValues("tstackh.DAT", EN_DATADIR); + initTstkiValues("tstacki.DAT", EN_DATADIR); + initTloopValues("tloop.DAT", EN_DATADIR); + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); } +int initStackValues(const string& fileName, const string& dirPath) { + std::string filePath; + std::ifstream cf; - int initStackValues(string fileName) { + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; - - // Initialize the array with INFINITY - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { stack[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // Read the thermodynamic parameters. - // The 24 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - stack[fourBaseIndex(ii,jj,kk,ll)] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + stack[fourBaseIndex(i,j,k,l)] = (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - /* jj = 1; */ - kk = (i % 4); - + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initMiscloopValues(string fileName) { - /* - miscloop.dat - Miscellaneous loop file. Contains : - 1. Extrapolation for large loops based on polymer theory - 2. Asymmetric internal loop correction parameters. - 3. the f(m) array (see Ninio for details) - 4. Paremeters for multibranch loops - 5. Paremeters for multibranch loops (for efn2 only) - 6. Terminal AU or GU penalty - 7. Bonus for GGG hairpin - 8,9,10. C hairpin rules: a) slope b) intercept c) value for size 3 - 11. Intermolecular initiation free energy - 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off) - */ +int initMiscloopValues(const string& fileName, const string& dirpath) { + std::string filePath; + std::ifstream cf; - char currentWord[256]; - string s; - ifstream cf; //cf = current file + filePath = dirpath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; -#if 0 - cout << "Getting miscloop values from " << fileName << endl; -#endif - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); } - s = ""; - cf >> currentWord; + char currentWord[256]; + std::string s; + for (int index = 1; index < 13; index++) { // There are total 12 values to read in. - while (strcmp(currentWord, "-->")) { - cf >> currentWord; - } if (index == 1) { cf >> currentWord; prelog = 100 * atof(currentWord); - //cout << "prelog = " << prelog << endl; } if (index == 2) { cf >> currentWord; maxpen = int(atof(currentWord) * 100.0 + .5); - //cout << "maxpen = " << maxpen << endl; } if (index == 3) { for (int count = 1; count <= 4; count++) { @@ -292,7 +202,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { s = currentWord; multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5); eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "\n multi " << multConst[count-1]; } } if (index == 5) { @@ -336,150 +245,86 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } } - cf.close(); + cf.close(); + return 0; } - int initDangleValues(string fileName) { - ifstream cf; //cf = current file - char currentLine[256]; - string currentString; - string s; - int index; - int i, j, k, l; - int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low - - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 2; l++) { +int initDangleValues(const std::string& fileName, + const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { dangle[i][j][k][l] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 8 first lines are junk - for (index = 1; index <= 8; index++) { - cf.getline(currentLine, 256); - } - - // 8 lines of useful data - i = 0; - ii = 0; - jj = 0; - kk = 0; - ll = 0; - - while (i < 8) { - - if (i != 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - kk++; - if (kk == 4) - kk = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - //if ( temp == 0 ) temp = -1; - dangle[ii][jj][kk][ll] = temp; - //cout<< "\n " << temp << " "<< ii <<" "<< jj << " "<< kk << " " << ll ; - r++; - z++; - if (r % 4 == 0) - jj++; - kk++; - if (kk == 4) - kk = 0; - + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count%4; + l = count/4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + + j = cols/4; + ss >> val; + k = cols%4; + if (!(val == "inf")) { + dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5); } - - } - - i++; - ii++; - if (ii == 4) - ii = 0; - - if (i == 4) - ll = 1; - + } + ++count; } - cf.close(); - -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initLoopValues(string fileName) { +int initLoopValues( const string& fileName, const string& dirPath) { // algorithm.c, line 2996 ifstream cf; // current file - char currentLine[256]; + std::string filePath; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + //char currentLine[256]; char currentWord[256]; string s; - int index; + int index= 0; int tempValue = 0; -#if 0 - cout << "Getting loop values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // The 4 first lines are junk we don't need - for (index = 1; index <= 4; index++) { - cf.getline(currentLine, 256); - //s = currentLine; - //cout << s << endl; - } + while (index < 30) { for (int j = 1; j <= 4; j++) { cf >> currentWord; if (j == 1) index = atoi(currentWord); if (j > 1) { - if (strcmp(currentWord, ".")) { + if (strcmp(currentWord, "inf")) { tempValue = (int) (100 * atof(currentWord) + 0.5); } else { tempValue = INFINITY_; @@ -500,228 +345,111 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initTstkhValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; +int initTstkhValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp; - - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - jj = 0; - kk = (i % 4); - + } + ++count; } - - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initTstkiValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { +int initTstkiValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; + int count = 0; - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } + while (cf.good()) { + int i, j, k, l; - else { - char value[10]; - int x = 0; + std::string line; + std::stringstream ss; - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } + getline(cf, line); + ss << line; + if (line.empty()) continue; - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstki[fourBaseIndex(ii,jj,kk,ll)] = temp; + i = count/4; + k = count%4; - //cout << "\n temp " << temp << " " <> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - jj = 0; - kk = (i % 4); - + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -//SH: Rewritten as an error was being generated by this function. - int initTloopValues(string fileName) { - ifstream cf; +int initTloopValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + int count; char currentLine[256]; char currentSeqNumbers[7]; @@ -732,20 +460,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { string s, temp; -#if 0 - cout << "Getting tloop values..."; -#endif - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - // skip 2 lines - cf.getline(currentLine, 256); - cf.getline(currentLine, 256); - numoftloops = 0; while (!cf.eof() && (++(numoftloops) < maxtloop)) { @@ -759,33 +473,23 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { for (count = 0; count < 6; count++) { temp = currentLine[count + clindex]; currentSeqNumbers[count] = baseToDigit(temp.c_str()); - //cout << currentSeqNumbers[count]; - //cout << currentLine[count+1]; } - //cout << endl; clindex=clindex+7; while(currentLine[clindex]== ' ') clindex++; count = 0; while(currentLine[clindex+count]!=' '&¤tLine[clindex+count]!='\0') { currentValue[count] = currentLine[count + clindex]; count++; - //cout << currentValue[count]; } - //cout << endl; tloop[numoftloops][0] = (int) atoi(currentSeqNumbers); tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); - //cout << " -- "<< tloop[numoftloops][0] << " | " << tloop[numoftloops][1] << endl; } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initInt22Values(string fileName) { - +int initInt22Values(const std::string& fileName, const std::string& dirPath) { //Read the 2x2 internal loops //key iloop22[a][b][c][d][j][l][k][m] = //a j l b @@ -803,66 +507,36 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { iloop22[i][j][k][r][q][t][y][z] = INFINITY_; ifstream cf; - int index, flag; char currentLine[256], currentValue[6]; - string s, s1, s2, temp; - string sre; int base[4]; int l, m; -#if 0 - cout << "Getting Int22 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; + string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + if (!cf.good()) { + cerr << "File open failed " << endl; exit(-1); } - // Get rid of the 38 1st lines - for (index = 1; index < 28; index++) { - cf.getline(currentLine, 256); - } - - sre = "Y"; - flag = 0; - - for (index = 1; index <= 36; index++) { // 36 tables 16x16 - // Go to the beginning of the tables - while (!flag) { - cf.getline(currentLine, 256); + const char* str[] = {"A-U","C-G","G-C","U-A","G-U","U-G"}; + - s = currentLine; + int outer, inner; - int z = 0; - while (s[z] != '\0') { + for (int index = 1; index <= 36; index++) { // 36 tables 16x16 + std::stringstream ss1; + std::string s ; - if (s[z] == 'Y') - flag = 1; - - z++; - } - } - flag = 0; - - // We skip 5 lines - for (i = 0; i < 5; ++i) { - cf.getline(currentLine, 256); - } - - // get the closing bases - cf.getline(currentLine, 256); - s1 = currentLine; - cf.getline(currentLine, 256); - s2 = currentLine; - s = s1 + s2; - - int z = 0; + outer = (index-1)/6; + inner = (index-1)%6; + ss1 << str[outer][0] << '-' << str[inner][0] << '-' << str[outer][2] << '-' << + str[inner][2]; + ss1 >> s; + int k = 0; + int z = 0; while (s[z] != '\0') { - if (s[z] == 'A') base[k++] = BASE_A; else if (s[z] == 'C') @@ -871,22 +545,15 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base[k++] = BASE_G; else if (s[z] == 'U') base[k++] = BASE_U; - z++; } - cf.getline(currentLine, 256); - - //key iloop22[a][b][c][d][j][l][k][m] = - //a j l b - //c k m d - - for (int rowIndex = 1; rowIndex <= 16; rowIndex++) { + cf.getline(currentLine, 256); + std::stringstream ss; + ss << currentLine; for (int colIndex = 1; colIndex <= 16; colIndex++) { - cf >> currentValue; - // rowIndex = j*4+k - // colIndex = l*4+m + ss >> currentValue; j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4; k = (rowIndex - 1) % 4; @@ -894,23 +561,17 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { l = ((colIndex - 1) - (colIndex - 1) % 4) / 4; m = (colIndex - 1) % 4; - iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] - = (int) floor(100.0 * atof(currentValue) + 0.5); - //int temp = (int) floor(100.0*atof(currentValue)+0.5); - //printf("\n temp is : %d %d %d %d %d %d %d %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m ); + iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] + = (int) floor(100.0 * atof(currentValue) + 0.5); } } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initInt21Values(string fileName) { - +int initInt21Values(const std::string& fileName, const std::string& dirPath) { // 24x6 arrays of 4x4 values // c // a f @@ -921,7 +582,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { char currentLine[256]; string sre; string s, s1, s2; - int a, b, c, d, e, f, g, index; + int a, b, c, d, e, f, g; int i, j, k, r, q, t, y; int z; @@ -958,87 +619,44 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base1[6] = BASE_U + 1; base2[6] = BASE_G + 1; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // Get rid of the 18 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - i = 1; - while (i <= 6) { - j = 1; - while (j <= 4) { - k = 1; - - for (index = 1; index <= 10; index++) - cf.getline(currentLine, 256); - - s = currentLine; - while (k <= 4) { - cf.getline(currentLine, 256); - - s = currentLine; - r = 0; - z = 0; int jj = 1; d = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - d++; - if (d == 5) - d = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[i]; - b = base2[i]; - f = base1[jj]; - g = base2[jj]; - c = k; - e = j; - - iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] - = temp; - //printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g); - r++; - z++; - if (r % 4 == 0) - jj++; - d++; - if (d == 5) - d = 1; - } + + std::stringstream ss; + ss << currentLine; + + for (z = 1; z <=24 ; z++) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[i]; + b = base2[i]; + f = base1[jj]; + g = base2[jj]; + c = k; + e = j; + + iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] + = temp; + r++; + if (r % 4 == 0) jj++; + d++; + if (d == 5) d = 1; } k++; } @@ -1050,13 +668,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { return 0; } - int initInt11Values(string fileName) { - - //Read the 1x1 internal loops - //key iloop11[a][b][c][d][j][l][k][m] = - //a b c - //d e f - +int initInt11Values(const std::string& fileName, const std::string& dirPath) { int i, j, k, r, q, t; for (i = 0; i < 4; i++) @@ -1068,37 +680,20 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { iloop11[i][j][k][r][q][t] = INFINITY_; ifstream cf; - int index; char currentLine[256]; string s; int base1[7]; int base2[7]; - //int j, k, l, m; int a, b, c, d, f; -#if 0 - cout << "Getting Int11 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // Get rid of the 19 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - - /* - Structure of the file: - array of 6x6 arrays - Order: - AU CG GC UA GU UG - */ - base1[1] = BASE_A + 1; base2[1] = BASE_U + 1; base1[2] = BASE_C + 1; @@ -1117,75 +712,38 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { while (k < 6) { k++; - index = 0; - for (index = 1; index <= 10; index++) { - cf.getline(currentLine, 256); - } - i = 0; b = 1; while (i < 4) { - int jj = 1; ++i; cf.getline(currentLine, 256); - s = currentLine; - j = 0; int r = 0; - int z = 0; int e = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - e++; - if (e == 5) - e = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; + std::stringstream ss; + ss << currentLine; - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[k]; - d = base2[k]; - c = base1[jj]; - f = base2[jj]; - iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - e++; - if (e == 5) - e = 1; - } + for (int z=1; z <= 24; ++z) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[k]; + d = base2[k]; + c = base1[jj]; + f = base2[jj]; + iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; + r++; + if (r % 4 == 0) jj++; + e++; + if (e == 5) e = 1; } b++; } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - - From b18929911eb1bbb5db85a29267502d7259a48edd Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 4 May 2011 11:05:23 -0400 Subject: [PATCH 014/187] fixed bug related to constraints --- gtfold-mfe/src/constraints.cc | 23 ++++++++++++++--------- 1 file changed, 14 insertions(+), 9 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 97cbc5e..d3cd01b 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -89,13 +89,16 @@ static int load_constraints(const char* constr_file, int verbose=0) { for(int k=1;k<= FBP[it][2];k++) v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); } - std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); - for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second <= v_fbp[ii+1].second) { - fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(-1); + + if (v_fbp.size() > 1) { + std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); + for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { + if (v_fbp[ii].second <= v_fbp[ii+1].second) { + fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); + exit(-1); + } + } - } @@ -134,18 +137,18 @@ int init_constraints(const char* constr_file,int length) { for (it = 0; it < nFBP; it++) { if (FBP[it][2] < 1) { printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]); - continue; + continue; // TODO: report and exit here } for(k=1; k <= FBP[it][2];k++) { int i1 = FBP[it][0]+k-1; int j1 = FBP[it][1]-k+1; if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) { printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1); - continue; + continue; // TODO: report and exit here } if (j1-i1 < TURN) { printf("Can't constrain (%d,%d)\n", i1, j1); - continue; + continue; // TODO: report and exit here } BP[FBP[it][0]+k-1] = FBP[it][1]+1-k; BP[FBP[it][1]+1-k] = FBP[it][0]+k-1; @@ -175,6 +178,8 @@ void print_constraints(int len) { printf("\n"); } + + int is_ss(int i, int j) { if (CONS_ENABLED) { int it; From 1a4dfa0130b4ebf396e684cab5e6b798dcf492d0 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sun, 8 May 2011 01:22:48 +0200 Subject: [PATCH 015/187] Commiting SHAPE support and the first attempt at fixing constraints. Still can't produce structures like (...)(...) --- gtfold-mfe/Makefile | 753 +++++++++++++++++++++++ gtfold-mfe/include/shapereader.h | 23 + gtfold-mfe/src/.deps/algorithms.Po | 131 ++++ gtfold-mfe/src/.deps/constraints.Po | 370 +++++++++++ gtfold-mfe/src/.deps/energy.Po | 116 ++++ gtfold-mfe/src/.deps/global.Po | 85 +++ gtfold-mfe/src/.deps/loader.Po | 367 +++++++++++ gtfold-mfe/src/.deps/main.Po | 437 +++++++++++++ gtfold-mfe/src/.deps/options.Po | 265 ++++++++ gtfold-mfe/src/.deps/shapereader.Po | 360 +++++++++++ gtfold-mfe/src/.deps/subopt_traceback.Po | 351 +++++++++++ gtfold-mfe/src/.deps/traceback.Po | 127 ++++ gtfold-mfe/src/.deps/utils.Po | 222 +++++++ gtfold-mfe/src/Makefile | 522 ++++++++++++++++ gtfold-mfe/src/shapereader.cc | 89 +++ 15 files changed, 4218 insertions(+) create mode 100644 gtfold-mfe/Makefile create mode 100644 gtfold-mfe/include/shapereader.h create mode 100644 gtfold-mfe/src/.deps/algorithms.Po create mode 100644 gtfold-mfe/src/.deps/constraints.Po create mode 100644 gtfold-mfe/src/.deps/energy.Po create mode 100644 gtfold-mfe/src/.deps/global.Po create mode 100644 gtfold-mfe/src/.deps/loader.Po create mode 100644 gtfold-mfe/src/.deps/main.Po create mode 100644 gtfold-mfe/src/.deps/options.Po create mode 100644 gtfold-mfe/src/.deps/shapereader.Po create mode 100644 gtfold-mfe/src/.deps/subopt_traceback.Po create mode 100644 gtfold-mfe/src/.deps/traceback.Po create mode 100644 gtfold-mfe/src/.deps/utils.Po create mode 100644 gtfold-mfe/src/Makefile create mode 100644 gtfold-mfe/src/shapereader.cc diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile new file mode 100644 index 0000000..75480ce --- /dev/null +++ b/gtfold-mfe/Makefile @@ -0,0 +1,753 @@ +# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile. 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+#endif diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po new file mode 100644 index 0000000..b84c3b7 --- /dev/null +++ b/gtfold-mfe/src/.deps/algorithms.Po @@ -0,0 +1,131 @@ +algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + 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\ + /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc \ + /usr/include/c++/4.4/bits/locale_classes.tcc \ + /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ + /usr/include/c++/4.4/bits/basic_ios.h \ + /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/wctype.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.4/bits/streambuf_iterator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.4/bits/locale_facets.tcc \ + /usr/include/c++/4.4/bits/basic_ios.tcc \ + /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ + /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ + /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/vector \ + /usr/include/c++/4.4/bits/stl_construct.h \ + /usr/include/c++/4.4/bits/stl_uninitialized.h \ + /usr/include/c++/4.4/bits/stl_vector.h \ + /usr/include/c++/4.4/bits/stl_bvector.h \ + /usr/include/c++/4.4/bits/vector.tcc /usr/include/c++/4.4/algorithm \ + /usr/include/c++/4.4/bits/stl_algo.h /usr/include/c++/4.4/cstdlib \ + /usr/include/c++/4.4/bits/algorithmfwd.h \ + /usr/include/c++/4.4/bits/stl_heap.h \ + /usr/include/c++/4.4/bits/stl_tempbuf.h ../include/global.h \ + ../include/constants.h ../include/options.h /usr/include/c++/4.4/cstring \ + ../include/constraints.h + +/usr/include/stdlib.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/xlocale.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/string.h: + +/usr/include/bits/string3.h: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/c++/4.4/iostream: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/ostream: + +/usr/include/c++/4.4/ios: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/c++/4.4/cstddef: + +/usr/include/bits/wchar.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/c++/4.4/bits/ios_base.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/bits/sched.h: + +/usr/include/signal.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/bits/locale_classes.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + +/usr/include/c++/4.4/new: + +/usr/include/c++/4.4/bits/ostream_insert.h: + +/usr/include/c++/4.4/cxxabi-forced.h: + +/usr/include/c++/4.4/bits/stl_function.h: + +/usr/include/c++/4.4/backward/binders.h: + +/usr/include/c++/4.4/bits/basic_string.h: + +/usr/include/c++/4.4/initializer_list: + +/usr/include/c++/4.4/bits/basic_string.tcc: + +/usr/include/c++/4.4/bits/locale_classes.tcc: + +/usr/include/c++/4.4/streambuf: + +/usr/include/c++/4.4/bits/streambuf.tcc: + +/usr/include/c++/4.4/bits/basic_ios.h: + +/usr/include/c++/4.4/bits/locale_facets.h: + +/usr/include/c++/4.4/cwctype: + +/usr/include/wctype.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: + +/usr/include/c++/4.4/bits/streambuf_iterator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: + +/usr/include/c++/4.4/bits/locale_facets.tcc: + +/usr/include/c++/4.4/bits/basic_ios.tcc: + +/usr/include/c++/4.4/bits/ostream.tcc: + +/usr/include/c++/4.4/istream: + +/usr/include/c++/4.4/bits/istream.tcc: + +/usr/include/c++/4.4/fstream: + +/usr/include/c++/4.4/bits/codecvt.h: + +/usr/include/c++/4.4/cstdio: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: + +/usr/include/c++/4.4/bits/fstream.tcc: + +/usr/include/c++/4.4/vector: + +/usr/include/c++/4.4/bits/stl_construct.h: + +/usr/include/c++/4.4/bits/stl_uninitialized.h: + +/usr/include/c++/4.4/bits/stl_vector.h: + +/usr/include/c++/4.4/bits/stl_bvector.h: + +/usr/include/c++/4.4/bits/vector.tcc: + +/usr/include/c++/4.4/algorithm: + +/usr/include/c++/4.4/bits/stl_algo.h: + +/usr/include/c++/4.4/cstdlib: + +/usr/include/c++/4.4/bits/algorithmfwd.h: + +/usr/include/c++/4.4/bits/stl_heap.h: + +/usr/include/c++/4.4/bits/stl_tempbuf.h: + +../include/global.h: + +../include/constants.h: + +../include/options.h: + +/usr/include/c++/4.4/cstring: + +../include/constraints.h: diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po new file mode 100644 index 0000000..7c1467f --- /dev/null +++ b/gtfold-mfe/src/.deps/energy.Po @@ -0,0 +1,116 @@ +energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ + /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/sys/types.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/include/bits/sigset.h /usr/include/bits/time.h \ + /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ + /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + ../include/energy.h ../include/data.h ../include/constants.h \ + ../include/utils.h ../include/global.h ../include/constants.h + +/usr/include/stdlib.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/stdio.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +../include/energy.h: + +../include/data.h: + +../include/constants.h: + +../include/utils.h: + +../include/global.h: + +../include/constants.h: diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po new file mode 100644 index 0000000..e2d1748 --- /dev/null +++ b/gtfold-mfe/src/.deps/global.Po @@ -0,0 +1,85 @@ +global.o: global.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ + /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \ + /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +../include/global.h: + +../include/constants.h: diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po new file mode 100644 index 0000000..290868e --- /dev/null +++ b/gtfold-mfe/src/.deps/loader.Po @@ -0,0 +1,367 @@ +loader.o: loader.cc /usr/include/c++/4.4/iostream \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/bits/predefs.h \ + /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ + /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ + /usr/include/c++/4.4/cstddef \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/c++/4.4/bits/ios_base.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc \ + /usr/include/c++/4.4/bits/locale_classes.tcc \ + /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ + /usr/include/c++/4.4/bits/basic_ios.h \ + /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/wctype.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.4/bits/streambuf_iterator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.4/bits/locale_facets.tcc \ + /usr/include/c++/4.4/bits/basic_ios.tcc \ + /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ + /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ + /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + /usr/include/c++/4.4/cstring /usr/include/string.h \ + /usr/include/bits/string3.h /usr/include/stdlib.h \ + /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ + /usr/include/sys/types.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/bits/stdlib.h ../include/data.h \ + ../include/constants.h ../include/utils.h ../include/constants.h \ + ../include/global.h ../include/loader.h ../include/data.h + +/usr/include/c++/4.4/iostream: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/ostream: + +/usr/include/c++/4.4/ios: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/c++/4.4/cstddef: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/c++/4.4/bits/ios_base.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/bits/locale_classes.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + +/usr/include/c++/4.4/new: + +/usr/include/c++/4.4/bits/ostream_insert.h: + +/usr/include/c++/4.4/cxxabi-forced.h: + +/usr/include/c++/4.4/bits/stl_function.h: + +/usr/include/c++/4.4/backward/binders.h: + +/usr/include/c++/4.4/bits/basic_string.h: + +/usr/include/c++/4.4/initializer_list: + +/usr/include/c++/4.4/bits/basic_string.tcc: + +/usr/include/c++/4.4/bits/locale_classes.tcc: + +/usr/include/c++/4.4/streambuf: + +/usr/include/c++/4.4/bits/streambuf.tcc: + +/usr/include/c++/4.4/bits/basic_ios.h: + +/usr/include/c++/4.4/bits/locale_facets.h: + +/usr/include/c++/4.4/cwctype: + +/usr/include/wctype.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: + +/usr/include/c++/4.4/bits/streambuf_iterator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: + +/usr/include/c++/4.4/bits/locale_facets.tcc: + +/usr/include/c++/4.4/bits/basic_ios.tcc: + +/usr/include/c++/4.4/bits/ostream.tcc: + +/usr/include/c++/4.4/istream: + +/usr/include/c++/4.4/bits/istream.tcc: + +/usr/include/c++/4.4/fstream: + +/usr/include/c++/4.4/bits/codecvt.h: + +/usr/include/c++/4.4/cstdio: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: + +/usr/include/c++/4.4/bits/fstream.tcc: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/c++/4.4/cstring: + +/usr/include/string.h: + +/usr/include/bits/string3.h: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +../include/data.h: + +../include/constants.h: + +../include/utils.h: + +../include/constants.h: + +../include/global.h: + +../include/loader.h: + +../include/data.h: diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po new file mode 100644 index 0000000..df8b6af --- /dev/null +++ b/gtfold-mfe/src/.deps/main.Po @@ -0,0 +1,437 @@ +main.o: main.cc /usr/include/c++/4.4/iostream \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/bits/predefs.h \ + /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ + /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ + /usr/include/c++/4.4/cstddef \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/c++/4.4/bits/ios_base.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc \ + /usr/include/c++/4.4/bits/locale_classes.tcc \ + /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ + /usr/include/c++/4.4/bits/basic_ios.h \ + /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/wctype.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.4/bits/streambuf_iterator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.4/bits/locale_facets.tcc \ + /usr/include/c++/4.4/bits/basic_ios.tcc \ + /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ + /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/iomanip \ + /usr/include/c++/4.4/fstream /usr/include/c++/4.4/bits/codecvt.h \ + /usr/include/c++/4.4/cstdio /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/include/bits/stdio2.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + /usr/include/sys/time.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/c++/4.4/sstream \ + /usr/include/c++/4.4/bits/sstream.tcc /usr/include/stdlib.h \ + /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ + /usr/include/sys/types.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \ + /usr/include/bits/string3.h ../include/main.h \ + /usr/include/c++/4.4/vector /usr/include/c++/4.4/bits/stl_construct.h \ + /usr/include/c++/4.4/bits/stl_uninitialized.h \ + /usr/include/c++/4.4/bits/stl_vector.h \ + /usr/include/c++/4.4/bits/stl_bvector.h \ + /usr/include/c++/4.4/bits/vector.tcc ../include/constants.h \ + ../include/utils.h ../include/loader.h ../include/data.h \ + ../include/options.h /usr/include/c++/4.4/cstring ../include/global.h \ + ../include/energy.h ../include/algorithms.h ../include/constraints.h \ + ../include/traceback.h ../include/subopt_traceback.h \ + /usr/include/c++/4.4/cassert /usr/include/assert.h \ + /usr/include/c++/4.4/stack /usr/include/c++/4.4/deque \ + /usr/include/c++/4.4/bits/stl_deque.h \ + /usr/include/c++/4.4/bits/deque.tcc \ + /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \ + /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \ + /usr/include/c++/4.4/bits/stl_multimap.h ../include/shapereader.h + +/usr/include/c++/4.4/iostream: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/ostream: + +/usr/include/c++/4.4/ios: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/c++/4.4/cstddef: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/c++/4.4/bits/ios_base.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/bits/locale_classes.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + +/usr/include/c++/4.4/new: + +/usr/include/c++/4.4/bits/ostream_insert.h: + +/usr/include/c++/4.4/cxxabi-forced.h: + +/usr/include/c++/4.4/bits/stl_function.h: + +/usr/include/c++/4.4/backward/binders.h: + +/usr/include/c++/4.4/bits/basic_string.h: + +/usr/include/c++/4.4/initializer_list: + +/usr/include/c++/4.4/bits/basic_string.tcc: + +/usr/include/c++/4.4/bits/locale_classes.tcc: + +/usr/include/c++/4.4/streambuf: + +/usr/include/c++/4.4/bits/streambuf.tcc: + +/usr/include/c++/4.4/bits/basic_ios.h: + +/usr/include/c++/4.4/bits/locale_facets.h: + +/usr/include/c++/4.4/cwctype: + +/usr/include/wctype.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: + +/usr/include/c++/4.4/bits/streambuf_iterator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: + +/usr/include/c++/4.4/bits/locale_facets.tcc: + +/usr/include/c++/4.4/bits/basic_ios.tcc: + +/usr/include/c++/4.4/bits/ostream.tcc: + +/usr/include/c++/4.4/istream: + +/usr/include/c++/4.4/bits/istream.tcc: + +/usr/include/c++/4.4/iomanip: + +/usr/include/c++/4.4/fstream: + +/usr/include/c++/4.4/bits/codecvt.h: + +/usr/include/c++/4.4/cstdio: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: + +/usr/include/c++/4.4/bits/fstream.tcc: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/sys/time.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/c++/4.4/sstream: + +/usr/include/c++/4.4/bits/sstream.tcc: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/string.h: + +/usr/include/bits/string3.h: + +../include/main.h: + +/usr/include/c++/4.4/vector: + +/usr/include/c++/4.4/bits/stl_construct.h: + +/usr/include/c++/4.4/bits/stl_uninitialized.h: + +/usr/include/c++/4.4/bits/stl_vector.h: + +/usr/include/c++/4.4/bits/stl_bvector.h: + +/usr/include/c++/4.4/bits/vector.tcc: + +../include/constants.h: + +../include/utils.h: + +../include/loader.h: + +../include/data.h: + +../include/options.h: + +/usr/include/c++/4.4/cstring: + +../include/global.h: + +../include/energy.h: + +../include/algorithms.h: + +../include/constraints.h: + +../include/traceback.h: + +../include/subopt_traceback.h: + +/usr/include/c++/4.4/cassert: + +/usr/include/assert.h: + +/usr/include/c++/4.4/stack: + +/usr/include/c++/4.4/deque: + +/usr/include/c++/4.4/bits/stl_deque.h: + +/usr/include/c++/4.4/bits/deque.tcc: + +/usr/include/c++/4.4/bits/stl_stack.h: + +/usr/include/c++/4.4/map: + +/usr/include/c++/4.4/bits/stl_tree.h: + +/usr/include/c++/4.4/bits/stl_map.h: + +/usr/include/c++/4.4/bits/stl_multimap.h: + +../include/shapereader.h: diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po new file mode 100644 index 0000000..52acdb4 --- /dev/null +++ b/gtfold-mfe/src/.deps/options.Po @@ -0,0 +1,265 @@ +options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/bits/predefs.h \ + /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \ + /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \ + /usr/include/c++/4.4/cctype /usr/include/ctype.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc ../include/constants.h \ + ../include/data.h ../include/options.h /usr/include/stdlib.h \ + /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ + /usr/include/sys/types.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/bits/stdlib.h \ + /usr/include/c++/4.4/cstring /usr/include/string.h \ + /usr/include/bits/string3.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ + /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ + /usr/include/bits/stdio2.h + +../include/loader.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/cstddef: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + +/usr/include/c++/4.4/new: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/c++/4.4/bits/ostream_insert.h: + +/usr/include/c++/4.4/cxxabi-forced.h: + +/usr/include/c++/4.4/bits/stl_function.h: + +/usr/include/c++/4.4/backward/binders.h: + +/usr/include/c++/4.4/bits/basic_string.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/initializer_list: + +/usr/include/c++/4.4/bits/basic_string.tcc: + +../include/constants.h: + +../include/data.h: + +../include/options.h: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/c++/4.4/cstring: + +/usr/include/string.h: + +/usr/include/bits/string3.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po new file mode 100644 index 0000000..4c5d9af --- /dev/null +++ b/gtfold-mfe/src/.deps/shapereader.Po @@ -0,0 +1,360 @@ +shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/bits/predefs.h \ + /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ + /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ + /usr/include/c++/4.4/cstddef \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/ctype.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/c++/4.4/bits/ios_base.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc \ + /usr/include/c++/4.4/bits/locale_classes.tcc \ + /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ + /usr/include/c++/4.4/bits/basic_ios.h \ + /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/wctype.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.4/bits/streambuf_iterator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.4/bits/locale_facets.tcc \ + /usr/include/c++/4.4/bits/basic_ios.tcc \ + /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ + /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ + /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ + /usr/include/libio.h /usr/include/_G_config.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.4/bits/fstream.tcc /usr/include/string.h \ + /usr/include/bits/string3.h /usr/include/stdlib.h \ + /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ + /usr/include/sys/types.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ + /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + ../include/shapereader.h ../include/global.h ../include/constants.h \ + ../include/options.h /usr/include/c++/4.4/cstring + +/usr/include/c++/4.4/iostream: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/ostream: + +/usr/include/c++/4.4/ios: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/c++/4.4/cstddef: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/wchar.h: + +/usr/include/stdio.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/c++/4.4/bits/ios_base.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/bits/locale_classes.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + +/usr/include/c++/4.4/new: + +/usr/include/c++/4.4/bits/ostream_insert.h: + +/usr/include/c++/4.4/cxxabi-forced.h: + +/usr/include/c++/4.4/bits/stl_function.h: + +/usr/include/c++/4.4/backward/binders.h: + +/usr/include/c++/4.4/bits/basic_string.h: + +/usr/include/c++/4.4/initializer_list: + +/usr/include/c++/4.4/bits/basic_string.tcc: + +/usr/include/c++/4.4/bits/locale_classes.tcc: + +/usr/include/c++/4.4/streambuf: + +/usr/include/c++/4.4/bits/streambuf.tcc: + +/usr/include/c++/4.4/bits/basic_ios.h: + +/usr/include/c++/4.4/bits/locale_facets.h: + +/usr/include/c++/4.4/cwctype: + +/usr/include/wctype.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: + +/usr/include/c++/4.4/bits/streambuf_iterator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: + +/usr/include/c++/4.4/bits/locale_facets.tcc: + +/usr/include/c++/4.4/bits/basic_ios.tcc: + +/usr/include/c++/4.4/bits/ostream.tcc: + +/usr/include/c++/4.4/istream: + +/usr/include/c++/4.4/bits/istream.tcc: + +/usr/include/c++/4.4/fstream: + +/usr/include/c++/4.4/bits/codecvt.h: + +/usr/include/c++/4.4/cstdio: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: + +/usr/include/c++/4.4/bits/fstream.tcc: + +/usr/include/string.h: + +/usr/include/bits/string3.h: + +/usr/include/stdlib.h: + +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: + +/usr/include/sys/types.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +../include/shapereader.h: + +../include/global.h: + +../include/constants.h: + +../include/options.h: + +/usr/include/c++/4.4/cstring: diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po new file mode 100644 index 0000000..375a33e --- /dev/null +++ b/gtfold-mfe/src/.deps/subopt_traceback.Po @@ -0,0 +1,351 @@ +subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/features.h /usr/include/bits/predefs.h \ + /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ + /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/cstddef \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/stdio.h /usr/include/bits/types.h \ + /usr/include/bits/typesizes.h /usr/include/libio.h \ + /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ + ../include/constants.h ../include/energy.h ../include/data.h \ + ../include/constants.h ../include/utils.h ../include/global.h \ + ../include/subopt_traceback.h /usr/include/c++/4.4/cassert \ + /usr/include/assert.h /usr/include/c++/4.4/iostream \ + /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ + /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ + /usr/include/bits/wchar.h /usr/include/xlocale.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ios_base.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc \ + /usr/include/c++/4.4/bits/locale_classes.tcc \ + /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ + /usr/include/c++/4.4/bits/basic_ios.h \ + /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/wctype.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.4/bits/streambuf_iterator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.4/bits/locale_facets.tcc \ + /usr/include/c++/4.4/bits/basic_ios.tcc \ + /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ + /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/sstream \ + /usr/include/c++/4.4/bits/sstream.tcc /usr/include/c++/4.4/stack \ + /usr/include/c++/4.4/deque /usr/include/c++/4.4/bits/stl_construct.h \ + /usr/include/c++/4.4/bits/stl_uninitialized.h \ + /usr/include/c++/4.4/bits/stl_deque.h \ + /usr/include/c++/4.4/bits/deque.tcc \ + /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \ + /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \ + /usr/include/c++/4.4/bits/stl_multimap.h /usr/include/c++/4.4/vector \ + /usr/include/c++/4.4/bits/stl_vector.h \ + /usr/include/c++/4.4/bits/stl_bvector.h \ + /usr/include/c++/4.4/bits/vector.tcc + +/usr/include/c++/4.4/cstdio: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/cstddef: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/stdio.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +../include/constants.h: + +../include/energy.h: + +../include/data.h: + +../include/constants.h: + +../include/utils.h: + +../include/global.h: + +../include/subopt_traceback.h: + +/usr/include/c++/4.4/cassert: + +/usr/include/assert.h: + +/usr/include/c++/4.4/iostream: + +/usr/include/c++/4.4/ostream: + +/usr/include/c++/4.4/ios: + +/usr/include/c++/4.4/iosfwd: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/postypes.h: + +/usr/include/c++/4.4/cwchar: + +/usr/include/bits/wchar.h: + +/usr/include/xlocale.h: + +/usr/include/bits/wchar2.h: + +/usr/include/c++/4.4/exception: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/bits/functexcept.h: + +/usr/include/c++/4.4/exception_defines.h: + +/usr/include/c++/4.4/bits/cpp_type_traits.h: + +/usr/include/c++/4.4/ext/type_traits.h: + +/usr/include/c++/4.4/ext/numeric_traits.h: + +/usr/include/c++/4.4/bits/stl_pair.h: + +/usr/include/c++/4.4/bits/move.h: + +/usr/include/c++/4.4/bits/concept_check.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_types.h: + +/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: + +/usr/include/c++/4.4/bits/stl_iterator.h: + +/usr/include/c++/4.4/debug/debug.h: + +/usr/include/c++/4.4/bits/localefwd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: + +/usr/include/c++/4.4/clocale: + +/usr/include/locale.h: + +/usr/include/bits/locale.h: + +/usr/include/c++/4.4/cctype: + +/usr/include/ctype.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/c++/4.4/bits/ios_base.h: + +/usr/include/c++/4.4/ext/atomicity.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: + +/usr/include/pthread.h: + +/usr/include/sched.h: + +/usr/include/time.h: + +/usr/include/bits/sched.h: + +/usr/include/bits/time.h: + +/usr/include/signal.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/bits/setjmp.h: + +/usr/include/unistd.h: + +/usr/include/bits/posix_opt.h: + +/usr/include/bits/environments.h: + +/usr/include/bits/confname.h: + +/usr/include/getopt.h: + +/usr/include/bits/unistd.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: + +/usr/include/c++/4.4/bits/locale_classes.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/bits/allocator.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: + +/usr/include/c++/4.4/ext/new_allocator.h: + 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+/usr/include/c++/4.4/sstream: + +/usr/include/c++/4.4/bits/sstream.tcc: + +/usr/include/c++/4.4/stack: + +/usr/include/c++/4.4/deque: + +/usr/include/c++/4.4/bits/stl_construct.h: + +/usr/include/c++/4.4/bits/stl_uninitialized.h: + +/usr/include/c++/4.4/bits/stl_deque.h: + +/usr/include/c++/4.4/bits/deque.tcc: + +/usr/include/c++/4.4/bits/stl_stack.h: + +/usr/include/c++/4.4/map: + +/usr/include/c++/4.4/bits/stl_tree.h: + +/usr/include/c++/4.4/bits/stl_map.h: + +/usr/include/c++/4.4/bits/stl_multimap.h: + +/usr/include/c++/4.4/vector: + +/usr/include/c++/4.4/bits/stl_vector.h: + +/usr/include/c++/4.4/bits/stl_bvector.h: + +/usr/include/c++/4.4/bits/vector.tcc: diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po new file mode 100644 index 0000000..c8b0c87 --- /dev/null +++ b/gtfold-mfe/src/.deps/traceback.Po @@ -0,0 +1,127 @@ +traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ + /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ + /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ + /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \ + /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/sys/select.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h /usr/include/math.h \ + /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ + /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ + /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ + /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ + /usr/include/assert.h ../include/data.h ../include/constants.h \ + ../include/constants.h ../include/constraints.h ../include/energy.h \ + ../include/data.h ../include/global.h ../include/traceback.h \ + ../include/utils.h + +/usr/include/stdio.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/libio.h: + +/usr/include/_G_config.h: + +/usr/include/wchar.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: + +/usr/include/bits/stdio_lim.h: + +/usr/include/bits/sys_errlist.h: + +/usr/include/bits/stdio.h: + +/usr/include/bits/stdio2.h: + +/usr/include/stdlib.h: + +/usr/include/sys/types.h: + +/usr/include/time.h: + +/usr/include/endian.h: + +/usr/include/bits/endian.h: + +/usr/include/bits/byteswap.h: + +/usr/include/sys/select.h: + +/usr/include/bits/select.h: + +/usr/include/bits/sigset.h: + +/usr/include/bits/time.h: + +/usr/include/sys/sysmacros.h: + +/usr/include/bits/pthreadtypes.h: + +/usr/include/alloca.h: + +/usr/include/bits/stdlib.h: + +/usr/include/math.h: + +/usr/include/bits/huge_val.h: + +/usr/include/bits/huge_valf.h: + +/usr/include/bits/huge_vall.h: + +/usr/include/bits/inf.h: + +/usr/include/bits/nan.h: + +/usr/include/bits/mathdef.h: + +/usr/include/bits/mathcalls.h: + +/usr/include/bits/mathinline.h: + +/usr/include/assert.h: + +../include/data.h: + +../include/constants.h: + +../include/constants.h: + +../include/constraints.h: + +../include/energy.h: + +../include/data.h: + +../include/global.h: + +../include/traceback.h: + +../include/utils.h: diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po new file mode 100644 index 0000000..61ad5ac --- /dev/null +++ b/gtfold-mfe/src/.deps/utils.Po @@ -0,0 +1,222 @@ +utils.o: utils.cc ../include/utils.h ../include/constants.h \ + /usr/include/string.h /usr/include/features.h \ + /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ + /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ + /usr/include/gnu/stubs-64.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/xlocale.h /usr/include/bits/string3.h \ + /usr/include/c++/4.4/string \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.4/bits/stringfwd.h \ + /usr/include/c++/4.4/bits/char_traits.h \ + /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \ + /usr/include/c++/4.4/bits/functexcept.h \ + /usr/include/c++/4.4/exception_defines.h \ + /usr/include/c++/4.4/bits/cpp_type_traits.h \ + /usr/include/c++/4.4/ext/type_traits.h \ + /usr/include/c++/4.4/ext/numeric_traits.h \ + /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ + /usr/include/c++/4.4/bits/concept_check.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.4/bits/stl_iterator.h \ + /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \ + /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \ + /usr/include/c++/4.4/bits/allocator.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ + /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.4/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \ + /usr/include/c++/4.4/cctype /usr/include/ctype.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \ + /usr/include/c++/4.4/cxxabi-forced.h \ + /usr/include/c++/4.4/bits/stl_function.h \ + /usr/include/c++/4.4/backward/binders.h \ + /usr/include/c++/4.4/bits/basic_string.h \ + /usr/include/c++/4.4/ext/atomicity.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ + /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ + /usr/include/bits/confname.h /usr/include/getopt.h \ + /usr/include/bits/unistd.h \ + /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.4/initializer_list \ + /usr/include/c++/4.4/bits/basic_string.tcc + +../include/utils.h: + +../include/constants.h: + +/usr/include/string.h: + +/usr/include/features.h: + +/usr/include/bits/predefs.h: + +/usr/include/sys/cdefs.h: + +/usr/include/bits/wordsize.h: + +/usr/include/gnu/stubs.h: + +/usr/include/gnu/stubs-64.h: + +/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: + +/usr/include/xlocale.h: + +/usr/include/bits/string3.h: + +/usr/include/c++/4.4/string: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + +/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: + +/usr/include/c++/4.4/bits/stringfwd.h: + +/usr/include/c++/4.4/bits/char_traits.h: + +/usr/include/c++/4.4/bits/stl_algobase.h: + +/usr/include/c++/4.4/cstddef: + +/usr/include/c++/4.4/bits/functexcept.h: + 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indicator (ignoring line): %s\n", line.c_str()); + } + }else{ + printf("Invalid line (ignoring): %s\n", line.c_str()); + } + } + +} + +int getShapeEnergy(int position){ + if(SHAPE_ENABLED){ + return SHAPEenergies[position]; + } + else{ + return 0; + } +} + +int calcShapeEnergy(double shapeNumber){ +//ZS: This function returns the free energy contribution as an integer. + if(shapeNumber<(double)0){ + return 0; + } + else{ + double energy = shapeModel(shapeNumber); + return (int)floor(100.0*energy+ .5); + } +} + + +double shapeModel(double SHAPE_value){ +//ZS: This function calculates the free energy contribution due to SHAPE. + double m = 2.6; + double b = -0.8; + return m*log(SHAPE_value+1)+b; +} + + + + From de4982d3154a87ebbbfdd6c4146915c37fcba2ac Mon Sep 17 00:00:00 2001 From: dsokus Date: Sat, 7 May 2011 20:07:52 -0400 Subject: [PATCH 016/187] Errors in thermodynamic paramters... commit long overdue!! (It is not clear what to do with the misc loop parameters.) Signed-off-by: dsokus --- .../Turner04-errors/Turner04-errors/Makefile | 405 ++++++++ .../Turner04-errors/Makefile.am | 27 + .../Turner04-errors/coaxial.dat | 63 ++ .../Turner04-errors/coaxstack.dat | 63 ++ .../Turner04-errors/dangle.dat | 72 ++ .../Turner04-errors/hexaloop.dat | 6 + .../Turner04-errors/Turner04-errors/int11.dat | 101 ++ .../Turner04-errors/Turner04-errors/int21.dat | 353 +++++++ .../Turner04-errors/Turner04-errors/int22.dat | 928 ++++++++++++++++++ .../Turner04-errors/Turner04-errors/loop.dat | 34 + .../Turner04-errors/miscloop.dat | 48 + .../Turner04-errors/Turner04-errors/stack.dat | 63 ++ .../Turner04-errors/Turner04-errors/tloop.dat | 17 + .../Turner04-errors/triloop.dat | 4 + .../Turner04-errors/tstack.dat | 63 ++ .../Turner04-errors/tstackcoax.dat | 63 ++ .../Turner04-errors/tstackh.dat | 63 ++ .../Turner04-errors/tstacki.dat | 63 ++ .../Turner04-errors/tstackm.dat | 63 ++ 19 files changed, 2499 insertions(+) create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/int22.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/loop.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat create mode 100644 gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile new file mode 100644 index 0000000..ba5abb0 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile @@ -0,0 +1,405 @@ +# Makefile.in generated by automake 1.11.1 from Makefile.am. +# data/Turner04/Makefile. 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+gtfold_datadir = $(datadir)/@PACKAGE@/Turner04 + +gtfold_data_DATA = \ + stack.dat\ + miscloop.dat\ + dangle.dat\ + loop.dat\ + coaxial.dat\ + coaxstack.dat\ + hexaloop.dat\ + int11.dat\ + int21.dat\ + int22.dat\ + tloop.dat\ + triloop.dat\ + tstack.dat\ + tstackcoax.dat\ + tstackh.dat\ + tstacki.dat\ + tstackm.dat + +EXTRA_DIST = $(gtfold_data_DATA) + +CLEANFILES = *~ + diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat new file mode 100644 index 0000000..1fb3051 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat new file mode 100644 index 0000000..cef509d --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat new file mode 100644 index 0000000..7c9161b --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat @@ -0,0 +1,72 @@ + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + A A A A + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + C C C C + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + G G G G + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + U U U U + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat new file mode 100644 index 0000000..66eb771 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat @@ -0,0 +1,6 @@ + Seq Energy + ------------- + ACAGUGCU 0 + ACAGUGAU 0 + ACAGUUCU 0 + ACAGUACU 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat new file mode 100644 index 0000000..67aa76a --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat @@ -0,0 +1,101 @@ +Data table for symetric interior loops of size 2 +Free energies at 37 degrees for RNA +Data Arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + Y + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 -0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat new file mode 100644 index 0000000..9966877 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat @@ -0,0 +1,353 @@ +Data tables for asymmetric interior loops of size 3 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + YA + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 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the ninio equation +the maximum correction +--> +3.0 +the f(m) array (see Ninio for details) +--> + .6 .6 .6 .6 +multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 -.0 -.9 +efn2 multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 0.0 -0.9 +miscloop asym +--> +0.9 +multiloop strain +--> +0.44 +terminal AU penalty +--> + 0.5 +bonus for GGG hairpin +--> +-2.2 +c hairpin slope +--> +0.3 +c hairpin intercept +--> +0.24 +c hairpin of 3 +--> +1.5 +Intermolecular initiation free energy +--> +4.1 +Bonus for Single C bulges adjacent to C +--> +0.3 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat new file mode 100644 index 0000000..81fa1e6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) 0 0 0 0 + (C) 0 0 0 0 + (G) 0 0 0 0 + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.03 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0.32 + 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0 0.24 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0.09 0 0.27 0 0 0 0 + 0 0 0 0 0 0 0 0 0.06 0 0.24 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0 0.28 + 0 0 0 0 0 0 0.08 0 0 0 0 0 0 0 0.25 0 + 0 0 0 0 0 0.07 0 0.27 0 0 0 0 0 0.25 0 0.96 + 0 0 0 0 0.06 0 0.25 0 0 0 0 0 0.24 0 0.56 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0.09 0 0 0 0 0 0 0 0.30 0 0 0 0 + 0 0 0.06 0 0 0 0 0 0 0 0.27 0 0 0 0 0 + 0 0.07 0 0.30 0 0 0 0 0 0.24 0 0.48 0 0 0 0 +0.03 0 0.28 0 0 0 0 0 0.32 0 0.96 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat new file mode 100644 index 0000000..3a63c62 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat @@ -0,0 +1,17 @@ + Seq Energy + ------------- +CUACGG 0 +CUCCGG 0 +CUUCGG 0 +CCAAGG 0 +CCCAGG 0 +CCGAGG 0 +CCUAGG 0 +CCACGG 0 +CCGCGG 0 +CCUCGG 0 +CUAAGG 0 +CUCAGG 0 +CUUAGG 0 +CUGCGG 0 +CAACGG 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat new file mode 100644 index 0000000..e66a4b6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat @@ -0,0 +1,4 @@ + Seq Energy + ------------- +CAACG 0 +GUUAC 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackcoax.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 From 0e3f085ba7c44f6b953b44298969d9104be4ff72 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sun, 8 May 2011 03:17:13 +0200 Subject: [PATCH 017/187] Contact distance implemented + missing SHAPE header included again in algorithms.c --- gtfold-mfe/include/constraints.h | 1 + gtfold-mfe/src/.deps/algorithms.Po | 3 +++ gtfold-mfe/src/algorithms.c | 3 ++- gtfold-mfe/src/constraints.cc | 6 ++++++ 4 files changed, 12 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h index a6b3370..8743d88 100644 --- a/gtfold-mfe/include/constraints.h +++ b/gtfold-mfe/include/constraints.h @@ -34,6 +34,7 @@ int check_pair(int i, int j) ; int check_stack(int i, int j) ; int check_hairpin(int i, int j) ; int can_dangle(int i); +int withinCD(int i, int j); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po index b84c3b7..c737d2e 100644 --- a/gtfold-mfe/src/.deps/algorithms.Po +++ b/gtfold-mfe/src/.deps/algorithms.Po @@ -22,6 +22,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ ../include/constants.h ../include/utils.h ../include/constants.h \ ../include/energy.h ../include/data.h ../include/global.h \ ../include/algorithms.h ../include/constraints.h \ + ../include/shapereader.h \ /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h /usr/include/stdio.h: @@ -128,4 +129,6 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ ../include/constraints.h: +../include/shapereader.h: + /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h: diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index eef7105..8986603 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -30,6 +30,7 @@ #include "global.h" #include "algorithms.h" #include "constraints.h" +#include "shapereader.h" #ifdef _OPENMP #include "omp.h" @@ -56,7 +57,7 @@ int calculate(int len, int nThreads) { j = i + b; int flag = 0, newWM = INFINITY_; - if (canPair(RNA[i], RNA[j])) { + if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) { flag = 1; int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index f97d214..0dd931d 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -451,5 +451,11 @@ int check_hairpin(int i, int j) { //return is_ss(i,j) || force_pair(i,j) || force_pair(j,i); } else return 0; +} +int withinCD(int i, int j){ + if (LIMIT_DISTANCE){ + return j-i+1>contactDistance; + } + else return 1; } From ff9ec67037510adabad78fba9e137d0d12ecfcb1 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sun, 8 May 2011 03:26:55 +0200 Subject: [PATCH 018/187] Removed unnecessary output --- gtfold-mfe/src/main.cc | 4 ---- 1 file changed, 4 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 8ab8888..b8edbf3 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -65,10 +65,6 @@ void init_fold(string seq) { init_constraints(constraintsFile.c_str(), len); } - if (LIMIT_DISTANCE){ - printf("Limit distance is currently not implemented."); - } - if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } From 48ee2aafe9f74c8164b90e892dfda25083490aac Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Mon, 9 May 2011 01:03:22 +0200 Subject: [PATCH 019/187] Fixed pseudoknotted constraint issue (issue nr. 3) --- gtfold-mfe/src/constraints.cc | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 0dd931d..e0913f5 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -116,7 +116,8 @@ static int load_constraints(const char* constr_file, int verbose=0) { if(v_fbp.size()>1){ std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second) { + if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second + && v_fbp[ii].second >= v_fbp[ii+1].first) { fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); exit(-1); } From 0d865669b29582ae27cdc1c2387b34c166676ce5 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sat, 14 May 2011 05:22:49 +0200 Subject: [PATCH 020/187] Fix to forcing constraints, traceback error, and some small problems in the multiloop optimization. --- gtfold-mfe/src/.deps/traceback.Po | 4 +++- gtfold-mfe/src/algorithms.c | 37 ++++++++++++++++++++-------- gtfold-mfe/src/constraints.cc | 11 +++++---- gtfold-mfe/src/traceback.c | 40 +++++++++++++++++++++++-------- 4 files changed, 67 insertions(+), 25 deletions(-) diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po index c8b0c87..c475c0e 100644 --- a/gtfold-mfe/src/.deps/traceback.Po +++ b/gtfold-mfe/src/.deps/traceback.Po @@ -22,7 +22,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/assert.h ../include/data.h ../include/constants.h \ ../include/constants.h ../include/constraints.h ../include/energy.h \ ../include/data.h ../include/global.h ../include/traceback.h \ - ../include/utils.h + ../include/utils.h ../include/shapereader.h /usr/include/stdio.h: @@ -125,3 +125,5 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ ../include/traceback.h: ../include/utils.h: + +../include/shapereader.h: diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 8986603..b1d9b6c 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -56,7 +56,6 @@ int calculate(int len, int nThreads) { for (i = 1; i <= len - b; i++) { j = i + b; int flag = 0, newWM = INFINITY_; - if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) { flag = 1; int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin @@ -65,14 +64,23 @@ int calculate(int len, int nThreads) { int p=0, q=0; int VBIij = INFINITY_; + int found_forced_pair = 0; for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { int minq = j-i+p-MAXLOOP-2; if (minq < p+1+TURN) minq = p+1+TURN; for (q = minq; q < j; q++) { if (!canPair(RNA[p], RNA[q])) continue; if (check_iloop(i,j,p,q)) continue; + if(force_pair1(p,q)){ + //ZS: if we know a pair should be forced, we should + //just enforce it and not care about other options. + VBIij = eL(i,j,p,q) + V(p,q); + found_forced_pair = 1; + break; + } VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); } + if(found_forced_pair){break;} } VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij; } // Internal Loop END @@ -87,7 +95,12 @@ int calculate(int len, int nThreads) { VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); - newWM = MIN(newWM, VMij); + //ZS: I don't think the following line is being checked in traceback, so + //if you enable it, sometimes huge parts of the structure will not be possible + //to trace. + //I don't know if it should be here or not. If it is here, it should be in traceback + //too. For now, I am removing it! + //newWM = MIN(newWM, VMij); } int d3 = can_dangle(j-1)?Ed3(i,j,j-1):INFINITY_; @@ -108,20 +121,24 @@ int calculate(int len, int nThreads) { if (j-i > 4) { // WM BEGIN int h; - if (!flag) { + //ZS: if we know that i,j are pairing, we just have to set WM(i,j) = V(i,j) in the best possible way. + //Conversely, we only need to find the best partitioning if we know that i,j are not forced to pair. + + //Prashant's original code had if(!flag) here... I don't know what that was supposed to do? + if (!force_pair1(i,j)) { for (h = i+TURN+1 ; h <= j-TURN-1; h++) { newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); } } newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; - newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; - newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_; - - newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_; - newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_; + //ZS: if i,j are forced to pair then can_dangle(i) and can_dangle(j) will be false + newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): newWM; + newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : newWM; + newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): newWM; + newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; + newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; WMU(i,j) = WML(i,j) = newWM; } // WM END } @@ -147,7 +164,7 @@ int calculate(int len, int nThreads) { else if (Wj==Wijd && force_pair1(i,j-1)) branch = 1; else if (force_pair1(i+1,j)) - branch = 1; + branch = 1; } } W[j] = branch?Wj:MIN(Wj, W[j-1]); diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index e0913f5..aca5419 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -377,10 +377,13 @@ int force_ss1(int i){ int force_ssregion1(int i, int j){ if(CONS_ENABLED){ + int value = 1; for(int p = i; p all should be ss Widjd = Wijd = Widj = INFINITY_; Wij = V(i,j) + auPenalty(i, j) + wim1; @@ -76,7 +79,8 @@ void traceW(int j) { Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); if (W[j] == Wj) { - if (W[j] == Wij) { + //if we know W[j] is pairing with something + if (W[j] == Wij || force_pair1(i,j)){ done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); @@ -86,7 +90,7 @@ void traceW(int j) { traceV(i, j); if (flag || force_ssregion1(1,i)) traceW(i - 1); break; - } else if (W[j] == Widjd && can_dangle(i) && can_dangle(j)) { + } else if ((W[j] == Widjd && can_dangle(i) && can_dangle(j)) || force_pair1(i+1,j-1)) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00); @@ -96,7 +100,7 @@ void traceW(int j) { traceV(i + 1, j - 1); if (flag || force_ssregion1(1,i)) traceW(i - 1); break; - } else if (W[j] == Wijd && can_dangle(j)) { + } else if ((W[j] == Wijd && can_dangle(j))||force_pair1(i,j-1)) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); @@ -106,7 +110,7 @@ void traceW(int j) { traceV(i, j - 1); if (flag || force_ssregion1(1,i)) traceW(i - 1); break; - } else if (W[j] == Widj && can_dangle(i)) { + } else if ((W[j] == Widj && can_dangle(i))||force_pair1(i+1,j)) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); @@ -126,14 +130,15 @@ void traceW(int j) { } int traceV(int i, int j) { + int a, b, c, d, Vij; if (j-i < TURN) return INFINITY_; - a = eH(i, j); - b = eS(i, j) + V(i + 1, j - 1); + a = eH(i, j)+getShapeEnergy(i) + getShapeEnergy(j); + b = eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j); if (eS(i, j) == 0) b = INFINITY_; - c = VBI(i,j); - d = VM(i,j); + c = VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j); + d = VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j); Vij = MIN(MIN(a, b), MIN(c, d)); @@ -251,6 +256,7 @@ int traceVM(int i, int j) { done = 1; eVM += traceWM(i + 2, h - 1); eVM += traceWM(h, j - 2); + break; } } @@ -260,7 +266,6 @@ int traceVM(int i, int j) { } int traceWM(int i, int j) { - int done; int h1, h; int eWM = 0; @@ -312,5 +317,20 @@ int traceWM(int i, int j) { } } } + //ZS: This is for debugging purposes. + if(!done){ + printf("ERROR: WM couldn't be traced!\n"); + printf("%d %d \n", i, j); + printf("WM(i,j) = %d\n", WM(i,j)); + printf("candangle i? %d\n", can_dangle(i)); + printf("candangle j? %d\n", can_dangle(j)); + printf("The options were: \n"); + printf("Option 1 %d \n" , V(i,j) + auPenalty(i, j) + Eb); + printf("Option 2 %d \n" , V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec); + printf("Option 3 %d \n", V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec); + printf("Option 4 %d \n", V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec); + printf("Option 5 %d \n", WM(i + 1,j) + Ec ); + printf("Option 6 %d \n", WM(i,j - 1) + Ec); + } return eWM; } From e6877be5ebb72d32820036ca534db0f22203c63b Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sat, 14 May 2011 15:37:42 +0200 Subject: [PATCH 021/187] fix to tracing W[i] even if it has positive energy, in the special case that something is forced to pair within it --- gtfold-mfe/src/traceback.c | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 9d7290e..9c961e8 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -68,7 +68,9 @@ void traceW(int j) { wim1 = MIN(0, W[i-1]); flag = 1; - if (wim1 != W[i-1]) flag = 0; //ZS: flag is false if the free energy of the best structure to W[i] is 0 --> all should be ss + if (wim1 != W[i-1] && !check_ssregion(1,i)) flag = 0; + //ZS: flag is false if the free energy of the best structure to W[i] is > 0 --> all should be ss + //UNLESS there is at least one base that is forced to pair in that region, this is revealed by check_ssregion(1,i) Widjd = Wijd = Widj = INFINITY_; Wij = V(i,j) + auPenalty(i, j) + wim1; @@ -123,7 +125,7 @@ void traceW(int j) { } } } - + if (W[j] == W[j - 1] && !done) traceW(j-1); return; From 4d8be8a072ebee2fdd357dc8c570ed059a7129aa Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Sat, 14 May 2011 16:19:27 +0200 Subject: [PATCH 022/187] fixed an out-of-scope reference in unconstrained predictions, and added verification function to check that prediction fulfills constraint criteria --- gtfold-mfe/include/constraints.h | 1 + gtfold-mfe/src/constraints.cc | 80 ++++++++++++++++++++++++++++++-- gtfold-mfe/src/main.cc | 10 ++++ gtfold-mfe/src/traceback.c | 2 +- 4 files changed, 88 insertions(+), 5 deletions(-) diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h index 8743d88..045ebad 100644 --- a/gtfold-mfe/include/constraints.h +++ b/gtfold-mfe/include/constraints.h @@ -35,6 +35,7 @@ int check_stack(int i, int j) ; int check_hairpin(int i, int j) ; int can_dangle(int i); int withinCD(int i, int j); +int verify_structure(); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index aca5419..86814b8 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -263,6 +263,76 @@ int init_constraints(const char* constr_file,int length) { return 0; } +int verify_structure(){ + //ZS: This method returns true if the structure (global.h) is consistent with + //the constraints, and false if it is not. + + if(CONS_ENABLED){ + int errorhappened = 0; + int it, k; + //Check prohibited constraints + if(nPBP != 0){ + for(it = 0; it < nPBP; it++){ + if(PBP[it][2] < 1 || PBP[it][1] == 0){ + //printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); + continue; + } + for(k = 1; k <= PBP[it][2]; k++){ + //correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1)) + if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){ + errorhappened = 1; + printf("Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]); + break; + } + } + } + } + + //Check forced constraints + if(nFBP != 0){ + for(it = 0; it Date: Tue, 17 May 2011 02:57:28 +0200 Subject: [PATCH 023/187] fix to prohibited constraints --- gtfold-mfe/src/algorithms.c | 3 +++ gtfold-mfe/src/constraints.cc | 20 ++++++++++++++++++++ gtfold-mfe/src/main.cc | 3 +++ 3 files changed, 26 insertions(+) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index b1d9b6c..c7b9a3d 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -39,6 +39,9 @@ int calculate(int len, int nThreads) { int b, i, j; + +// printf("%d\n", BP(1145, 13)); + #ifdef _OPENMP if (nThreads>0) omp_set_num_threads(nThreads); #endif diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 86814b8..3d50a5f 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -174,6 +174,17 @@ int init_constraints(const char* constr_file,int length) { //ZS: set prohibited basepairs if(nPBP != 0){ + int temp; + //Make sure smallest one is first + for(it = 0; it < nPBP; it++){ + if(PBP[it][0] > PBP[it][1]){ + temp = PBP[it][0]; + PBP[it][0] = PBP[it][1]; + PBP[it][1] = temp; + } + printf("%d\n", it); + } + for(it = 0; it < nPBP; it++){ if(PBP[it][2] < 1 || PBP[it][1] == 0){ printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); @@ -194,6 +205,15 @@ int init_constraints(const char* constr_file,int length) { //ZS: set forced basepairs and single-stranded nucleotides if(nFBP != 0){ + int temp; + for(it = 0; it < nFBP; it++){ + if(FBP[it][0] > FBP[it][1]){ + temp = FBP[it][0]; + FBP[it][0] = FBP[it][1]; + FBP[it][1] = temp; + } + printf("%d\n", it); + } for(it = 0; it Date: Tue, 17 May 2011 09:53:30 -0400 Subject: [PATCH 024/187] I need to move this to another computer to go to a ballgame --- gtfold-mfe/src/partition-dangle.cc | 57 ++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 gtfold-mfe/src/partition-dangle.cc diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc new file mode 100644 index 0000000..53b889e --- /dev/null +++ b/gtfold-mfe/src/partition-dangle.cc @@ -0,0 +1,57 @@ +/**s1 -> partial_external +* s2 -> partial_multi +* s3 -> partial_multi2 +* u1 -> u_helper +* f -> cond_dangle (conditional) +**/ + +/**TODO cond_dangle, ed3, ed5,**/ + +/** +* For each spot in partial_external at index h,j we'll need: +**/ + +double RT = 0.00198721 * 310.15; + +int l; + +for(l = i+2; l < j; l++){ + upm[i][j] += up[i+1][l] * exp(-(a + 2 * c + /**TODO terminal pair i+1,l**/)/RT) * + (exp(-ed3(i+1,l,l+1)/RT) * + u_helper[l+2][j-1] + + u_helper[l+1][j-1] - + u_helper[l+2][j-1]); + if(l != i+2){ //goes from i + 2 < l < j + upm[i][j] += up[i + 2][l] * + exp(-(a + 2c + b + ed3(j,i,i + 1) + /**TODO terminal pair i+2, l**/)/RT) * + (exp(-ed3(i+2,l,l+1)/RT)*u_helper[l+2][j-1] + u_helper[l+1][j-1] - + u_helper[l+2][j-1]); + + if(l != j - 1){ + upm[i][j] += exp(-ed3(j,i,i+1)/RT)*exp(-(a + 2 * c + (h - i -1) * b)/RT) * + partial_multi[l][j]; + //Changed h in the paper to l it makes no difference + //other than unifying loops + } + } +} + + +for(l = h+1; l < j; l++){ + partial_external[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * + (exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j] - + u_helper[l+2][j]); + + partial_multi[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * + (exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j-1] - + u_helper[l+2][j-1]); + + partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j) + +u_helper(l + 1,j) - u1(l + 2,j)); + +} +/** partial_multi2 goes up to j **/ +partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j) + +u_helper(l + 1,j) - u1(l + 3,j)); From 83f7fe5caa4b99e7ff571c52b1d1c6700ab154e2 Mon Sep 17 00:00:00 2001 From: Joshua Anderson Date: Wed, 18 May 2011 09:17:43 -0400 Subject: [PATCH 025/187] First draft of matrix filling --- gtfold-mfe/src/partition-dangle.cc | 159 +++++++++++++++++++++-------- 1 file changed, 116 insertions(+), 43 deletions(-) diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc index 53b889e..d07064c 100644 --- a/gtfold-mfe/src/partition-dangle.cc +++ b/gtfold-mfe/src/partition-dangle.cc @@ -1,57 +1,130 @@ +//The paper (Dirks, Pierce) offhandedly mentions a G-U terminal pair penalty +//I don't think we do that... + /**s1 -> partial_external * s2 -> partial_multi * s3 -> partial_multi2 -* u1 -> u_helper +* u1 -> u_multi * f -> cond_dangle (conditional) **/ -/**TODO cond_dangle, ed3, ed5,**/ +#include energy.h -/** -* For each spot in partial_external at index h,j we'll need: -**/ -double RT = 0.00198721 * 310.15; - -int l; - -for(l = i+2; l < j; l++){ - upm[i][j] += up[i+1][l] * exp(-(a + 2 * c + /**TODO terminal pair i+1,l**/)/RT) * - (exp(-ed3(i+1,l,l+1)/RT) * - u_helper[l+2][j-1] + - u_helper[l+1][j-1] - - u_helper[l+2][j-1]); - if(l != i+2){ //goes from i + 2 < l < j - upm[i][j] += up[i + 2][l] * - exp(-(a + 2c + b + ed3(j,i,i + 1) + /**TODO terminal pair i+2, l**/)/RT) * - (exp(-ed3(i+2,l,l+1)/RT)*u_helper[l+2][j-1] + u_helper[l+1][j-1] - - u_helper[l+2][j-1]); - - if(l != j - 1){ - upm[i][j] += exp(-ed3(j,i,i+1)/RT)*exp(-(a + 2 * c + (h - i -1) * b)/RT) * - partial_multi[l][j]; - //Changed h in the paper to l it makes no difference - //other than unifying loops - } - } +int cond_dangle(int j, int h, int l){ + return j - 1 == l ? 1 : exp(-Ed3(h,l,l+1)/RT); } +double RT = (0.00198721 * 310.15)/100.00; +//So that we don't have the /100 in every exponent +//Seeing as we missed some last time + +int seg_length; +int i; +for(seg_length = MIN_TURN; seg_length < len; len ++){ + for(i = 1; i < seg_length - MIN_TURN; i++){ + j = i + seg_length; + int l; + /** + * For each spot in partial_external at index h,j we'll need: + **/ + for(l = i+2; l < j; l++){ + upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) * + (exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + if(l != i+2){ //goes from i + 2 < l < j + upm[i][j] += up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) * + (exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); -for(l = h+1; l < j; l++){ - partial_external[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * - (exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j] - - u_helper[l+2][j]); + if(l != j - 1){ + upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * + partial_multi[l][j]; + //Changed h in the paper to l it makes no difference + //other than unifying loops + } + } + } - partial_multi[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * - (exp(-ed3(h,l,l+1)/RT)*u_helper[l+2,j-1] + u_helper[l+1][j-1] - - u_helper[l+2][j-1]); - partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * - (cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j) - +u_helper(l + 1,j) - u1(l + 2,j)); - + up[i][j] += exp(-eh(i,j)/RT) + exp(-es(i,j)/RT) * up[i + 1][j - 1] + upm[i][j]; + for(l = j - 1; l > i + 1; l--){ + if((j - l) - 2> MAX_LOOP){ + break; + } + for(h = i + 1 ; h < l; h++){ + if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack + up[i][j] += exp(-ebi(i,j,h,l)/RT); + } + if((j - l) + (h - i) - 2> MAX_LOOP){ + break; + } + } + } + + for(l = i + 1; l <= j ; l++){ + u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) * + (cond_dangle(j + 1, i, l) * exp(-(j - l) * Eb/RT) + + exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != i+1){ + u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)* + (cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + + exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != j){ + u_multi[i][j] += exp(-(Ec + (h - i) * Eb)/RT) * partial_multi2[l][j]; + + } + } + } + + + int h = i; //To stay consistant with the notation in the paper. + + for(l = h+1; l < j; l++){ + partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u[l + 2,j - 1] + + u[l + 1][j] - + u[l + 2][j]); + + partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + } + /** partial_multi2 goes up to j **/ + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + //Finally we do the u matrix + u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT); + + for(l = i + 1; l < j; l++){ + //Replaced l with h in the next line to unify loops + u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT) + + u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] + + u[l + 1][j] - u[l + 2][j]); + if(l != j - 1) { + u[i][j] += partial_external[l][j]; + } + + } + } } -/** partial_multi2 goes up to j **/ -partial_multi2[h][j] += up[h][l] * exp( -(ed5(h,l,h-1) + /**TODO terminal pair hl**/) / RT) * - (cond_dangle(j + 1, h, l)*exp(-(j-l) * b / RT) + exp(-ed3(h,l,l + 1)/RT)*u_helper(l+2,j) - +u_helper(l + 1,j) - u1(l + 3,j)); From d814038e5fc3aab31b13ad257a79dcb725a8d10a Mon Sep 17 00:00:00 2001 From: Janderson Date: Wed, 18 May 2011 17:32:30 -0400 Subject: [PATCH 026/187] Compiles does not link --- gtfold-mfe/Makefile | 24 +- gtfold-mfe/configure | 343 +++++++++++----------- gtfold-mfe/include/Makefile.am | 2 +- gtfold-mfe/include/Makefile.in | 2 +- gtfold-mfe/src/.deps/algorithms.Po | 33 ++- gtfold-mfe/src/.deps/constraints.Po | 311 ++++++++++---------- gtfold-mfe/src/.deps/energy.Po | 33 ++- gtfold-mfe/src/.deps/global.Po | 23 +- gtfold-mfe/src/.deps/loader.Po | 286 +++++++++--------- gtfold-mfe/src/.deps/main.Po | 352 +++++++++++------------ gtfold-mfe/src/.deps/options.Po | 197 +++++++------ gtfold-mfe/src/.deps/shapereader.Po | 282 +++++++++--------- gtfold-mfe/src/.deps/subopt_traceback.Po | 321 ++++++++++----------- gtfold-mfe/src/.deps/traceback.Po | 23 +- gtfold-mfe/src/.deps/utils.Po | 185 ++++++------ gtfold-mfe/src/Makefile | 29 +- gtfold-mfe/src/Makefile.am | 1 + gtfold-mfe/src/Makefile.in | 5 +- gtfold-mfe/src/algorithms-partition.c | 1 - gtfold-mfe/src/partition-dangle.cc | 130 --------- 20 files changed, 1241 insertions(+), 1342 deletions(-) delete mode 100644 gtfold-mfe/src/partition-dangle.cc diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile index 75480ce..cdd52e6 100644 --- a/gtfold-mfe/Makefile +++ b/gtfold-mfe/Makefile @@ -126,12 +126,12 @@ DIST_ARCHIVES = $(distdir).tar.gz GZIP_ENV = --best distuninstallcheck_listfiles = find . -type f -print distcleancheck_listfiles = find . -type f -print -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -158,7 +158,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -174,10 +174,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -205,7 +205,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index da30cd9..c5acafe 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -1,11 +1,11 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.65 for gtfold 1.18. +# Generated by GNU Autoconf 2.67 for gtfold 1.18. # # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, -# Inc. +# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software +# Foundation, Inc. # # # This configure script is free software; the Free Software Foundation @@ -316,7 +316,7 @@ $as_echo X"$as_dir" | test -d "$as_dir" && break done test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" } # as_fn_mkdir_p @@ -356,19 +356,19 @@ else fi # as_fn_arith -# as_fn_error ERROR [LINENO LOG_FD] -# --------------------------------- +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are # provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with status $?, using 1 if that was 0. +# script with STATUS, using 1 if that was 0. as_fn_error () { - as_status=$?; test $as_status -eq 0 && as_status=1 - if test "$3"; then - as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi - $as_echo "$as_me: error: $1" >&2 + $as_echo "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error @@ -530,7 +530,7 @@ test -n "$DJDIR" || exec 7<&0 &1 # Name of the host. -# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` @@ -778,8 +778,9 @@ do fi case $ac_option in - *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; - *) ac_optarg=yes ;; + *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *=) ac_optarg= ;; + *) ac_optarg=yes ;; esac # Accept the important Cygnus configure options, so we can diagnose typos. @@ -824,7 +825,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error "invalid feature name: $ac_useropt" + as_fn_error $? "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -850,7 +851,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error "invalid feature name: $ac_useropt" + as_fn_error $? "invalid feature name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1054,7 +1055,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error "invalid package name: $ac_useropt" + as_fn_error $? "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1070,7 +1071,7 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error "invalid package name: $ac_useropt" + as_fn_error $? "invalid package name: $ac_useropt" ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1100,8 +1101,8 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) as_fn_error "unrecognized option: \`$ac_option' -Try \`$0 --help' for more information." + -*) as_fn_error $? "unrecognized option: \`$ac_option' +Try \`$0 --help' for more information" ;; *=*) @@ -1109,7 +1110,7 @@ Try \`$0 --help' for more information." # Reject names that are not valid shell variable names. case $ac_envvar in #( '' | [0-9]* | *[!_$as_cr_alnum]* ) - as_fn_error "invalid variable name: \`$ac_envvar'" ;; + as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; esac eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1127,13 +1128,13 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - as_fn_error "missing argument to $ac_option" + as_fn_error $? "missing argument to $ac_option" fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; - fatal) as_fn_error "unrecognized options: $ac_unrecognized_opts" ;; + fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1156,7 +1157,7 @@ do [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac - as_fn_error "expected an absolute directory name for --$ac_var: $ac_val" + as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" done # There might be people who depend on the old broken behavior: `$host' @@ -1170,8 +1171,8 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. - If a cross compiler is detected then cross compile mode will be used." >&2 + $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host. + If a cross compiler is detected then cross compile mode will be used" >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi @@ -1186,9 +1187,9 @@ test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || - as_fn_error "working directory cannot be determined" + as_fn_error $? "working directory cannot be determined" test "X$ac_ls_di" = "X$ac_pwd_ls_di" || - as_fn_error "pwd does not report name of working directory" + as_fn_error $? "pwd does not report name of working directory" # Find the source files, if location was not specified. @@ -1227,11 +1228,11 @@ else fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." - as_fn_error "cannot find sources ($ac_unique_file) in $srcdir" + as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( - cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error "$ac_msg" + cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then @@ -1271,7 +1272,7 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print \`checking...' messages + -q, --quiet, --silent do not print \`checking ...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files @@ -1421,9 +1422,9 @@ test -n "$ac_init_help" && exit $ac_status if $ac_init_version; then cat <<\_ACEOF gtfold configure 1.18 -generated by GNU Autoconf 2.65 +generated by GNU Autoconf 2.67 -Copyright (C) 2009 Free Software Foundation, Inc. +Copyright (C) 2010 Free Software Foundation, Inc. This configure script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it. _ACEOF @@ -1577,7 +1578,7 @@ $as_echo "$ac_try_echo"; } >&5 mv -f conftest.er1 conftest.err fi $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } >/dev/null && { + test $ac_status = 0; } > conftest.i && { test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || test ! -s conftest.err }; then : @@ -1643,10 +1644,10 @@ fi ac_fn_c_check_header_mongrel () { as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : + if eval "test \"\${$3+set}\"" = set; then : { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } -if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${$3+set}\"" = set; then : $as_echo_n "(cached) " >&6 fi eval ac_res=\$$3 @@ -1682,7 +1683,7 @@ if ac_fn_c_try_cpp "$LINENO"; then : else ac_header_preproc=no fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_header_preproc" >&5 $as_echo "$ac_header_preproc" >&6; } @@ -1709,7 +1710,7 @@ $as_echo "$as_me: WARNING: $2: proceeding with the compiler's result" >&2;} esac { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } -if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${$3+set}\"" = set; then : $as_echo_n "(cached) " >&6 else eval "$3=\$ac_header_compiler" @@ -1731,7 +1732,7 @@ ac_fn_c_check_header_compile () as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } -if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${$3+set}\"" = set; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext @@ -1762,7 +1763,7 @@ ac_fn_c_check_type () as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } -if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${$3+set}\"" = set; then : $as_echo_n "(cached) " >&6 else eval "$3=no" @@ -1815,7 +1816,7 @@ ac_fn_c_check_func () as_lineno=${as_lineno-"$1"} as_lineno_stack=as_lineno_stack=$as_lineno_stack { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $2" >&5 $as_echo_n "checking for $2... " >&6; } -if { as_var=$3; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${$3+set}\"" = set; then : $as_echo_n "(cached) " >&6 else cat confdefs.h - <<_ACEOF >conftest.$ac_ext @@ -1878,7 +1879,7 @@ This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by gtfold $as_me 1.18, which was -generated by GNU Autoconf 2.65. Invocation command line was +generated by GNU Autoconf 2.67. Invocation command line was $ $0 $@ @@ -1988,11 +1989,9 @@ trap 'exit_status=$? { echo - cat <<\_ASBOX -## ---------------- ## + $as_echo "## ---------------- ## ## Cache variables. ## -## ---------------- ## -_ASBOX +## ---------------- ##" echo # The following way of writing the cache mishandles newlines in values, ( @@ -2026,11 +2025,9 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; ) echo - cat <<\_ASBOX -## ----------------- ## + $as_echo "## ----------------- ## ## Output variables. ## -## ----------------- ## -_ASBOX +## ----------------- ##" echo for ac_var in $ac_subst_vars do @@ -2043,11 +2040,9 @@ _ASBOX echo if test -n "$ac_subst_files"; then - cat <<\_ASBOX -## ------------------- ## + $as_echo "## ------------------- ## ## File substitutions. ## -## ------------------- ## -_ASBOX +## ------------------- ##" echo for ac_var in $ac_subst_files do @@ -2061,11 +2056,9 @@ _ASBOX fi if test -s confdefs.h; then - cat <<\_ASBOX -## ----------- ## + $as_echo "## ----------- ## ## confdefs.h. ## -## ----------- ## -_ASBOX +## ----------- ##" echo cat confdefs.h echo @@ -2120,7 +2113,12 @@ _ACEOF ac_site_file1=NONE ac_site_file2=NONE if test -n "$CONFIG_SITE"; then - ac_site_file1=$CONFIG_SITE + # We do not want a PATH search for config.site. + case $CONFIG_SITE in #(( + -*) ac_site_file1=./$CONFIG_SITE;; + */*) ac_site_file1=$CONFIG_SITE;; + *) ac_site_file1=./$CONFIG_SITE;; + esac elif test "x$prefix" != xNONE; then ac_site_file1=$prefix/share/config.site ac_site_file2=$prefix/etc/config.site @@ -2135,7 +2133,11 @@ do { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 - . "$ac_site_file" + . "$ac_site_file" \ + || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +as_fn_error $? "failed to load site script $ac_site_file +See \`config.log' for more details" "$LINENO" 5 ; } fi done @@ -2211,7 +2213,7 @@ if $ac_cache_corrupted; then $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 + as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 fi ## -------------------- ## ## Main body of script. ## @@ -2232,16 +2234,22 @@ ac_config_headers="$ac_config_headers gtfold_config.h" ac_aux_dir= for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do - for ac_t in install-sh install.sh shtool; do - if test -f "$ac_dir/$ac_t"; then - ac_aux_dir=$ac_dir - ac_install_sh="$ac_aux_dir/$ac_t -c" - break 2 - fi - done + if test -f "$ac_dir/install-sh"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install-sh -c" + break + elif test -f "$ac_dir/install.sh"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/install.sh -c" + break + elif test -f "$ac_dir/shtool"; then + ac_aux_dir=$ac_dir + ac_install_sh="$ac_aux_dir/shtool install -c" + break + fi done if test -z "$ac_aux_dir"; then - as_fn_error "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 + as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 fi # These three variables are undocumented and unsupported, @@ -2255,7 +2263,7 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. # Make sure we can run config.sub. $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || - as_fn_error "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 + as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 { $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 $as_echo_n "checking build system type... " >&6; } @@ -2266,16 +2274,16 @@ else test "x$ac_build_alias" = x && ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` test "x$ac_build_alias" = x && - as_fn_error "cannot guess build type; you must specify one" "$LINENO" 5 + as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || - as_fn_error "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 $as_echo "$ac_cv_build" >&6; } case $ac_cv_build in *-*-*) ;; -*) as_fn_error "invalid value of canonical build" "$LINENO" 5;; +*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' @@ -2300,7 +2308,7 @@ else ac_cv_host=$ac_cv_build else ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || - as_fn_error "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 fi fi @@ -2308,7 +2316,7 @@ fi $as_echo "$ac_cv_host" >&6; } case $ac_cv_host in *-*-*) ;; -*) as_fn_error "invalid value of canonical host" "$LINENO" 5;; +*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' @@ -2333,7 +2341,7 @@ else ac_cv_target=$ac_cv_host else ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || - as_fn_error "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 + as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 fi fi @@ -2341,7 +2349,7 @@ fi $as_echo "$ac_cv_target" >&6; } case $ac_cv_target in *-*-*) ;; -*) as_fn_error "invalid value of canonical target" "$LINENO" 5;; +*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;; esac target=$ac_cv_target ac_save_IFS=$IFS; IFS='-' @@ -2471,11 +2479,11 @@ am_lf=' ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) - as_fn_error "unsafe absolute working directory name" "$LINENO" 5;; + as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) - as_fn_error "unsafe srcdir value: \`$srcdir'" "$LINENO" 5;; + as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; esac # Do `set' in a subshell so we don't clobber the current shell's @@ -2497,7 +2505,7 @@ if ( # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". - as_fn_error "ls -t appears to fail. Make sure there is not a broken + as_fn_error $? "ls -t appears to fail. Make sure there is not a broken alias in your environment" "$LINENO" 5 fi @@ -2507,7 +2515,7 @@ then # Ok. : else - as_fn_error "newly created file is older than distributed files! + as_fn_error $? "newly created file is older than distributed files! Check your system clock" "$LINENO" 5 fi { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 @@ -2745,7 +2753,7 @@ done $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } set x ${MAKE-make} ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` -if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then : +if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then : $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2753,7 +2761,7 @@ SHELL = /bin/sh all: @echo '@@@%%%=$(MAKE)=@@@%%%' _ACEOF -# GNU make sometimes prints "make[1]: Entering...", which would confuse us. +# GNU make sometimes prints "make[1]: Entering ...", which would confuse us. case `${MAKE-make} -f conftest.make 2>/dev/null` in *@@@%%%=?*=@@@%%%*) eval ac_cv_prog_make_${ac_make}_set=yes;; @@ -2787,7 +2795,7 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then am__isrc=' -I$(srcdir)' # test to see if srcdir already configured if test -f $srcdir/config.status; then - as_fn_error "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 + as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 fi fi @@ -2849,7 +2857,7 @@ if test "${enable_64bit+set}" = set; then : enableval=$enable_64bit; case "${enableval}" in "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;; n | no) gtfold_cv_enable_64bit=no ;; - *) as_fn_error "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;; + *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;; esac else gtfold_cv_enable_64bit=no @@ -2978,8 +2986,8 @@ fi test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error "no acceptable C compiler found in \$PATH -See \`config.log' for more details." "$LINENO" 5; } +as_fn_error $? "no acceptable C compiler found in \$PATH +See \`config.log' for more details" "$LINENO" 5 ; } # Provide some information about the compiler. $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 @@ -3093,9 +3101,8 @@ sed 's/^/| /' conftest.$ac_ext >&5 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -{ as_fn_set_status 77 -as_fn_error "C compiler cannot create executables -See \`config.log' for more details." "$LINENO" 5; }; } +as_fn_error 77 "C compiler cannot create executables +See \`config.log' for more details" "$LINENO" 5 ; } else { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 $as_echo "yes" >&6; } @@ -3137,8 +3144,8 @@ done else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error "cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details." "$LINENO" 5; } +as_fn_error $? "cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details" "$LINENO" 5 ; } fi rm -f conftest conftest$ac_cv_exeext { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 @@ -3195,9 +3202,9 @@ $as_echo "$ac_try_echo"; } >&5 else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error "cannot run C compiled programs. +as_fn_error $? "cannot run C compiled programs. If you meant to cross compile, use \`--host'. -See \`config.log' for more details." "$LINENO" 5; } +See \`config.log' for more details" "$LINENO" 5 ; } fi fi fi @@ -3248,8 +3255,8 @@ sed 's/^/| /' conftest.$ac_ext >&5 { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error "cannot compute suffix of object files: cannot compile -See \`config.log' for more details." "$LINENO" 5; } +as_fn_error $? "cannot compute suffix of object files: cannot compile +See \`config.log' for more details" "$LINENO" 5 ; } fi rm -f conftest.$ac_cv_objext conftest.$ac_ext fi @@ -4199,7 +4206,7 @@ else # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. @@ -4215,11 +4222,11 @@ else ac_preproc_ok=: break fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.err conftest.$ac_ext +rm -f conftest.i conftest.err conftest.$ac_ext if $ac_preproc_ok; then : break fi @@ -4258,7 +4265,7 @@ else # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. @@ -4274,18 +4281,18 @@ else ac_preproc_ok=: break fi -rm -f conftest.err conftest.$ac_ext +rm -f conftest.err conftest.i conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.err conftest.$ac_ext +rm -f conftest.i conftest.err conftest.$ac_ext if $ac_preproc_ok; then : else { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error "C preprocessor \"$CPP\" fails sanity check -See \`config.log' for more details." "$LINENO" 5; } +as_fn_error $? "C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details" "$LINENO" 5 ; } fi ac_ext=c @@ -4346,7 +4353,7 @@ esac done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then - as_fn_error "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_GREP=$GREP @@ -4412,7 +4419,7 @@ esac done IFS=$as_save_IFS if test -z "$ac_cv_path_EGREP"; then - as_fn_error "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 fi else ac_cv_path_EGREP=$EGREP @@ -4546,8 +4553,7 @@ do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default " -eval as_val=\$$as_ac_Header - if test "x$as_val" = x""yes; then : +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -4561,8 +4567,7 @@ for ac_header in stdlib.h string.h sys/time.h do : as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" -eval as_val=\$$as_ac_Header - if test "x$as_val" = x""yes; then : +if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -5073,8 +5078,7 @@ for ac_func in floor gettimeofday pow do : as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" -eval as_val=\$$as_ac_var - if test "x$as_val" = x""yes; then : +if eval test \"x\$"$as_ac_var"\" = x"yes"; then : cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 _ACEOF @@ -5089,7 +5093,7 @@ if test "${enable_debug+set}" = set; then : "" | y | ye | yes) debug=true; CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;; n | no) debug=false ;; - *) as_fn_error "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;; + *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;; esac else debug=false @@ -5192,6 +5196,7 @@ DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= +U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' @@ -5215,19 +5220,19 @@ else fi if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then - as_fn_error "conditional \"AMDEP\" was never defined. + as_fn_error $? "conditional \"AMDEP\" was never defined. Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then - as_fn_error "conditional \"am__fastdepCC\" was never defined. + as_fn_error $? "conditional \"am__fastdepCC\" was never defined. Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then - as_fn_error "conditional \"am__fastdepCXX\" was never defined. + as_fn_error $? "conditional \"am__fastdepCXX\" was never defined. Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then - as_fn_error "conditional \"GTFOLD_DEBUG\" was never defined. + as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined. Usually this means the macro was only invoked conditionally." "$LINENO" 5 fi @@ -5377,19 +5382,19 @@ export LANGUAGE (unset CDPATH) >/dev/null 2>&1 && unset CDPATH -# as_fn_error ERROR [LINENO LOG_FD] -# --------------------------------- +# as_fn_error STATUS ERROR [LINENO LOG_FD] +# ---------------------------------------- # Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are # provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with status $?, using 1 if that was 0. +# script with STATUS, using 1 if that was 0. as_fn_error () { - as_status=$?; test $as_status -eq 0 && as_status=1 - if test "$3"; then - as_lineno=${as_lineno-"$2"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $1" >&$3 + as_status=$1; test $as_status -eq 0 && as_status=1 + if test "$4"; then + as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack + $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 fi - $as_echo "$as_me: error: $1" >&2 + $as_echo "$as_me: error: $2" >&2 as_fn_exit $as_status } # as_fn_error @@ -5585,7 +5590,7 @@ $as_echo X"$as_dir" | test -d "$as_dir" && break done test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error "cannot create directory $as_dir" + } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" } # as_fn_mkdir_p @@ -5639,7 +5644,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # values after options handling. ac_log=" This file was extended by gtfold $as_me 1.18, which was -generated by GNU Autoconf 2.65. Invocation command line was +generated by GNU Autoconf 2.67. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -5705,10 +5710,10 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ gtfold config.status 1.18 -configured by $0, generated by GNU Autoconf 2.65, +configured by $0, generated by GNU Autoconf 2.67, with options \\"\$ac_cs_config\\" -Copyright (C) 2009 Free Software Foundation, Inc. +Copyright (C) 2010 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -5726,11 +5731,16 @@ ac_need_defaults=: while test $# != 0 do case $1 in - --*=*) + --*=?*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; + --*=) + ac_option=`expr "X$1" : 'X\([^=]*\)='` + ac_optarg= + ac_shift=: + ;; *) ac_option=$1 ac_optarg=$2 @@ -5752,6 +5762,7 @@ do $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; + '') as_fn_error $? "missing file argument" ;; esac as_fn_append CONFIG_FILES " '$ac_optarg'" ac_need_defaults=false;; @@ -5764,7 +5775,7 @@ do ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - as_fn_error "ambiguous option: \`$1' + as_fn_error $? "ambiguous option: \`$1' Try \`$0 --help' for more information.";; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; @@ -5773,7 +5784,7 @@ Try \`$0 --help' for more information.";; ac_cs_silent=: ;; # This is an error. - -*) as_fn_error "unrecognized option: \`$1' + -*) as_fn_error $? "unrecognized option: \`$1' Try \`$0 --help' for more information." ;; *) as_fn_append ac_config_targets " $1" @@ -5837,7 +5848,7 @@ do "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;; "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;; - *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;; + *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; esac done @@ -5875,7 +5886,7 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || as_fn_error "cannot create a temporary directory in ." "$LINENO" 5 +} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -5892,7 +5903,7 @@ if test "x$ac_cr" = x; then fi ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then - ac_cs_awk_cr='\r' + ac_cs_awk_cr='\\r' else ac_cs_awk_cr=$ac_cr fi @@ -5906,18 +5917,18 @@ _ACEOF echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || - as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 -ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 +ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || - as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then - as_fn_error "could not make $CONFIG_STATUS" "$LINENO" 5 + as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6006,20 +6017,28 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || as_fn_error "could not setup config files machinery" "$LINENO" 5 + || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 _ACEOF -# VPATH may cause trouble with some makes, so we remove $(srcdir), -# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and +# VPATH may cause trouble with some makes, so we remove sole $(srcdir), +# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=/{ -s/:*\$(srcdir):*/:/ -s/:*\${srcdir}:*/:/ -s/:*@srcdir@:*/:/ -s/^\([^=]*=[ ]*\):*/\1/ + ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ +h +s/// +s/^/:/ +s/[ ]*$/:/ +s/:\$(srcdir):/:/g +s/:\${srcdir}:/:/g +s/:@srcdir@:/:/g +s/^:*// s/:*$// +x +s/\(=[ ]*\).*/\1/ +G +s/\n// s/^[^=]*=[ ]*$// }' fi @@ -6047,7 +6066,7 @@ for ac_last_try in false false :; do if test -z "$ac_t"; then break elif $ac_last_try; then - as_fn_error "could not make $CONFIG_HEADERS" "$LINENO" 5 + as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5 else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6132,7 +6151,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - as_fn_error "could not setup config headers machinery" "$LINENO" 5 + as_fn_error $? "could not setup config headers machinery" "$LINENO" 5 fi # test -n "$CONFIG_HEADERS" @@ -6145,7 +6164,7 @@ do esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error "invalid tag \`$ac_tag'" "$LINENO" 5;; + :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -6173,7 +6192,7 @@ do [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error "cannot find input file: \`$ac_f'" "$LINENO" 5;; + as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac as_fn_append ac_file_inputs " '$ac_f'" @@ -6200,7 +6219,7 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || as_fn_error "could not create $ac_file" "$LINENO" 5 ;; + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; esac ;; esac @@ -6337,22 +6356,22 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || as_fn_error "could not create $ac_file" "$LINENO" 5 + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined." >&5 +which seems to be undefined. Please make sure it is defined" >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined." >&2;} +which seems to be undefined. Please make sure it is defined" >&2;} rm -f "$tmp/stdin" case $ac_file in -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || as_fn_error "could not create $ac_file" "$LINENO" 5 + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; :H) # @@ -6363,19 +6382,19 @@ which seems to be undefined. Please make sure it is defined." >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || as_fn_error "could not create $ac_file" "$LINENO" 5 + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || as_fn_error "could not create $ac_file" "$LINENO" 5 + || as_fn_error $? "could not create $ac_file" "$LINENO" 5 fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || as_fn_error "could not create -" "$LINENO" 5 + || as_fn_error $? "could not create -" "$LINENO" 5 fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -6525,7 +6544,7 @@ _ACEOF ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || - as_fn_error "write failure creating $CONFIG_STATUS" "$LINENO" 5 + as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 # configure is writing to config.log, and then calls config.status. @@ -6546,7 +6565,7 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit $? + $ac_cs_success || as_fn_exit 1 fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index 545325a..b73b2f6 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,3 @@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index 1fc5099..a0bf52b 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -155,7 +155,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h CLEANFILES = *~ all: all-am diff --git a/gtfold-mfe/src/.deps/algorithms.Po b/gtfold-mfe/src/.deps/algorithms.Po index c737d2e..d5d1ad2 100644 --- a/gtfold-mfe/src/.deps/algorithms.Po +++ b/gtfold-mfe/src/.deps/algorithms.Po @@ -2,10 +2,10 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/bits/types.h /usr/include/bits/typesizes.h \ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ @@ -15,15 +15,16 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/time.h /usr/include/bits/time.h /usr/include/xlocale.h \ /usr/include/sys/time.h /usr/include/sys/select.h \ /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/endian.h \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/assert.h \ - ../include/constants.h ../include/utils.h ../include/constants.h \ - ../include/energy.h ../include/data.h ../include/global.h \ - ../include/algorithms.h ../include/constraints.h \ - ../include/shapereader.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h + /usr/include/sys/types.h /usr/include/sys/sysmacros.h \ + /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h /usr/include/assert.h ../include/constants.h \ + ../include/utils.h ../include/constants.h ../include/energy.h \ + ../include/data.h ../include/global.h ../include/algorithms.h \ + ../include/constraints.h ../include/shapereader.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h /usr/include/stdio.h: @@ -39,7 +40,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/bits/types.h: @@ -51,7 +52,7 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -95,7 +96,9 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/stdlib.h: -/usr/include/sys/types.h: +/usr/include/bits/waitflags.h: + +/usr/include/bits/waitstatus.h: /usr/include/endian.h: @@ -103,6 +106,8 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/byteswap.h: +/usr/include/sys/types.h: + /usr/include/sys/sysmacros.h: /usr/include/bits/pthreadtypes.h: @@ -131,4 +136,4 @@ algorithms.o: algorithms.c /usr/include/stdio.h /usr/include/features.h \ ../include/shapereader.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/omp.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/omp.h: diff --git a/gtfold-mfe/src/.deps/constraints.Po b/gtfold-mfe/src/.deps/constraints.Po index ec27b91..891773e 100644 --- a/gtfold-mfe/src/.deps/constraints.Po +++ b/gtfold-mfe/src/.deps/constraints.Po @@ -2,7 +2,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ /usr/include/endian.h /usr/include/bits/endian.h \ /usr/include/bits/byteswap.h /usr/include/xlocale.h \ @@ -14,81 +14,82 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \ /usr/include/bits/string3.h /usr/include/stdio.h /usr/include/libio.h \ /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ - /usr/include/c++/4.4/cstddef /usr/include/bits/wchar.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ - /usr/include/ctype.h /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/c++/4.5/iostream \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ + /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ + /usr/include/c++/4.5/cstddef /usr/include/bits/wchar.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ + /usr/include/ctype.h /usr/include/c++/4.5/bits/ios_base.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/bits/sched.h \ - /usr/include/signal.h /usr/include/bits/setjmp.h /usr/include/unistd.h \ + /usr/include/bits/setjmp.h /usr/include/unistd.h \ /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ /usr/include/bits/confname.h /usr/include/getopt.h \ /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc \ + /usr/include/c++/4.5/bits/locale_classes.tcc \ + /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ + /usr/include/c++/4.5/bits/basic_ios.h \ + /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ - /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/vector \ - /usr/include/c++/4.4/bits/stl_construct.h \ - /usr/include/c++/4.4/bits/stl_uninitialized.h \ - /usr/include/c++/4.4/bits/stl_vector.h \ - /usr/include/c++/4.4/bits/stl_bvector.h \ - /usr/include/c++/4.4/bits/vector.tcc /usr/include/c++/4.4/algorithm \ - /usr/include/c++/4.4/bits/stl_algo.h /usr/include/c++/4.4/cstdlib \ - /usr/include/c++/4.4/bits/algorithmfwd.h \ - /usr/include/c++/4.4/bits/stl_heap.h \ - /usr/include/c++/4.4/bits/stl_tempbuf.h ../include/global.h \ - ../include/constants.h ../include/options.h /usr/include/c++/4.4/cstring \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.5/bits/streambuf_iterator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.5/bits/locale_facets.tcc \ + /usr/include/c++/4.5/bits/basic_ios.tcc \ + /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ + /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \ + /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/vector \ + /usr/include/c++/4.5/bits/stl_construct.h \ + /usr/include/c++/4.5/bits/stl_uninitialized.h \ + /usr/include/c++/4.5/bits/stl_vector.h \ + /usr/include/c++/4.5/bits/stl_bvector.h \ + /usr/include/c++/4.5/bits/vector.tcc /usr/include/c++/4.5/algorithm \ + /usr/include/c++/4.5/utility /usr/include/c++/4.5/bits/stl_relops.h \ + /usr/include/c++/4.5/bits/stl_algo.h /usr/include/c++/4.5/cstdlib \ + /usr/include/c++/4.5/bits/algorithmfwd.h \ + /usr/include/c++/4.5/bits/stl_heap.h \ + /usr/include/c++/4.5/bits/stl_tempbuf.h ../include/global.h \ + ../include/constants.h ../include/options.h /usr/include/c++/4.5/cstring \ ../include/constraints.h /usr/include/stdlib.h: @@ -105,7 +106,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/bits/waitflags.h: @@ -155,7 +156,7 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -165,83 +166,83 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/bits/stdio2.h: -/usr/include/c++/4.4/iostream: +/usr/include/c++/4.5/iostream: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/ostream: +/usr/include/c++/4.5/ostream: -/usr/include/c++/4.4/ios: +/usr/include/c++/4.5/ios: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: /usr/include/bits/wchar.h: /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: -/usr/include/c++/4.4/bits/ios_base.h: +/usr/include/c++/4.5/bits/ios_base.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -249,8 +250,6 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/bits/sched.h: -/usr/include/signal.h: - /usr/include/bits/setjmp.h: /usr/include/unistd.h: @@ -265,99 +264,103 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/bits/locale_classes.h: +/usr/include/c++/4.5/bits/locale_classes.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: -/usr/include/c++/4.4/bits/locale_classes.tcc: +/usr/include/c++/4.5/bits/locale_classes.tcc: -/usr/include/c++/4.4/streambuf: +/usr/include/c++/4.5/streambuf: -/usr/include/c++/4.4/bits/streambuf.tcc: +/usr/include/c++/4.5/bits/streambuf.tcc: -/usr/include/c++/4.4/bits/basic_ios.h: +/usr/include/c++/4.5/bits/basic_ios.h: -/usr/include/c++/4.4/bits/locale_facets.h: +/usr/include/c++/4.5/bits/locale_facets.h: -/usr/include/c++/4.4/cwctype: +/usr/include/c++/4.5/cwctype: /usr/include/wctype.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: + +/usr/include/c++/4.5/bits/streambuf_iterator.h: + +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: -/usr/include/c++/4.4/bits/streambuf_iterator.h: +/usr/include/c++/4.5/bits/locale_facets.tcc: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: +/usr/include/c++/4.5/bits/basic_ios.tcc: -/usr/include/c++/4.4/bits/locale_facets.tcc: +/usr/include/c++/4.5/bits/ostream.tcc: -/usr/include/c++/4.4/bits/basic_ios.tcc: +/usr/include/c++/4.5/istream: -/usr/include/c++/4.4/bits/ostream.tcc: +/usr/include/c++/4.5/bits/istream.tcc: -/usr/include/c++/4.4/istream: +/usr/include/c++/4.5/fstream: -/usr/include/c++/4.4/bits/istream.tcc: +/usr/include/c++/4.5/bits/codecvt.h: -/usr/include/c++/4.4/fstream: +/usr/include/c++/4.5/cstdio: -/usr/include/c++/4.4/bits/codecvt.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: -/usr/include/c++/4.4/cstdio: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: +/usr/include/c++/4.5/bits/fstream.tcc: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: +/usr/include/c++/4.5/vector: -/usr/include/c++/4.4/bits/fstream.tcc: +/usr/include/c++/4.5/bits/stl_construct.h: -/usr/include/c++/4.4/vector: +/usr/include/c++/4.5/bits/stl_uninitialized.h: -/usr/include/c++/4.4/bits/stl_construct.h: +/usr/include/c++/4.5/bits/stl_vector.h: -/usr/include/c++/4.4/bits/stl_uninitialized.h: +/usr/include/c++/4.5/bits/stl_bvector.h: -/usr/include/c++/4.4/bits/stl_vector.h: +/usr/include/c++/4.5/bits/vector.tcc: -/usr/include/c++/4.4/bits/stl_bvector.h: +/usr/include/c++/4.5/algorithm: -/usr/include/c++/4.4/bits/vector.tcc: +/usr/include/c++/4.5/utility: -/usr/include/c++/4.4/algorithm: +/usr/include/c++/4.5/bits/stl_relops.h: -/usr/include/c++/4.4/bits/stl_algo.h: +/usr/include/c++/4.5/bits/stl_algo.h: -/usr/include/c++/4.4/cstdlib: +/usr/include/c++/4.5/cstdlib: -/usr/include/c++/4.4/bits/algorithmfwd.h: +/usr/include/c++/4.5/bits/algorithmfwd.h: -/usr/include/c++/4.4/bits/stl_heap.h: +/usr/include/c++/4.5/bits/stl_heap.h: -/usr/include/c++/4.4/bits/stl_tempbuf.h: +/usr/include/c++/4.5/bits/stl_tempbuf.h: ../include/global.h: @@ -365,6 +368,6 @@ constraints.o: constraints.cc /usr/include/stdlib.h \ ../include/options.h: -/usr/include/c++/4.4/cstring: +/usr/include/c++/4.5/cstring: ../include/constraints.h: diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po index 7c1467f..daea2c1 100644 --- a/gtfold-mfe/src/.deps/energy.Po +++ b/gtfold-mfe/src/.deps/energy.Po @@ -2,16 +2,17 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ - /usr/include/sys/types.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/sys/select.h /usr/include/bits/select.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ + /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ + /usr/include/endian.h /usr/include/bits/endian.h \ + /usr/include/bits/byteswap.h /usr/include/sys/types.h \ + /usr/include/bits/types.h /usr/include/bits/typesizes.h \ + /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \ /usr/include/bits/sigset.h /usr/include/bits/time.h \ /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ @@ -35,15 +36,11 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: -/usr/include/sys/types.h: - -/usr/include/bits/types.h: +/usr/include/bits/waitflags.h: -/usr/include/bits/typesizes.h: - -/usr/include/time.h: +/usr/include/bits/waitstatus.h: /usr/include/endian.h: @@ -51,6 +48,14 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ /usr/include/bits/byteswap.h: +/usr/include/sys/types.h: + +/usr/include/bits/types.h: + +/usr/include/bits/typesizes.h: + +/usr/include/time.h: + /usr/include/sys/select.h: /usr/include/bits/select.h: @@ -75,7 +80,7 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po index e2d1748..613e0c5 100644 --- a/gtfold-mfe/src/.deps/global.Po +++ b/gtfold-mfe/src/.deps/global.Po @@ -2,15 +2,16 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/bits/types.h /usr/include/bits/typesizes.h \ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \ - /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/sys/select.h \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ /usr/include/bits/select.h /usr/include/bits/sigset.h \ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ @@ -30,7 +31,7 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/bits/types.h: @@ -42,7 +43,7 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -54,9 +55,9 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/stdlib.h: -/usr/include/sys/types.h: +/usr/include/bits/waitflags.h: -/usr/include/time.h: +/usr/include/bits/waitstatus.h: /usr/include/endian.h: @@ -64,6 +65,10 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/byteswap.h: +/usr/include/sys/types.h: + +/usr/include/time.h: + /usr/include/sys/select.h: /usr/include/bits/select.h: diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po index 290868e..41da0fe 100644 --- a/gtfold-mfe/src/.deps/loader.Po +++ b/gtfold-mfe/src/.deps/loader.Po @@ -1,98 +1,98 @@ -loader.o: loader.cc /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ +loader.o: loader.cc /usr/include/c++/4.5/iostream \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ - /usr/include/c++/4.4/cstddef \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ + /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ + /usr/include/c++/4.5/cstddef \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ /usr/include/ctype.h /usr/include/bits/types.h \ /usr/include/bits/typesizes.h /usr/include/endian.h \ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/c++/4.5/bits/ios_base.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc \ + /usr/include/c++/4.5/bits/locale_classes.tcc \ + /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ + /usr/include/c++/4.5/bits/basic_ios.h \ + /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ - /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.5/bits/streambuf_iterator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.5/bits/locale_facets.tcc \ + /usr/include/c++/4.5/bits/basic_ios.tcc \ + /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ + /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \ + /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \ /usr/include/libio.h /usr/include/_G_config.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - /usr/include/c++/4.4/cstring /usr/include/string.h \ + /usr/include/c++/4.5/cstring /usr/include/string.h \ /usr/include/bits/string3.h /usr/include/stdlib.h \ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h ../include/data.h \ - ../include/constants.h ../include/utils.h ../include/constants.h \ - ../include/global.h ../include/loader.h ../include/data.h + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h ../include/data.h ../include/constants.h \ + ../include/utils.h ../include/constants.h ../include/global.h \ + ../include/loader.h ../include/data.h -/usr/include/c++/4.4/iostream: +/usr/include/c++/4.5/iostream: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: /usr/include/features.h: @@ -106,29 +106,29 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/gnu/stubs-64.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/ostream: +/usr/include/c++/4.5/ostream: -/usr/include/c++/4.4/ios: +/usr/include/c++/4.5/ios: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/wchar.h: /usr/include/stdio.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/wchar.h: @@ -136,47 +136,47 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -190,13 +190,13 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ios_base.h: +/usr/include/c++/4.5/bits/ios_base.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -208,10 +208,6 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -228,69 +224,69 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/bits/locale_classes.h: +/usr/include/c++/4.5/bits/locale_classes.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: -/usr/include/c++/4.4/bits/locale_classes.tcc: +/usr/include/c++/4.5/bits/locale_classes.tcc: -/usr/include/c++/4.4/streambuf: +/usr/include/c++/4.5/streambuf: -/usr/include/c++/4.4/bits/streambuf.tcc: +/usr/include/c++/4.5/bits/streambuf.tcc: -/usr/include/c++/4.4/bits/basic_ios.h: +/usr/include/c++/4.5/bits/basic_ios.h: -/usr/include/c++/4.4/bits/locale_facets.h: +/usr/include/c++/4.5/bits/locale_facets.h: -/usr/include/c++/4.4/cwctype: +/usr/include/c++/4.5/cwctype: /usr/include/wctype.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: -/usr/include/c++/4.4/bits/streambuf_iterator.h: +/usr/include/c++/4.5/bits/streambuf_iterator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: -/usr/include/c++/4.4/bits/locale_facets.tcc: +/usr/include/c++/4.5/bits/locale_facets.tcc: -/usr/include/c++/4.4/bits/basic_ios.tcc: +/usr/include/c++/4.5/bits/basic_ios.tcc: -/usr/include/c++/4.4/bits/ostream.tcc: +/usr/include/c++/4.5/bits/ostream.tcc: -/usr/include/c++/4.4/istream: +/usr/include/c++/4.5/istream: -/usr/include/c++/4.4/bits/istream.tcc: +/usr/include/c++/4.5/bits/istream.tcc: -/usr/include/c++/4.4/fstream: +/usr/include/c++/4.5/fstream: -/usr/include/c++/4.4/bits/codecvt.h: +/usr/include/c++/4.5/bits/codecvt.h: -/usr/include/c++/4.4/cstdio: +/usr/include/c++/4.5/cstdio: /usr/include/libio.h: @@ -304,11 +300,11 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/stdio2.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: -/usr/include/c++/4.4/bits/fstream.tcc: +/usr/include/c++/4.5/bits/fstream.tcc: /usr/include/math.h: @@ -328,7 +324,7 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/mathinline.h: -/usr/include/c++/4.4/cstring: +/usr/include/c++/4.5/cstring: /usr/include/string.h: @@ -346,6 +342,8 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/select.h: +/usr/include/bits/sigset.h: + /usr/include/sys/sysmacros.h: /usr/include/alloca.h: diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po index df8b6af..73ec5ce 100644 --- a/gtfold-mfe/src/.deps/main.Po +++ b/gtfold-mfe/src/.deps/main.Po @@ -1,114 +1,114 @@ -main.o: main.cc /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ +main.o: main.cc /usr/include/c++/4.5/iostream \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ - /usr/include/c++/4.4/cstddef \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ + /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ + /usr/include/c++/4.5/cstddef \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ /usr/include/ctype.h /usr/include/bits/types.h \ /usr/include/bits/typesizes.h /usr/include/endian.h \ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/c++/4.5/bits/ios_base.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc \ + /usr/include/c++/4.5/bits/locale_classes.tcc \ + /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ + /usr/include/c++/4.5/bits/basic_ios.h \ + /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/iomanip \ - /usr/include/c++/4.4/fstream /usr/include/c++/4.4/bits/codecvt.h \ - /usr/include/c++/4.4/cstdio /usr/include/libio.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.5/bits/streambuf_iterator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.5/bits/locale_facets.tcc \ + /usr/include/c++/4.5/bits/basic_ios.tcc \ + /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ + /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/iomanip \ + /usr/include/c++/4.5/fstream /usr/include/c++/4.5/bits/codecvt.h \ + /usr/include/c++/4.5/cstdio /usr/include/libio.h \ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ /usr/include/bits/stdio2.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ /usr/include/sys/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/c++/4.4/sstream \ - /usr/include/c++/4.4/bits/sstream.tcc /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/sys/types.h /usr/include/sys/sysmacros.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/string.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/c++/4.5/sstream /usr/include/c++/4.5/bits/sstream.tcc \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h /usr/include/string.h \ /usr/include/bits/string3.h ../include/main.h \ - /usr/include/c++/4.4/vector /usr/include/c++/4.4/bits/stl_construct.h \ - /usr/include/c++/4.4/bits/stl_uninitialized.h \ - /usr/include/c++/4.4/bits/stl_vector.h \ - /usr/include/c++/4.4/bits/stl_bvector.h \ - /usr/include/c++/4.4/bits/vector.tcc ../include/constants.h \ + /usr/include/c++/4.5/vector /usr/include/c++/4.5/bits/stl_construct.h \ + /usr/include/c++/4.5/bits/stl_uninitialized.h \ + /usr/include/c++/4.5/bits/stl_vector.h \ + /usr/include/c++/4.5/bits/stl_bvector.h \ + /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \ ../include/utils.h ../include/loader.h ../include/data.h \ - ../include/options.h /usr/include/c++/4.4/cstring ../include/global.h \ + ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \ ../include/energy.h ../include/algorithms.h ../include/constraints.h \ ../include/traceback.h ../include/subopt_traceback.h \ - /usr/include/c++/4.4/cassert /usr/include/assert.h \ - /usr/include/c++/4.4/stack /usr/include/c++/4.4/deque \ - /usr/include/c++/4.4/bits/stl_deque.h \ - /usr/include/c++/4.4/bits/deque.tcc \ - /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \ - /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \ - /usr/include/c++/4.4/bits/stl_multimap.h ../include/shapereader.h + /usr/include/c++/4.5/cassert /usr/include/assert.h \ + /usr/include/c++/4.5/stack /usr/include/c++/4.5/deque \ + /usr/include/c++/4.5/bits/stl_deque.h \ + /usr/include/c++/4.5/bits/deque.tcc \ + /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \ + /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \ + /usr/include/c++/4.5/bits/stl_multimap.h ../include/shapereader.h -/usr/include/c++/4.4/iostream: +/usr/include/c++/4.5/iostream: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: /usr/include/features.h: @@ -122,29 +122,29 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/gnu/stubs-64.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/ostream: +/usr/include/c++/4.5/ostream: -/usr/include/c++/4.4/ios: +/usr/include/c++/4.5/ios: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/wchar.h: /usr/include/stdio.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/wchar.h: @@ -152,47 +152,47 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -206,13 +206,13 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ios_base.h: +/usr/include/c++/4.5/bits/ios_base.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -224,10 +224,6 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -244,71 +240,71 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/bits/locale_classes.h: +/usr/include/c++/4.5/bits/locale_classes.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: -/usr/include/c++/4.4/bits/locale_classes.tcc: +/usr/include/c++/4.5/bits/locale_classes.tcc: -/usr/include/c++/4.4/streambuf: +/usr/include/c++/4.5/streambuf: -/usr/include/c++/4.4/bits/streambuf.tcc: +/usr/include/c++/4.5/bits/streambuf.tcc: -/usr/include/c++/4.4/bits/basic_ios.h: +/usr/include/c++/4.5/bits/basic_ios.h: -/usr/include/c++/4.4/bits/locale_facets.h: +/usr/include/c++/4.5/bits/locale_facets.h: -/usr/include/c++/4.4/cwctype: +/usr/include/c++/4.5/cwctype: /usr/include/wctype.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: -/usr/include/c++/4.4/bits/streambuf_iterator.h: +/usr/include/c++/4.5/bits/streambuf_iterator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: -/usr/include/c++/4.4/bits/locale_facets.tcc: +/usr/include/c++/4.5/bits/locale_facets.tcc: -/usr/include/c++/4.4/bits/basic_ios.tcc: +/usr/include/c++/4.5/bits/basic_ios.tcc: -/usr/include/c++/4.4/bits/ostream.tcc: +/usr/include/c++/4.5/bits/ostream.tcc: -/usr/include/c++/4.4/istream: +/usr/include/c++/4.5/istream: -/usr/include/c++/4.4/bits/istream.tcc: +/usr/include/c++/4.5/bits/istream.tcc: -/usr/include/c++/4.4/iomanip: +/usr/include/c++/4.5/iomanip: -/usr/include/c++/4.4/fstream: +/usr/include/c++/4.5/fstream: -/usr/include/c++/4.4/bits/codecvt.h: +/usr/include/c++/4.5/bits/codecvt.h: -/usr/include/c++/4.4/cstdio: +/usr/include/c++/4.5/cstdio: /usr/include/libio.h: @@ -322,11 +318,11 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/stdio2.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: -/usr/include/c++/4.4/bits/fstream.tcc: +/usr/include/c++/4.5/bits/fstream.tcc: /usr/include/math.h: @@ -352,9 +348,11 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/select.h: -/usr/include/c++/4.4/sstream: +/usr/include/bits/sigset.h: + +/usr/include/c++/4.5/sstream: -/usr/include/c++/4.4/bits/sstream.tcc: +/usr/include/c++/4.5/bits/sstream.tcc: /usr/include/stdlib.h: @@ -376,17 +374,17 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ ../include/main.h: -/usr/include/c++/4.4/vector: +/usr/include/c++/4.5/vector: -/usr/include/c++/4.4/bits/stl_construct.h: +/usr/include/c++/4.5/bits/stl_construct.h: -/usr/include/c++/4.4/bits/stl_uninitialized.h: +/usr/include/c++/4.5/bits/stl_uninitialized.h: -/usr/include/c++/4.4/bits/stl_vector.h: +/usr/include/c++/4.5/bits/stl_vector.h: -/usr/include/c++/4.4/bits/stl_bvector.h: +/usr/include/c++/4.5/bits/stl_bvector.h: -/usr/include/c++/4.4/bits/vector.tcc: +/usr/include/c++/4.5/bits/vector.tcc: ../include/constants.h: @@ -398,7 +396,7 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ ../include/options.h: -/usr/include/c++/4.4/cstring: +/usr/include/c++/4.5/cstring: ../include/global.h: @@ -412,26 +410,26 @@ main.o: main.cc /usr/include/c++/4.4/iostream \ ../include/subopt_traceback.h: -/usr/include/c++/4.4/cassert: +/usr/include/c++/4.5/cassert: /usr/include/assert.h: -/usr/include/c++/4.4/stack: +/usr/include/c++/4.5/stack: -/usr/include/c++/4.4/deque: +/usr/include/c++/4.5/deque: -/usr/include/c++/4.4/bits/stl_deque.h: +/usr/include/c++/4.5/bits/stl_deque.h: -/usr/include/c++/4.4/bits/deque.tcc: +/usr/include/c++/4.5/bits/deque.tcc: -/usr/include/c++/4.4/bits/stl_stack.h: +/usr/include/c++/4.5/bits/stl_stack.h: -/usr/include/c++/4.4/map: +/usr/include/c++/4.5/map: -/usr/include/c++/4.4/bits/stl_tree.h: +/usr/include/c++/4.5/bits/stl_tree.h: -/usr/include/c++/4.4/bits/stl_map.h: +/usr/include/c++/4.5/bits/stl_map.h: -/usr/include/c++/4.4/bits/stl_multimap.h: +/usr/include/c++/4.5/bits/stl_multimap.h: ../include/shapereader.h: diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po index 52acdb4..7d4de3a 100644 --- a/gtfold-mfe/src/.deps/options.Po +++ b/gtfold-mfe/src/.deps/options.Po @@ -1,74 +1,73 @@ -options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ +options.o: options.cc ../include/loader.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \ - /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \ + /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \ - /usr/include/c++/4.4/cctype /usr/include/ctype.h \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \ + /usr/include/c++/4.5/cctype /usr/include/ctype.h \ /usr/include/bits/types.h /usr/include/bits/typesizes.h \ /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc ../include/constants.h \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc ../include/constants.h \ ../include/data.h ../include/options.h /usr/include/stdlib.h \ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h \ - /usr/include/c++/4.4/cstring /usr/include/string.h \ - /usr/include/bits/string3.h /usr/include/libio.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h /usr/include/c++/4.5/cstring \ + /usr/include/string.h /usr/include/bits/string3.h /usr/include/libio.h \ /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ /usr/include/bits/stdio2.h ../include/loader.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: /usr/include/features.h: @@ -82,51 +81,51 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/gnu/stubs-64.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: /usr/include/wchar.h: /usr/include/stdio.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/wchar.h: @@ -134,29 +133,29 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -170,21 +169,21 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -196,10 +195,6 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -216,11 +211,11 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: ../include/constants.h: @@ -240,13 +235,15 @@ options.o: options.cc ../include/loader.h /usr/include/c++/4.4/string \ /usr/include/bits/select.h: +/usr/include/bits/sigset.h: + /usr/include/sys/sysmacros.h: /usr/include/alloca.h: /usr/include/bits/stdlib.h: -/usr/include/c++/4.4/cstring: +/usr/include/c++/4.5/cstring: /usr/include/string.h: diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po index 4c5d9af..aa9b3a0 100644 --- a/gtfold-mfe/src/.deps/shapereader.Po +++ b/gtfold-mfe/src/.deps/shapereader.Po @@ -1,97 +1,97 @@ -shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ +shapereader.o: shapereader.cc /usr/include/c++/4.5/iostream \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ - /usr/include/c++/4.4/cstddef \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ + /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ + /usr/include/c++/4.5/cstddef \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ /usr/include/ctype.h /usr/include/bits/types.h \ /usr/include/bits/typesizes.h /usr/include/endian.h \ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/c++/4.5/bits/ios_base.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc \ + /usr/include/c++/4.5/bits/locale_classes.tcc \ + /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ + /usr/include/c++/4.5/bits/basic_ios.h \ + /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/fstream \ - /usr/include/c++/4.4/bits/codecvt.h /usr/include/c++/4.4/cstdio \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.5/bits/streambuf_iterator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.5/bits/locale_facets.tcc \ + /usr/include/c++/4.5/bits/basic_ios.tcc \ + /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ + /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \ + /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \ /usr/include/libio.h /usr/include/_G_config.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/string.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.5/bits/fstream.tcc /usr/include/string.h \ /usr/include/bits/string3.h /usr/include/stdlib.h \ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/sys/sysmacros.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/math.h \ + /usr/include/bits/select.h /usr/include/bits/sigset.h \ + /usr/include/sys/sysmacros.h /usr/include/alloca.h \ + /usr/include/bits/stdlib.h /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ ../include/shapereader.h ../include/global.h ../include/constants.h \ - ../include/options.h /usr/include/c++/4.4/cstring + ../include/options.h /usr/include/c++/4.5/cstring -/usr/include/c++/4.4/iostream: +/usr/include/c++/4.5/iostream: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: /usr/include/features.h: @@ -105,29 +105,29 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/gnu/stubs-64.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/ostream: +/usr/include/c++/4.5/ostream: -/usr/include/c++/4.4/ios: +/usr/include/c++/4.5/ios: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/wchar.h: /usr/include/stdio.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/wchar.h: @@ -135,47 +135,47 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -189,13 +189,13 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ios_base.h: +/usr/include/c++/4.5/bits/ios_base.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -207,10 +207,6 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -227,69 +223,69 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/bits/locale_classes.h: +/usr/include/c++/4.5/bits/locale_classes.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: -/usr/include/c++/4.4/bits/locale_classes.tcc: +/usr/include/c++/4.5/bits/locale_classes.tcc: -/usr/include/c++/4.4/streambuf: +/usr/include/c++/4.5/streambuf: -/usr/include/c++/4.4/bits/streambuf.tcc: +/usr/include/c++/4.5/bits/streambuf.tcc: -/usr/include/c++/4.4/bits/basic_ios.h: +/usr/include/c++/4.5/bits/basic_ios.h: -/usr/include/c++/4.4/bits/locale_facets.h: +/usr/include/c++/4.5/bits/locale_facets.h: -/usr/include/c++/4.4/cwctype: +/usr/include/c++/4.5/cwctype: /usr/include/wctype.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: -/usr/include/c++/4.4/bits/streambuf_iterator.h: +/usr/include/c++/4.5/bits/streambuf_iterator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: -/usr/include/c++/4.4/bits/locale_facets.tcc: +/usr/include/c++/4.5/bits/locale_facets.tcc: -/usr/include/c++/4.4/bits/basic_ios.tcc: +/usr/include/c++/4.5/bits/basic_ios.tcc: -/usr/include/c++/4.4/bits/ostream.tcc: +/usr/include/c++/4.5/bits/ostream.tcc: -/usr/include/c++/4.4/istream: +/usr/include/c++/4.5/istream: -/usr/include/c++/4.4/bits/istream.tcc: +/usr/include/c++/4.5/bits/istream.tcc: -/usr/include/c++/4.4/fstream: +/usr/include/c++/4.5/fstream: -/usr/include/c++/4.4/bits/codecvt.h: +/usr/include/c++/4.5/bits/codecvt.h: -/usr/include/c++/4.4/cstdio: +/usr/include/c++/4.5/cstdio: /usr/include/libio.h: @@ -303,11 +299,11 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/stdio2.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: -/usr/include/c++/4.4/bits/fstream.tcc: +/usr/include/c++/4.5/bits/fstream.tcc: /usr/include/string.h: @@ -325,6 +321,8 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/select.h: +/usr/include/bits/sigset.h: + /usr/include/sys/sysmacros.h: /usr/include/alloca.h: @@ -357,4 +355,4 @@ shapereader.o: shapereader.cc /usr/include/c++/4.4/iostream \ ../include/options.h: -/usr/include/c++/4.4/cstring: +/usr/include/c++/4.5/cstring: diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po index 375a33e..6dac6fe 100644 --- a/gtfold-mfe/src/.deps/subopt_traceback.Po +++ b/gtfold-mfe/src/.deps/subopt_traceback.Po @@ -1,96 +1,95 @@ -subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ +subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.5/cstdio \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ /usr/include/features.h /usr/include/bits/predefs.h \ /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/cstddef \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/cstddef \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/stdio.h /usr/include/bits/types.h \ /usr/include/bits/typesizes.h /usr/include/libio.h \ /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ ../include/constants.h ../include/energy.h ../include/data.h \ ../include/constants.h ../include/utils.h ../include/global.h \ - ../include/subopt_traceback.h /usr/include/c++/4.4/cassert \ - /usr/include/assert.h /usr/include/c++/4.4/iostream \ - /usr/include/c++/4.4/ostream /usr/include/c++/4.4/ios \ - /usr/include/c++/4.4/iosfwd /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/postypes.h /usr/include/c++/4.4/cwchar \ + ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \ + /usr/include/assert.h /usr/include/c++/4.5/iostream \ + /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ + /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.4/exception \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/cctype \ + /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ios_base.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ios_base.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/bits/locale_classes.h /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc \ - /usr/include/c++/4.4/bits/locale_classes.tcc \ - /usr/include/c++/4.4/streambuf /usr/include/c++/4.4/bits/streambuf.tcc \ - /usr/include/c++/4.4/bits/basic_ios.h \ - /usr/include/c++/4.4/bits/locale_facets.h /usr/include/c++/4.4/cwctype \ + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc \ + /usr/include/c++/4.5/bits/locale_classes.tcc \ + /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ + /usr/include/c++/4.5/bits/basic_ios.h \ + /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ /usr/include/wctype.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.4/bits/streambuf_iterator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.4/bits/locale_facets.tcc \ - /usr/include/c++/4.4/bits/basic_ios.tcc \ - /usr/include/c++/4.4/bits/ostream.tcc /usr/include/c++/4.4/istream \ - /usr/include/c++/4.4/bits/istream.tcc /usr/include/c++/4.4/sstream \ - /usr/include/c++/4.4/bits/sstream.tcc /usr/include/c++/4.4/stack \ - /usr/include/c++/4.4/deque /usr/include/c++/4.4/bits/stl_construct.h \ - /usr/include/c++/4.4/bits/stl_uninitialized.h \ - /usr/include/c++/4.4/bits/stl_deque.h \ - /usr/include/c++/4.4/bits/deque.tcc \ - /usr/include/c++/4.4/bits/stl_stack.h /usr/include/c++/4.4/map \ - /usr/include/c++/4.4/bits/stl_tree.h /usr/include/c++/4.4/bits/stl_map.h \ - /usr/include/c++/4.4/bits/stl_multimap.h /usr/include/c++/4.4/vector \ - /usr/include/c++/4.4/bits/stl_vector.h \ - /usr/include/c++/4.4/bits/stl_bvector.h \ - /usr/include/c++/4.4/bits/vector.tcc - -/usr/include/c++/4.4/cstdio: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ + /usr/include/c++/4.5/bits/streambuf_iterator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ + /usr/include/c++/4.5/bits/locale_facets.tcc \ + /usr/include/c++/4.5/bits/basic_ios.tcc \ + /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ + /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/sstream \ + /usr/include/c++/4.5/bits/sstream.tcc /usr/include/c++/4.5/stack \ + /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_construct.h \ + /usr/include/c++/4.5/bits/stl_uninitialized.h \ + /usr/include/c++/4.5/bits/stl_deque.h \ + /usr/include/c++/4.5/bits/deque.tcc \ + /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \ + /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \ + /usr/include/c++/4.5/bits/stl_multimap.h /usr/include/c++/4.5/vector \ + /usr/include/c++/4.5/bits/stl_vector.h \ + /usr/include/c++/4.5/bits/stl_bvector.h \ + /usr/include/c++/4.5/bits/vector.tcc + +/usr/include/c++/4.5/cstdio: + +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: + +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: /usr/include/features.h: @@ -104,11 +103,11 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/gnu/stubs-64.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/stdio.h: @@ -122,7 +121,7 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -146,23 +145,23 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ ../include/subopt_traceback.h: -/usr/include/c++/4.4/cassert: +/usr/include/c++/4.5/cassert: /usr/include/assert.h: -/usr/include/c++/4.4/iostream: +/usr/include/c++/4.5/iostream: -/usr/include/c++/4.4/ostream: +/usr/include/c++/4.5/ostream: -/usr/include/c++/4.4/ios: +/usr/include/c++/4.5/ios: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: /usr/include/bits/wchar.h: @@ -170,47 +169,47 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -220,13 +219,13 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ios_base.h: +/usr/include/c++/4.5/bits/ios_base.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -238,10 +237,6 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -258,94 +253,94 @@ subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.4/cstdio \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/bits/locale_classes.h: +/usr/include/c++/4.5/bits/locale_classes.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: -/usr/include/c++/4.4/bits/locale_classes.tcc: +/usr/include/c++/4.5/bits/locale_classes.tcc: -/usr/include/c++/4.4/streambuf: +/usr/include/c++/4.5/streambuf: -/usr/include/c++/4.4/bits/streambuf.tcc: +/usr/include/c++/4.5/bits/streambuf.tcc: -/usr/include/c++/4.4/bits/basic_ios.h: +/usr/include/c++/4.5/bits/basic_ios.h: -/usr/include/c++/4.4/bits/locale_facets.h: +/usr/include/c++/4.5/bits/locale_facets.h: -/usr/include/c++/4.4/cwctype: +/usr/include/c++/4.5/cwctype: /usr/include/wctype.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_base.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: -/usr/include/c++/4.4/bits/streambuf_iterator.h: +/usr/include/c++/4.5/bits/streambuf_iterator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/ctype_inline.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: -/usr/include/c++/4.4/bits/locale_facets.tcc: +/usr/include/c++/4.5/bits/locale_facets.tcc: -/usr/include/c++/4.4/bits/basic_ios.tcc: +/usr/include/c++/4.5/bits/basic_ios.tcc: -/usr/include/c++/4.4/bits/ostream.tcc: +/usr/include/c++/4.5/bits/ostream.tcc: -/usr/include/c++/4.4/istream: +/usr/include/c++/4.5/istream: -/usr/include/c++/4.4/bits/istream.tcc: +/usr/include/c++/4.5/bits/istream.tcc: -/usr/include/c++/4.4/sstream: +/usr/include/c++/4.5/sstream: -/usr/include/c++/4.4/bits/sstream.tcc: +/usr/include/c++/4.5/bits/sstream.tcc: -/usr/include/c++/4.4/stack: +/usr/include/c++/4.5/stack: -/usr/include/c++/4.4/deque: +/usr/include/c++/4.5/deque: -/usr/include/c++/4.4/bits/stl_construct.h: +/usr/include/c++/4.5/bits/stl_construct.h: -/usr/include/c++/4.4/bits/stl_uninitialized.h: +/usr/include/c++/4.5/bits/stl_uninitialized.h: -/usr/include/c++/4.4/bits/stl_deque.h: +/usr/include/c++/4.5/bits/stl_deque.h: -/usr/include/c++/4.4/bits/deque.tcc: +/usr/include/c++/4.5/bits/deque.tcc: -/usr/include/c++/4.4/bits/stl_stack.h: +/usr/include/c++/4.5/bits/stl_stack.h: -/usr/include/c++/4.4/map: +/usr/include/c++/4.5/map: -/usr/include/c++/4.4/bits/stl_tree.h: +/usr/include/c++/4.5/bits/stl_tree.h: -/usr/include/c++/4.4/bits/stl_map.h: +/usr/include/c++/4.5/bits/stl_map.h: -/usr/include/c++/4.4/bits/stl_multimap.h: +/usr/include/c++/4.5/bits/stl_multimap.h: -/usr/include/c++/4.4/vector: +/usr/include/c++/4.5/vector: -/usr/include/c++/4.4/bits/stl_vector.h: +/usr/include/c++/4.5/bits/stl_vector.h: -/usr/include/c++/4.4/bits/stl_bvector.h: +/usr/include/c++/4.5/bits/stl_bvector.h: -/usr/include/c++/4.4/bits/vector.tcc: +/usr/include/c++/4.5/bits/vector.tcc: diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po index c475c0e..28cf049 100644 --- a/gtfold-mfe/src/.deps/traceback.Po +++ b/gtfold-mfe/src/.deps/traceback.Po @@ -2,15 +2,16 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/bits/types.h /usr/include/bits/typesizes.h \ /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \ - /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/sys/select.h \ + /usr/include/stdlib.h /usr/include/bits/waitflags.h \ + /usr/include/bits/waitstatus.h /usr/include/endian.h \ + /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ + /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ /usr/include/bits/select.h /usr/include/bits/sigset.h \ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ @@ -38,7 +39,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/bits/types.h: @@ -50,7 +51,7 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/wchar.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/stdio_lim.h: @@ -62,9 +63,9 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/stdlib.h: -/usr/include/sys/types.h: +/usr/include/bits/waitflags.h: -/usr/include/time.h: +/usr/include/bits/waitstatus.h: /usr/include/endian.h: @@ -72,6 +73,10 @@ traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/byteswap.h: +/usr/include/sys/types.h: + +/usr/include/time.h: + /usr/include/sys/select.h: /usr/include/bits/select.h: diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po index 61ad5ac..d92a43a 100644 --- a/gtfold-mfe/src/.deps/utils.Po +++ b/gtfold-mfe/src/.deps/utils.Po @@ -3,57 +3,56 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \ /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ /usr/include/gnu/stubs-64.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ /usr/include/xlocale.h /usr/include/bits/string3.h \ - /usr/include/c++/4.4/string \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.4/bits/stringfwd.h \ - /usr/include/c++/4.4/bits/char_traits.h \ - /usr/include/c++/4.4/bits/stl_algobase.h /usr/include/c++/4.4/cstddef \ - /usr/include/c++/4.4/bits/functexcept.h \ - /usr/include/c++/4.4/exception_defines.h \ - /usr/include/c++/4.4/bits/cpp_type_traits.h \ - /usr/include/c++/4.4/ext/type_traits.h \ - /usr/include/c++/4.4/ext/numeric_traits.h \ - /usr/include/c++/4.4/bits/stl_pair.h /usr/include/c++/4.4/bits/move.h \ - /usr/include/c++/4.4/bits/concept_check.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.4/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.4/bits/stl_iterator.h \ - /usr/include/c++/4.4/debug/debug.h /usr/include/c++/4.4/bits/postypes.h \ - /usr/include/c++/4.4/cwchar /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h \ + /usr/include/c++/4.5/string \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ + /usr/include/c++/4.5/bits/stringfwd.h \ + /usr/include/c++/4.5/bits/char_traits.h \ + /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \ + /usr/include/c++/4.5/bits/functexcept.h \ + /usr/include/c++/4.5/exception_defines.h \ + /usr/include/c++/4.5/bits/cpp_type_traits.h \ + /usr/include/c++/4.5/ext/type_traits.h \ + /usr/include/c++/4.5/ext/numeric_traits.h \ + /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ + /usr/include/c++/4.5/bits/concept_check.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ + /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ + /usr/include/c++/4.5/bits/stl_iterator.h \ + /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \ + /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \ + /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \ - /usr/include/c++/4.4/bits/allocator.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.4/ext/new_allocator.h /usr/include/c++/4.4/new \ - /usr/include/c++/4.4/exception /usr/include/c++/4.4/bits/localefwd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.4/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.4/iosfwd \ - /usr/include/c++/4.4/cctype /usr/include/ctype.h \ + /usr/include/c++/4.5/bits/allocator.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ + /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ + /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ + /usr/include/c++/4.5/clocale /usr/include/locale.h \ + /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \ + /usr/include/c++/4.5/cctype /usr/include/ctype.h \ /usr/include/bits/types.h /usr/include/bits/typesizes.h \ /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.4/bits/ostream_insert.h \ - /usr/include/c++/4.4/cxxabi-forced.h \ - /usr/include/c++/4.4/bits/stl_function.h \ - /usr/include/c++/4.4/backward/binders.h \ - /usr/include/c++/4.4/bits/basic_string.h \ - /usr/include/c++/4.4/ext/atomicity.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h \ + /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \ + /usr/include/c++/4.5/cxxabi-forced.h \ + /usr/include/c++/4.5/bits/stl_function.h \ + /usr/include/c++/4.5/backward/binders.h \ + /usr/include/c++/4.5/bits/basic_string.h \ + /usr/include/c++/4.5/ext/atomicity.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h /usr/include/signal.h \ - /usr/include/bits/sigset.h /usr/include/bits/pthreadtypes.h \ - /usr/include/bits/setjmp.h /usr/include/unistd.h \ - /usr/include/bits/posix_opt.h /usr/include/bits/environments.h \ - /usr/include/bits/confname.h /usr/include/getopt.h \ - /usr/include/bits/unistd.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.4/initializer_list \ - /usr/include/c++/4.4/bits/basic_string.tcc + /usr/include/bits/sched.h /usr/include/bits/time.h \ + /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ + /usr/include/unistd.h /usr/include/bits/posix_opt.h \ + /usr/include/bits/environments.h /usr/include/bits/confname.h \ + /usr/include/getopt.h /usr/include/bits/unistd.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ + /usr/include/c++/4.5/initializer_list \ + /usr/include/c++/4.5/bits/basic_string.tcc ../include/utils.h: @@ -73,89 +72,89 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \ /usr/include/gnu/stubs-64.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stddef.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: /usr/include/xlocale.h: /usr/include/bits/string3.h: -/usr/include/c++/4.4/string: +/usr/include/c++/4.5/string: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++config.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/os_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/cpu_defines.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: -/usr/include/c++/4.4/bits/stringfwd.h: +/usr/include/c++/4.5/bits/stringfwd.h: -/usr/include/c++/4.4/bits/char_traits.h: +/usr/include/c++/4.5/bits/char_traits.h: -/usr/include/c++/4.4/bits/stl_algobase.h: +/usr/include/c++/4.5/bits/stl_algobase.h: -/usr/include/c++/4.4/cstddef: +/usr/include/c++/4.5/cstddef: -/usr/include/c++/4.4/bits/functexcept.h: +/usr/include/c++/4.5/bits/functexcept.h: -/usr/include/c++/4.4/exception_defines.h: +/usr/include/c++/4.5/exception_defines.h: -/usr/include/c++/4.4/bits/cpp_type_traits.h: +/usr/include/c++/4.5/bits/cpp_type_traits.h: -/usr/include/c++/4.4/ext/type_traits.h: +/usr/include/c++/4.5/ext/type_traits.h: -/usr/include/c++/4.4/ext/numeric_traits.h: +/usr/include/c++/4.5/ext/numeric_traits.h: -/usr/include/c++/4.4/bits/stl_pair.h: +/usr/include/c++/4.5/bits/stl_pair.h: -/usr/include/c++/4.4/bits/move.h: +/usr/include/c++/4.5/bits/move.h: -/usr/include/c++/4.4/bits/concept_check.h: +/usr/include/c++/4.5/bits/concept_check.h: -/usr/include/c++/4.4/bits/stl_iterator_base_types.h: +/usr/include/c++/4.5/bits/stl_iterator_base_types.h: -/usr/include/c++/4.4/bits/stl_iterator_base_funcs.h: +/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: -/usr/include/c++/4.4/bits/stl_iterator.h: +/usr/include/c++/4.5/bits/stl_iterator.h: -/usr/include/c++/4.4/debug/debug.h: +/usr/include/c++/4.5/debug/debug.h: -/usr/include/c++/4.4/bits/postypes.h: +/usr/include/c++/4.5/bits/postypes.h: -/usr/include/c++/4.4/cwchar: +/usr/include/c++/4.5/cwchar: /usr/include/wchar.h: /usr/include/stdio.h: -/usr/lib/gcc/x86_64-linux-gnu/4.4.3/include/stdarg.h: +/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: /usr/include/bits/wchar.h: /usr/include/bits/wchar2.h: -/usr/include/c++/4.4/bits/allocator.h: +/usr/include/c++/4.5/bits/allocator.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++allocator.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: -/usr/include/c++/4.4/ext/new_allocator.h: +/usr/include/c++/4.5/ext/new_allocator.h: -/usr/include/c++/4.4/new: +/usr/include/c++/4.5/new: -/usr/include/c++/4.4/exception: +/usr/include/c++/4.5/exception: -/usr/include/c++/4.4/bits/localefwd.h: +/usr/include/c++/4.5/bits/localefwd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/c++locale.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: -/usr/include/c++/4.4/clocale: +/usr/include/c++/4.5/clocale: /usr/include/locale.h: /usr/include/bits/locale.h: -/usr/include/c++/4.4/iosfwd: +/usr/include/c++/4.5/iosfwd: -/usr/include/c++/4.4/cctype: +/usr/include/c++/4.5/cctype: /usr/include/ctype.h: @@ -169,21 +168,21 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \ /usr/include/bits/byteswap.h: -/usr/include/c++/4.4/bits/ostream_insert.h: +/usr/include/c++/4.5/bits/ostream_insert.h: -/usr/include/c++/4.4/cxxabi-forced.h: +/usr/include/c++/4.5/cxxabi-forced.h: -/usr/include/c++/4.4/bits/stl_function.h: +/usr/include/c++/4.5/bits/stl_function.h: -/usr/include/c++/4.4/backward/binders.h: +/usr/include/c++/4.5/backward/binders.h: -/usr/include/c++/4.4/bits/basic_string.h: +/usr/include/c++/4.5/bits/basic_string.h: -/usr/include/c++/4.4/ext/atomicity.h: +/usr/include/c++/4.5/ext/atomicity.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/gthr-default.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: /usr/include/pthread.h: @@ -195,10 +194,6 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \ /usr/include/bits/time.h: -/usr/include/signal.h: - -/usr/include/bits/sigset.h: - /usr/include/bits/pthreadtypes.h: /usr/include/bits/setjmp.h: @@ -215,8 +210,8 @@ utils.o: utils.cc ../include/utils.h ../include/constants.h \ /usr/include/bits/unistd.h: -/usr/include/c++/4.4/x86_64-linux-gnu/bits/atomic_word.h: +/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: -/usr/include/c++/4.4/initializer_list: +/usr/include/c++/4.5/initializer_list: -/usr/include/c++/4.4/bits/basic_string.tcc: +/usr/include/c++/4.5/bits/basic_string.tcc: diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile index 0f50f74..53081de 100644 --- a/gtfold-mfe/src/Makefile +++ b/gtfold-mfe/src/Makefile @@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS) am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT) + subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \ + shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -74,12 +75,12 @@ DIST_SOURCES = $(gtfold_SOURCES) ETAGS = etags CTAGS = ctags DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -106,7 +107,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -122,10 +123,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/src -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/src -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/src +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/src +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -153,7 +154,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -191,6 +192,7 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + partition-dangle.c\ shapereader.cc gtfold_LDFLAGS = @@ -284,6 +286,7 @@ include ./$(DEPDIR)/global.Po include ./$(DEPDIR)/loader.Po include ./$(DEPDIR)/main.Po include ./$(DEPDIR)/options.Po +include ./$(DEPDIR)/partition-dangle.Po include ./$(DEPDIR)/shapereader.Po include ./$(DEPDIR)/subopt_traceback.Po include ./$(DEPDIR)/traceback.Po diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 1dea460..797391e 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -16,6 +16,7 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + partition-dangle.c\ shapereader.cc gtfold_LDFLAGS = diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index 8d3f880..0de321f 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS) am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) shapereader.$(OBJEXT) + subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \ + shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -191,6 +192,7 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + partition-dangle.c\ shapereader.cc gtfold_LDFLAGS = @@ -284,6 +286,7 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index f87e190..c39128e 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -217,7 +217,6 @@ double **mallocTwoD(int r, int c) { return NULL; } } - return arr; } diff --git a/gtfold-mfe/src/partition-dangle.cc b/gtfold-mfe/src/partition-dangle.cc deleted file mode 100644 index d07064c..0000000 --- a/gtfold-mfe/src/partition-dangle.cc +++ /dev/null @@ -1,130 +0,0 @@ -//The paper (Dirks, Pierce) offhandedly mentions a G-U terminal pair penalty -//I don't think we do that... - -/**s1 -> partial_external -* s2 -> partial_multi -* s3 -> partial_multi2 -* u1 -> u_multi -* f -> cond_dangle (conditional) -**/ - -#include energy.h - - -int cond_dangle(int j, int h, int l){ - return j - 1 == l ? 1 : exp(-Ed3(h,l,l+1)/RT); -} - -double RT = (0.00198721 * 310.15)/100.00; -//So that we don't have the /100 in every exponent -//Seeing as we missed some last time - -int seg_length; -int i; -for(seg_length = MIN_TURN; seg_length < len; len ++){ - for(i = 1; i < seg_length - MIN_TURN; i++){ - j = i + seg_length; - int l; - /** - * For each spot in partial_external at index h,j we'll need: - **/ - for(l = i+2; l < j; l++){ - upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) * - (exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + - u_multi[l + 1][j - 1] - - u_multi[l + 2][j - 1]); - if(l != i+2){ //goes from i + 2 < l < j - upm[i][j] += up[i + 2][l] * - exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) * - (exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + - u_multi[l + 1][j - 1] - - u_multi[l + 2][j - 1]); - - if(l != j - 1){ - upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * - partial_multi[l][j]; - //Changed h in the paper to l it makes no difference - //other than unifying loops - } - } - } - - - up[i][j] += exp(-eh(i,j)/RT) + exp(-es(i,j)/RT) * up[i + 1][j - 1] + upm[i][j]; - for(l = j - 1; l > i + 1; l--){ - if((j - l) - 2> MAX_LOOP){ - break; - } - for(h = i + 1 ; h < l; h++){ - if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack - up[i][j] += exp(-ebi(i,j,h,l)/RT); - } - if((j - l) + (h - i) - 2> MAX_LOOP){ - break; - } - } - } - - for(l = i + 1; l <= j ; l++){ - u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) * - (cond_dangle(j + 1, i, l) * exp(-(j - l) * Eb/RT) + - exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + - u_multi[l + 1][j] - - u_multi[l + 2][j]); - if(l != i+1){ - u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)* - (cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + - exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + - u_multi[l + 1][j] - - u_multi[l + 2][j]); - if(l != j){ - u_multi[i][j] += exp(-(Ec + (h - i) * Eb)/RT) * partial_multi2[l][j]; - - } - } - } - - - int h = i; //To stay consistant with the notation in the paper. - - for(l = h+1; l < j; l++){ - partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * - (exp(-Ed3(h,l,l + 1)/RT)*u[l + 2,j - 1] + - u[l + 1][j] - - u[l + 2][j]); - - partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * - (exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + - u_multi[l + 1][j - 1] - - u_multi[l + 2][j - 1]); - - partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * - (cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + - exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + - u_multi[l + 1][j] - - u_multi[l + 2][j]); - - } - /** partial_multi2 goes up to j **/ - partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * - (cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + - exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + - u_multi[l + 1][j] - - u_multi[l + 2][j]); - - //Finally we do the u matrix - u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT); - - for(l = i + 1; l < j; l++){ - //Replaced l with h in the next line to unify loops - u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT) - - u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] + - u[l + 1][j] - u[l + 2][j]); - if(l != j - 1) { - u[i][j] += partial_external[l][j]; - } - - } - } -} From 294a55615f0b0230046db1af2b390e4f2751c07f Mon Sep 17 00:00:00 2001 From: Janderson Date: Fri, 20 May 2011 11:13:29 -0400 Subject: [PATCH 027/187] Finished writing all probability functions --- gtfold-mfe/src/random-sample.cc | 187 ++++++++++++++++++++++++++++++++ 1 file changed, 187 insertions(+) create mode 100644 gtfold-mfe/src/random-sample.cc diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc new file mode 100644 index 0000000..3290e38 --- /dev/null +++ b/gtfold-mfe/src/random-sample.cc @@ -0,0 +1,187 @@ +#include +#include + +#include "parition-dangle.h" +#include "energy.h" + +double RT=(0.00198721 * 310.15)/100.00; + +double randdouble(){ + return rand()/(double(RAND_MAX)+1); +} + +//P_0 +double single_stranded_prob(int i, int j, dangle_struct d_struct){ + return 1 / d_struct.u[i][j]; +} + +//P_{ij} +double ends_pair_prob(int i, int j, dangle_struct d_struct){ + return d_struct.up[i][j] * exp(-auPenalty(i,j)/RT)/d_struct.u[i][j]; +} + +//P_{hj} +double prob_h_pairs_with_5_end + (int i, int h, int j, dangle_struct d_struct){ + + return d_struct.up[h][j] * + exp(-(ed5(h,j,h - 1) + + auPenalty(h,j))/RT) / + d_struct.u[i][j]; +} + +//P_{il} +double prob_l_pairs_with_3_end + (int i, int l, int j dangle_struct d_struct){ + + return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) * + (exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.u[i][j]; +} + +//P_{s1h} +double prob_h_pairs_in_ij(int i, int h, int j, dangle_struct d_struct){ + return d_struct.s1[h][j] / d_struct.u[i][j]; +} + +//P_{hl} +//This is the probability h pairs with l +//**Given that h pairs before j** +double prob_h_pairs_with_l(int h, int l, int j, dangle_struct d_struct){ + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (exp(-Ed3(h,l,l + 1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.s1[h][j]; +} + +//Q_{ijH} +double prob_ij_pair_is_hairpin(int i, int j, dangle_struct d_struct){ + return exp(-eH(i,j)/RT)/d_struct.up[i][j]; +} + +//Q_{ijS} +double prob_ij_pair_is_stack(int i, int j, dangle_struct d_struct){ + return exp(-eS(i,j)/RT) * d_struct.up[i + 1][j - 1]/d_struct.u[i][j]; +} +//To find Q_{ijBl} take the rest of the probabilities and subtract +//them from 1. + +//Q_{ijM} +double prob_ij_pair_is_multiloop(int i, int j, dangle_struct d_struct){ + return d_struct.upm[i][j]/d_struct.up[i][j]; +} + +//This the probability hl closes a multiloop +//**GIVEN IJ CLOSES A MULTILOOP** +double prob_ijhl_is_internal_loop + (int i, int j, int h, int l, double partition_sum, dangle_struct d_struct){ + return exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / partition_sum; +} + +//P_{ij(1+1)l} +double first_multi_prob_pair_next_base + (int i, int l, int j, dangle_struct d_struct){ + return d_struct.up[i + 1][l] * + (exp( - (Ea + 2 * Ec + auPenalty(i + 1, l))/RT) * + (exp(-Ed3(i + 1,l,l +1))/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ij(1+2)l} +double first_multi_prob_pair_after_base + (int i, int l, int j, dangle_struct d_struct){ + + return d_struct[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) * + (exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ijs2h) +double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){ + return exp(-(Ea + 2 * Ec + (h - i - 1) * b + Ed3(j,i,i+1))/RT) * + d_struct.s2[h][j] / d_struct.upm[i][j]; +} +//P_{ijhl} +double first_multi_prob_base_rest + (int i, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h-1) + auPenalty(h,l))/RT) * + (exp( -Ed3(h,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1])/d_struct.s2[h][j]; +} + +//Q_{(l1 + 1)(j -1)(l1 +1)} +double rest_multi_prob_next_base_pairs + (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 +1][l] * exp( - (Ec + auPenalty(l1 + 1, l))/RT) + (cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) + + exp(-(j - 1 - l) * Eb) / RT + + exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(l1 + 1)(j - 1)(l1 + 2)l} +double rest_multi_prob_after_base_pairs + (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 + 2][l] * exp(-(Ec + Eb + auPenalty(l1 + 2,l))/RT) * + (cond_dangle(j, l1 + 2, l) * exp( -(j - 1 - l) * Eb / RT) + + exp(-Ed3(l1 + 1,l ,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; + +} + +//Q_{(l1 + 1)(j - 1)s3h} +double rest_multi_prob_rest_base_pairs + (int l1, int h, int j, dangle_struct d_struct){ + + return exp( -(Ec + (h - l1 - 1) * Eb)/RT) * d_struct.s3[h][j - 1] / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(j-1)hl} +//GIVEN THAT H PAIRS BEFORE J +double rest_multi_prob_h_pairs_with_l + (int l1, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (cond_dangle(j,h,l) * exp(-(j - 1 -l) * Eb/RT) + + exp(-Ed3(h,l,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.s3[h][j - 1]; +} + +int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){ + double counter = randdouble(); + double coin-flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) / + (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + + exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] + + d_struct.u1[l2 + 1][j - 1] - + d_struct.u1[l2 + 2][j - 1]); + + //If I was slick and mean I would have put + + //return counter > coin-flip + + if(counter <= coin-flip){ + return 0; + } + else{ + return 1; + } +} From 9008ee9021e249c35d620b6042064c49470f76aa Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 20 May 2011 13:24:55 -0400 Subject: [PATCH 028/187] fixed internal loop calculation --- gtfold-mfe/src/algorithms.c | 36 ++++++++++++++++++++++++++++++++++-- 1 file changed, 34 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index a10f0f7..0dcf4cb 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -63,17 +63,49 @@ int calculate(int len, int nThreads) { if (j-i > 6) { // Internal Loop BEGIN int p=0, q=0; int VBIij = INFINITY_; - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { int minq = j-i+p-MAXLOOP-2; if (minq < p+1+TURN) minq = p+1+TURN; - for (q = minq; q < j; q++) { + int maxq = (p==i+1)?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { if (!canPair(RNA[p], RNA[q])) continue; if (check_iloop(i,j,p,q)) continue; VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); } } VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij; + + /* + int ip,jp; + int ifinal, jfinal, temp; + + ip = i + 1; + int thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); // Minimum size of a hairpin loop is 3. So, start jp from ip+4 + for (jp = thres1; jp <= j - 2; jp++) { + if (canPair(RNA[ip], RNA[jp])) { + temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; // Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp) + if (VBIij > temp) { + VBIij = temp; + ifinal = ip; + jfinal = jp; + } + } + } + + for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) { + thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); + for (jp = thres1; jp <= j - 1; jp++) { + if (canPair(RNA[ip], RNA[jp])) { + temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; + if (VBIij > temp) { + VBIij = temp; + ifinal = ip; + jfinal = jp; + } + } + } + } */ + } // Internal Loop END if (j-i > 10) { // Multi Loop BEGIN From 9e0612c75ec5e17b4b1fb96ff307a7c457d20f0f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 12:40:34 -0400 Subject: [PATCH 029/187] removed flag optimization --- gtfold-mfe/src/algorithms.c | 45 +++++-------------------------------- 1 file changed, 5 insertions(+), 40 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 0dcf4cb..7f76aa5 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -54,12 +54,12 @@ int calculate(int len, int nThreads) { #endif for (i = 1; i <= len - b; i++) { j = i + b; - int flag = 0, newWM = INFINITY_; + int newWM = INFINITY_; if (canPair(RNA[i], RNA[j])) { - flag = 1; int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack + if (j-i > 6) { // Internal Loop BEGIN int p=0, q=0; int VBIij = INFINITY_; @@ -74,38 +74,6 @@ int calculate(int len, int nThreads) { } } VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij; - - /* - int ip,jp; - int ifinal, jfinal, temp; - - ip = i + 1; - int thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); // Minimum size of a hairpin loop is 3. So, start jp from ip+4 - for (jp = thres1; jp <= j - 2; jp++) { - if (canPair(RNA[ip], RNA[jp])) { - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; // Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp) - if (VBIij > temp) { - VBIij = temp; - ifinal = ip; - jfinal = jp; - } - } - } - - for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) { - thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); - for (jp = thres1; jp <= j - 1; jp++) { - if (canPair(RNA[ip], RNA[jp])) { - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > temp) { - VBIij = temp; - ifinal = ip; - jfinal = jp; - } - } - } - } */ - } // Internal Loop END if (j-i > 10) { // Multi Loop BEGIN @@ -118,7 +86,6 @@ int calculate(int len, int nThreads) { VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); - newWM = MIN(newWM, VMij); } int d3 = Ed3(i,j,j-1); @@ -138,12 +105,10 @@ int calculate(int len, int nThreads) { if (j-i > 4) { // WM BEGIN int h; - if (!flag) { - for (h = i+TURN+1 ; h <= j-TURN-1; h++) { - newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); - } + for (h = i+TURN+1 ; h <= j-TURN-1; h++) { + newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); } - + newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); newWM = check_base(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; newWM = check_base(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; From b85fbafbcaed713ea2358c77aee7d65d4a5492a6 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 16:44:42 -0400 Subject: [PATCH 030/187] added -p option to allow --- gtfold-mfe/src/constraints.cc | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index d3cd01b..1e840cc 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -24,8 +24,8 @@ bool compare_bp(const std::pair& o1, static int load_constraints(const char* constr_file, int verbose=0) { + fprintf(stdout, "- Running with constraints %s\n", constr_file); std::ifstream cfcons; - fprintf(stdout, "- Running with constraints\n"); cfcons.open(constr_file, std::ios::in); if (cfcons == 0) { @@ -83,7 +83,7 @@ static int load_constraints(const char* constr_file, int verbose=0) { pit++; } } - + /* std::vector > v_fbp; for(it=0; it< nFBP; it++) { for(int k=1;k<= FBP[it][2];k++) @@ -100,7 +100,7 @@ static int load_constraints(const char* constr_file, int verbose=0) { } } - +*/ return 0; } From 3e117e6079ee36b712e57c5920cacaec3be41827 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 16:45:22 -0400 Subject: [PATCH 031/187] added -p option to allow dir name for param files --- gtfold-mfe/src/loader.cc | 6 +----- gtfold-mfe/src/main.cc | 6 ++++-- gtfold-mfe/src/options.cc | 21 ++++++++++++++++----- 3 files changed, 21 insertions(+), 12 deletions(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 18066c6..e8354a1 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -76,8 +76,7 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo float prelog; void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { - -#ifndef GENBIN + cout << userdatalogic << ' ' << userdatadir << std::endl; if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; @@ -85,9 +84,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } else { EN_DATADIR.assign(userdatadir); } -#else - EN_DATADIR = "data"; -#endif //Handle the ending forward slash case if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index e976d49..a67c887 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -39,6 +39,8 @@ #include "constraints.h" #include "traceback.h" #include "subopt_traceback.h" +#include "shapereader.h" + using namespace std; @@ -173,7 +175,7 @@ int main(int argc, char** argv) { std::string seq; int energy; double t1; - + print_header(); parse_options(argc, argv); @@ -184,7 +186,7 @@ int main(int argc, char** argv) { } // Read in thermodynamic parameters. Always use Turner99 data (for now) - readThermodynamicParameters("Turner99",false); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR); printRunConfiguration(seq); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 1bc103c..a8be69b 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -5,8 +5,9 @@ using namespace std; bool ILSA; bool NOISOLATE; -bool USERDATA; -bool PARAMS; +//bool USERDATA; +//bool PARAMS; +bool PARAM_DIR = false; bool LIMIT_DISTANCE; bool BPP_ENABLED; bool SUBOPT_ENABLED; @@ -15,7 +16,8 @@ bool VERBOSE = false; string seqfile = ""; string constraintsFile = ""; -string outputFile = ""; +string outputFile = ""; +string paramDir = "Turner99"; // default value int suboptDelta = -1; int nThreads = -1; @@ -34,7 +36,8 @@ void help() { printf(" Load constraints from FILE. See Constraint syntax below\n"); printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); + printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); + printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); printf(" -t, --threads num Limit number of threads used\n"); @@ -83,7 +86,15 @@ void parse_options(int argc, char** argv) { outputFile = argv[++i]; else help(); - } else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { if(i < argc) nThreads = atoi(argv[++i]); else From 7e421b5762cd36e09ad88c4a948c9a8135c2be33 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 16:46:23 -0400 Subject: [PATCH 032/187] added -p option to allow dir name for param files --- gtfold-mfe/include/options.h | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 7772be1..1e46851 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -10,17 +10,19 @@ using namespace std; extern bool ILSA; extern bool NOISOLATE; -extern bool USERDATA; -extern bool PARAMS; +//extern bool USERDATA; +//extern bool PARAMS; extern bool LIMIT_DISTANCE; extern bool BPP_ENABLED; extern bool SUBOPT_ENABLED; extern bool CONS_ENABLED; extern bool VERBOSE; +extern bool PARAM_DIR; extern string seqfile; extern string constraintsFile; extern string outputFile; +extern string paramDir; extern int suboptDelta; extern int nThreads; From ec8dcb9830516cb8ffb57e7105ceac2c69a4c9bf Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 23:04:06 -0400 Subject: [PATCH 033/187] removed unrequired header --- gtfold-mfe/src/main.cc | 2 -- 1 file changed, 2 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index a67c887..2327ca0 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -39,8 +39,6 @@ #include "constraints.h" #include "traceback.h" #include "subopt_traceback.h" -#include "shapereader.h" - using namespace std; From fd23a9d001a671efcbb43be6e8695ef7b7c1dd7d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 23 May 2011 23:14:55 -0400 Subject: [PATCH 034/187] removed cout statement --- gtfold-mfe/src/loader.cc | 1 - 1 file changed, 1 deletion(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index e8354a1..c68ee22 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -76,7 +76,6 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo float prelog; void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { - cout << userdatalogic << ' ' << userdatadir << std::endl; if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; From 14e822e63e4fa717a423d343a482ca3eb944a32b Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Tue, 24 May 2011 15:05:02 +0200 Subject: [PATCH 035/187] fixed MFE and constraints. constraint check included with -v option --- gtfold-mfe/include/constraints.h | 24 ++--- gtfold-mfe/src/algorithms.c | 180 +++++++++++++------------------ gtfold-mfe/src/constraints.cc | 140 ++++++++---------------- gtfold-mfe/src/traceback.c | 86 ++++++--------- 4 files changed, 163 insertions(+), 267 deletions(-) diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h index 045ebad..9805dbd 100644 --- a/gtfold-mfe/include/constraints.h +++ b/gtfold-mfe/include/constraints.h @@ -21,19 +21,17 @@ void print_constraints(int length) ; #ifdef __cplusplus extern "C" { #endif -//int is_ss(int i, int j); -//int prohibit_base(int i) ; -int check_ssregion(int i, int j); -//int check_base(int i) ; -//int force_pair(int i, int j) ; -int force_pair1(int i, int j) ; -int force_ss1(int i); -int force_ssregion1(int i, int j); -int check_iloop(int i, int j, int p, int q) ; -int check_pair(int i, int j) ; -int check_stack(int i, int j) ; -int check_hairpin(int i, int j) ; -int can_dangle(int i); +int canStack(int i, int j); +int canSS(int i); +int canSSregion(int i, int j); +int canHairpin(int i, int j); +int canILoop(int i, int j, int p, int q); + +int forceSS(int i); +int forceSSregion(int i, int j); +int forcePair(int i, int j); + + int withinCD(int i, int j); int verify_structure(); #ifdef __cplusplus diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index c7b9a3d..c5a71c5 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -1,29 +1,24 @@ /* - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . */ - #include #include #include #include #include #include - #include "constants.h" #include "utils.h" #include "energy.h" @@ -31,27 +26,19 @@ #include "algorithms.h" #include "constraints.h" #include "shapereader.h" - -#ifdef _OPENMP +#ifdef _OPENMP #include "omp.h" #endif - int calculate(int len, int nThreads) { int b, i, j; - - -// printf("%d\n", BP(1145, 13)); - #ifdef _OPENMP if (nThreads>0) omp_set_num_threads(nThreads); #endif - #ifdef _OPENMP #pragma omp parallel #pragma omp master fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif - for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) @@ -59,119 +46,104 @@ int calculate(int len, int nThreads) { for (i = 1; i <= len - b; i++) { j = i + b; int flag = 0, newWM = INFINITY_; - if (canPair(RNA[i], RNA[j]) && withinCD(i,j)) { + if (canPair(RNA[i], RNA[j])) { flag = 1; - int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin - int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack - if (j-i > 6) { // Internal Loop BEGIN + int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin + int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack + if (j-i > 6) { // Internal Loop BEGIN int p=0, q=0; int VBIij = INFINITY_; - - int found_forced_pair = 0; for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { int minq = j-i+p-MAXLOOP-2; if (minq < p+1+TURN) minq = p+1+TURN; - for (q = minq; q < j; q++) { + int maxq = (p==i+1)?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { if (!canPair(RNA[p], RNA[q])) continue; - if (check_iloop(i,j,p,q)) continue; - if(force_pair1(p,q)){ - //ZS: if we know a pair should be forced, we should - //just enforce it and not care about other options. - VBIij = eL(i,j,p,q) + V(p,q); - found_forced_pair = 1; - break; - } + if (!canILoop(i,j,p,q)) continue; VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); } - if(found_forced_pair){break;} } - VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij; - } // Internal Loop END - - if (j-i > 10) { // Multi Loop BEGIN + VBI(i,j) = VBIij; + V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); + + } // Internal Loop END + if (j-i > 10) { // Multi Loop BEGIN int h; int VMij, VMijd, VMidj, VMidjd; VMij = VMijd = VMidj = VMidjd = INFINITY_; - for (h = i+TURN+1; h <= j-1-TURN; h++) { - VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); - VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); - VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); - VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); - //ZS: I don't think the following line is being checked in traceback, so - //if you enable it, sometimes huge parts of the structure will not be possible - //to trace. - //I don't know if it should be here or not. If it is here, it should be in traceback - //too. For now, I am removing it! - //newWM = MIN(newWM, VMij); + VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); + VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); + VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); + VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); } - - int d3 = can_dangle(j-1)?Ed3(i,j,j-1):INFINITY_; - int d5 = can_dangle(i+1)?Ed5(i,j,i+1):INFINITY_; - + int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; + int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; VMij = MIN(VMij, (VMidj + d5 +Ec)) ; VMij = MIN(VMij, (VMijd + d3 +Ec)); - VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); + VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); VMij = VMij + Ea + Eb + auPenalty(i,j); - VM(i,j) = check_pair(i,j)?INFINITY_:VMij; + VM(i,j) = canStack(i,j)?VMij:INFINITY_; } // Multi Loop END - - V(i,j) = check_pair(i,j)?INFINITY_:MIN4(eh,es,VBI(i,j),VM(i,j)); - V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); + V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); } - else - V(i,j) = INFINITY_; - - if (j-i > 4) { // WM BEGIN + else V(i,j) = INFINITY_; + if (j-i > 4) { // WM BEGIN int h; - //ZS: if we know that i,j are pairing, we just have to set WM(i,j) = V(i,j) in the best possible way. - //Conversely, we only need to find the best partitioning if we know that i,j are not forced to pair. - - //Prashant's original code had if(!flag) here... I don't know what that was supposed to do? - if (!force_pair1(i,j)) { - for (h = i+TURN+1 ; h <= j-TURN-1; h++) { - newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); - } + for (h = i+TURN+1 ; h <= j-TURN-1; h++) { + //ZS: This sum corresponds to when i,j are NOT paired with each other. + //So we need to make sure only terms where i,j aren't pairing are considered. + newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; } - newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - - //ZS: if i,j are forced to pair then can_dangle(i) and can_dangle(j) will be false - newWM = can_dangle(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): newWM; - newWM = can_dangle(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : newWM; - newWM = (can_dangle(i)&&can_dangle(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): newWM; - newWM = can_dangle(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; - newWM = can_dangle(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; + newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle + newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle + newWM = (canSS(i)&&canSS(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM):newWM; //i,j dangle + newWM = canSS(i)?MIN(WMU(i+1,j) + Ec, newWM):newWM; //i dangle + newWM = canSS(j)?MIN(WML(i,j-1) + Ec, newWM):newWM; //j dangle WMU(i,j) = WML(i,j) = newWM; } // WM END } } - - for (j = TURN+2; j <= len; j++) { - int i, branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1; + for (j = TURN+2; j <= len; j++) { + int i, must_branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1; Wj = INFINITY_; for (i = 1; i < j-TURN; i++) { Wij = Widjd = Wijd = Widj = INFINITY_; Wim1 = MIN(0, W[i-1]); Wij = V(i, j) + auPenalty(i, j) + Wim1; - Widjd = (can_dangle(i)&&can_dangle(j))?(V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1):INFINITY_; - Wijd = can_dangle(j)?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1):INFINITY_; - Widj = (can_dangle(i))?(V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1):INFINITY_; + Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1:Widjd; + Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd; + Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj; Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); - + + /* if (Wj 0) return 1; - } - return 0; - } - else - return 0; - -return 0; -} - - -int prohibit_base(int i) { -// return (BP[i] == -1); -return 0; -} - -*/ -//int check_base(int i) { - -// if (CONS_ENABLED) -// return (BP[i] <= 0); -// else -// return 1; - -//return 1; -//} - -/*int force_pair(int i, int j) { - - return (BP[i] > 0 && j != BP[i]); - -return 0; -}*/ - -int force_pair1(int i, int j) { -//ZS: this function returns true if a pair between i and j is forced. +int forcePair(int i, int j) { +//ZS: this function returns true if the pair i-j is forced. if (CONS_ENABLED) return BP(i,j)==1; else return 0; } -int force_ss1(int i){ -//ZS: this function returns true if a base is forced to be single-stranded - +int forceSS(int i){ +//ZS: this function returns true if base i is forced to be single-stranded if(CONS_ENABLED) return BP(i,i)==3; else return 0; } -int force_ssregion1(int i, int j){ +int forceSSregion(int i, int j){ + //ZS: This returns 1 if all nucleotides between i and j are forced to be single-stranded, 0 if there is at least one that is not if(CONS_ENABLED){ - int value = 1; for(int p = i; pcontactDistance; } diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 7d25b32..15a2f0c 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -61,28 +61,24 @@ void traceW(int j) { if (j == 0 || j == 1) return; - for (i = 1; i < j && !done; i++) { - if (j-i < TURN) continue; wim1 = MIN(0, W[i-1]); flag = 1; - if (wim1 != W[i-1] && !check_ssregion(1,i)) flag = 0; - //ZS: flag is false if the free energy of the best structure to W[i] is > 0 --> all should be ss - //UNLESS there is at least one base that is forced to pair in that region, this is revealed by check_ssregion(1,i) + if ( wim1 != W[i-1]) flag = 0; Widjd = Wijd = Widj = INFINITY_; Wij = V(i,j) + auPenalty(i, j) + wim1; - Widjd =(can_dangle(i)&&can_dangle(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_; - Wijd = (can_dangle(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_; - Widj = (can_dangle(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_; + Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1; + Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; + Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; Wj_temp=Wj; + Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); if (W[j] == Wj) { - //if we know W[j] is pairing with something - if (W[j] == Wij || force_pair1(i,j)){ + if (W[j] == Wij) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); @@ -90,9 +86,9 @@ void traceW(int j) { structure[i] = j; structure[j] = i; traceV(i, j); - if (flag || force_ssregion1(1,i)) traceW(i - 1); + if (flag ) traceW(i - 1); break; - } else if ((W[j] == Widjd && can_dangle(i) && can_dangle(j)) || force_pair1(i+1,j-1)) { + } else if (W[j] == Widjd) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00); @@ -100,9 +96,9 @@ void traceW(int j) { structure[i + 1] = j - 1; structure[j - 1] = i + 1; traceV(i + 1, j - 1); - if (flag || force_ssregion1(1,i)) traceW(i - 1); + if (flag ) traceW(i - 1); break; - } else if ((W[j] == Wijd && can_dangle(j))||force_pair1(i,j-1)) { + } else if (W[j] == Wijd) { done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); @@ -110,9 +106,9 @@ void traceW(int j) { structure[i] = j - 1; structure[j - 1] = i; traceV(i, j - 1); - if (flag || force_ssregion1(1,i)) traceW(i - 1); + if (flag ) traceW(i - 1); break; - } else if ((W[j] == Widj && can_dangle(i))||force_pair1(i+1,j)) { + } else if (W[j] == Widj){ done = 1; if (verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); @@ -120,29 +116,31 @@ void traceW(int j) { structure[i + 1] = j; structure[j] = i + 1; traceV(i + 1, j); - if (flag || force_ssregion1(1,i)) traceW(i - 1); + if (flag ) traceW(i - 1); break; } } } - + if (W[j] == W[j - 1] && !done) traceW(j-1); return; } int traceV(int i, int j) { - int a, b, c, d, Vij; if (j-i < TURN) return INFINITY_; - a = eH(i, j)+getShapeEnergy(i) + getShapeEnergy(j); - b = eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j); + a = canHairpin(i,j)?eH(i, j)+ getShapeEnergy(i) + getShapeEnergy(j):INFINITY_; + b = canStack(i,j)?eS(i, j) + V(i + 1, j - 1) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_; if (eS(i, j) == 0) b = INFINITY_; - c = VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j); - d = VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j); + c = canStack(i,j)?VBI(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_; + d = canStack(i,j)?VM(i,j) + getShapeEnergy(i) + getShapeEnergy(j):INFINITY_; + + - Vij = MIN(MIN(a, b), MIN(c, d)); + //Vij = MIN(MIN(a, b), MIN(c, d)); + Vij = V(i,j); if (Vij == a && Vij != b && Vij != c && Vij != d) { if (verbose == 1) @@ -183,7 +181,6 @@ int traceVBI(int i, int j) { for (ip = i + 1; ip < j - 1; ip++) { for (jp = ip + 1; jp < j; jp++) { - if (check_iloop(i,j,ip,jp)) continue; el = eL(i, j, ip, jp); v = V(ip, jp); VBIij_temp = el + v; @@ -227,7 +224,7 @@ int traceVM(int i, int j) { } } - if (can_dangle(i+1)) { + //if (check_base(i+1)) { for (h = i + 3; h <= j - 1 && !done; h++) { A_temp = WM(i + 2,h - 1) + WM(h,j - 1) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1); if (A_temp == VMij) { @@ -237,9 +234,9 @@ int traceVM(int i, int j) { break; } } - } + //} - if (can_dangle(j-1)) { + //if (check_base(j-1)) { for (h = i + 2; h <= j - 2 && !done; h++) { A_temp = WM(i + 1,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i, j) + Ed3(i,j,j - 1); if (A_temp == VMij) { @@ -249,25 +246,25 @@ int traceVM(int i, int j) { break; } } - } + //} - if (can_dangle(i+1)&&can_dangle(j-1)) { + //if (check_base(i+1)&&check_base(j-1)) { for (h = i + 3; h <= j - 2 && !done; h++) { A_temp = WM(i + 2,h - 1) + WM(h,j - 2) + Ea + Eb + auPenalty(i,j) + Ed5(i,j,i + 1) + Ed3(i,j,j - 1); if (A_temp == VMij) { done = 1; eVM += traceWM(i + 2, h - 1); eVM += traceWM(h, j - 2); - break; } } - } + //} return eVM; } int traceWM(int i, int j) { + int done; int h1, h; int eWM = 0; @@ -295,44 +292,29 @@ int traceWM(int i, int j) { structure[i] = j; structure[j] = i; eWM += traceV(i, j); - } else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && can_dangle(i)) { + } else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec) { done = 1; eWM += traceV(i + 1, j); structure[i + 1] = j; structure[j] = i + 1; - } else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && can_dangle(j) ) { + } else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec ) { done = 1; eWM += traceV(i, j - 1); structure[i] = j - 1; structure[j - 1] = i; - } else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec && can_dangle(i) && can_dangle(j)) { + } else if (WM(i,j) == V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec) { done = 1; eWM += traceV(i + 1, j - 1); structure[i + 1] = j - 1; structure[j - 1] = i + 1; - } else if (WM(i,j) == WM(i + 1,j) + Ec && can_dangle(i)) { + } else if (WM(i,j) == WM(i + 1,j) + Ec) { done = 1; eWM += traceWM(i + 1, j); - } else if (WM(i,j) == WM(i,j - 1) + Ec && can_dangle(j)) { + } else if (WM(i,j) == WM(i,j - 1) + Ec) { done = 1; eWM += traceWM(i, j - 1); } } } - //ZS: This is for debugging purposes. - if(!done){ - printf("ERROR: WM couldn't be traced!\n"); - printf("%d %d \n", i, j); - printf("WM(i,j) = %d\n", WM(i,j)); - printf("candangle i? %d\n", can_dangle(i)); - printf("candangle j? %d\n", can_dangle(j)); - printf("The options were: \n"); - printf("Option 1 %d \n" , V(i,j) + auPenalty(i, j) + Eb); - printf("Option 2 %d \n" , V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec); - printf("Option 3 %d \n", V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec); - printf("Option 4 %d \n", V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1, j-1) + Eb + 2*Ec); - printf("Option 5 %d \n", WM(i + 1,j) + Ec ); - printf("Option 6 %d \n", WM(i,j - 1) + Ec); - } return eWM; } From 3eee5c204703337e9539eecf53a3438dd82870ff Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Tue, 24 May 2011 18:13:27 +0200 Subject: [PATCH 036/187] Fixed constraints, removed unnecessary output --- gtfold-mfe/src/.deps/energy.Po | 5 +++- gtfold-mfe/src/algorithms.c | 30 ++------------------- gtfold-mfe/src/constraints.cc | 2 -- gtfold-mfe/src/energy.c | 7 +++-- gtfold-mfe/src/traceback.c | 49 ++++++++++++++++++---------------- 5 files changed, 37 insertions(+), 56 deletions(-) diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po index 7c1467f..de8d5e9 100644 --- a/gtfold-mfe/src/.deps/energy.Po +++ b/gtfold-mfe/src/.deps/energy.Po @@ -19,7 +19,8 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ ../include/energy.h ../include/data.h ../include/constants.h \ - ../include/utils.h ../include/global.h ../include/constants.h + ../include/utils.h ../include/global.h ../include/constants.h \ + ../include/shapereader.h /usr/include/stdlib.h: @@ -114,3 +115,5 @@ energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ ../include/global.h: ../include/constants.h: + +../include/shapereader.h: diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index c5a71c5..59a1824 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -49,7 +49,7 @@ int calculate(int len, int nThreads) { if (canPair(RNA[i], RNA[j])) { flag = 1; int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack + int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack if (j-i > 6) { // Internal Loop BEGIN int p=0, q=0; int VBIij = INFINITY_; @@ -106,7 +106,7 @@ int calculate(int len, int nThreads) { } } for (j = TURN+2; j <= len; j++) { - int i, must_branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1; + int i, Wj, Widjd, Wijd, Widj, Wij, Wim1; Wj = INFINITY_; for (i = 1; i < j-TURN; i++) { Wij = Widjd = Wijd = Widj = INFINITY_; @@ -116,34 +116,8 @@ int calculate(int len, int nThreads) { Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd; Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj; Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); - - /* - if (Wj Date: Wed, 25 May 2011 03:55:47 +0200 Subject: [PATCH 037/187] merged Prashant's rewrite branch --- gtfold-mfe/data/Turner99/Makefile.am | 15 + gtfold-mfe/data/Turner99/Makefile.in | 13 + gtfold-mfe/data/Turner99/dangle.DAT | 8 + gtfold-mfe/data/Turner99/int11.DAT | 24 + gtfold-mfe/data/Turner99/int21.DAT | 96 +++ gtfold-mfe/data/Turner99/int22.DAT | 576 ++++++++++++++++ gtfold-mfe/data/Turner99/loop.DAT | 30 + gtfold-mfe/data/Turner99/miscloop.DAT | 12 + gtfold-mfe/data/Turner99/sint2.DAT | 24 + gtfold-mfe/data/Turner99/sint4.DAT | 576 ++++++++++++++++ gtfold-mfe/data/Turner99/stack.DAT | 16 + gtfold-mfe/data/Turner99/tloop.DAT | 30 + gtfold-mfe/data/Turner99/tstackh.DAT | 16 + gtfold-mfe/data/Turner99/tstacki.DAT | 16 + gtfold-mfe/data/Turner99/tstackm.DAT | 16 + gtfold-mfe/include/loader.h | 20 +- gtfold-mfe/include/options.h | 11 + gtfold-mfe/scripts/dats2DATs.py | 53 ++ gtfold-mfe/src/algorithms.c | 23 + gtfold-mfe/src/constraints.cc | 57 +- gtfold-mfe/src/energy.c | 46 +- gtfold-mfe/src/loader.cc | 949 +++++++------------------- gtfold-mfe/src/main.cc | 14 +- gtfold-mfe/src/options.cc | 26 +- 24 files changed, 1921 insertions(+), 746 deletions(-) create mode 100644 gtfold-mfe/data/Turner99/dangle.DAT create mode 100644 gtfold-mfe/data/Turner99/int11.DAT create mode 100644 gtfold-mfe/data/Turner99/int21.DAT create mode 100644 gtfold-mfe/data/Turner99/int22.DAT create mode 100644 gtfold-mfe/data/Turner99/loop.DAT create mode 100644 gtfold-mfe/data/Turner99/miscloop.DAT create mode 100644 gtfold-mfe/data/Turner99/sint2.DAT create mode 100644 gtfold-mfe/data/Turner99/sint4.DAT create mode 100644 gtfold-mfe/data/Turner99/stack.DAT create mode 100644 gtfold-mfe/data/Turner99/tloop.DAT create mode 100644 gtfold-mfe/data/Turner99/tstackh.DAT create mode 100644 gtfold-mfe/data/Turner99/tstacki.DAT create mode 100644 gtfold-mfe/data/Turner99/tstackm.DAT create mode 100755 gtfold-mfe/scripts/dats2DATs.py diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index 4cf8fa7..cb09a05 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -3,6 +3,19 @@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + sint2.DAT\ + sint4.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstackm.DAT\ stack.dat\ miscloop.dat\ dangle.dat\ @@ -23,6 +36,8 @@ gtfold_data_DATA = \ tstacki.dat\ tstackm.dat + + EXTRA_DIST = $(gtfold_data_DATA) CLEANFILES = *~ diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index d9a1eb3..d042a79 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -176,6 +176,19 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + sint2.DAT\ + sint4.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstackm.DAT\ stack.dat\ miscloop.dat\ dangle.dat\ diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT new file mode 100644 index 0000000..9fb7c28 --- /dev/null +++ b/gtfold-mfe/data/Turner99/dangle.DAT @@ -0,0 +1,8 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -0.50 -0.80 -0.60 +inf inf inf inf inf inf inf inf -1.70 -0.80 -1.70 -1.20 inf inf inf inf +inf inf inf inf -1.10 -0.40 -1.30 -0.60 inf inf inf inf -0.80 -0.50 -0.80 -0.60 +-0.70 -0.10 -0.70 -0.10 inf inf inf inf -0.70 -0.10 -0.70 -0.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.10 -0.20 -0.20 +inf inf inf inf inf inf inf inf -0.20 -0.30 -0.0 -0.0 inf inf inf inf +inf inf inf inf -0.50 -0.30 -0.20 -0.10 inf inf inf inf -0.30 -0.10 -0.20 -0.20 +-0.30 -0.30 -0.40 -0.20 inf inf inf inf -0.30 -0.30 -0.40 -0.20 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/int11.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 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1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/Turner99/int21.DAT b/gtfold-mfe/data/Turner99/int21.DAT new file mode 100644 index 0000000..0dfe3c4 --- /dev/null +++ b/gtfold-mfe/data/Turner99/int21.DAT @@ -0,0 +1,96 @@ +3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 +3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 +3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 +3.60 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a/gtfold-mfe/data/Turner99/miscloop.DAT b/gtfold-mfe/data/Turner99/miscloop.DAT new file mode 100644 index 0000000..2ba7508 --- /dev/null +++ b/gtfold-mfe/data/Turner99/miscloop.DAT @@ -0,0 +1,12 @@ +1.079 +3.00 +.50 .50 .50 .50 +3.40 .00 .40 +10.10 -0.30 -0.30 +0.50 +-2.20 +0.30 +1.60 +1.40 +4.10 +1 diff --git a/gtfold-mfe/data/Turner99/sint2.DAT b/gtfold-mfe/data/Turner99/sint2.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/sint2.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 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1.60 +1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 +2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 +1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 +2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 +2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 +2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 +1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 +3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 +1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 +2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 +1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 +2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/Turner99/stack.DAT b/gtfold-mfe/data/Turner99/stack.DAT new file mode 100644 index 0000000..04a6889 --- /dev/null +++ b/gtfold-mfe/data/Turner99/stack.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf inf inf inf -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf inf inf -2.20 inf +inf inf inf inf inf inf inf inf inf inf inf inf inf -2.10 inf -0.60 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 inf -1.40 inf +inf inf inf inf inf inf inf inf inf inf inf -2.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf -3.30 inf inf inf inf inf +inf inf inf inf inf inf inf inf inf -2.40 inf -1.40 inf inf inf inf +inf inf inf inf inf inf inf inf -2.10 inf -2.10 inf inf inf inf inf +inf inf inf inf inf inf inf -2.40 inf inf inf inf inf inf inf -1.30 +inf inf inf inf inf inf -3.40 inf inf inf inf inf inf inf -2.50 inf +inf inf inf inf inf -3.30 inf -1.50 inf inf inf inf inf -2.10 inf -0.50 +inf inf inf inf -2.20 inf -2.50 inf inf inf inf inf -1.40 inf 1.30 inf +inf inf inf -1.30 inf inf inf inf inf inf inf -1.00 inf inf inf inf +inf inf -2.40 inf inf inf inf inf inf inf -1.50 inf inf inf inf inf +inf -2.10 inf -1.00 inf inf inf inf inf -1.40 inf 0.30 inf inf inf inf +-0.90 inf -1.30 inf inf inf inf inf -0.60 inf -0.50 inf inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tloop.DAT b/gtfold-mfe/data/Turner99/tloop.DAT new file mode 100644 index 0000000..dda2750 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tloop.DAT @@ -0,0 +1,30 @@ +GGGGAC -3.00 +GGUGAC -3.00 +CGAAAG -3.00 +GGAGAC -3.00 +CGCAAG -3.00 +GGAAAC -3.00 +CGGAAG -3.00 +CUUCGG -3.00 +CGUGAG -3.00 +CGAAGG -2.50 +CUACGG -2.50 +GGCAAC -2.50 +CGCGAG -2.50 +UGAGAG -2.50 +CGAGAG -2.00 +AGAAAU -2.00 +CGUAAG -2.00 +CUAACG -2.00 +UGAAAG -2.00 +GGAAGC -1.50 +GGGAAC -1.50 +UGAAAA -1.50 +AGCAAU -1.50 +AGUAAU -1.50 +CGGGAG -1.50 +AGUGAU -1.50 +GGCGAC -1.50 +GGGAGC -1.50 +GUGAAC -1.50 +UGGAAA -1.50 diff --git a/gtfold-mfe/data/Turner99/tstackh.DAT b/gtfold-mfe/data/Turner99/tstackh.DAT new file mode 100644 index 0000000..7648650 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstackh.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.50 -0.30 -0.30 +inf inf inf inf inf inf inf inf inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -1.20 -0.20 0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.30 -0.60 -1.10 +inf inf inf inf inf inf inf inf -1.50 -1.50 -1.40 -1.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -0.90 -2.90 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -2.20 -2.00 -1.60 -1.10 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -1.40 -1.80 -2.00 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -2.10 inf inf inf inf 0.20 -0.50 -0.30 -0.30 +inf inf inf inf -1.10 -0.70 -2.40 -0.50 inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf -2.40 -2.90 -1.40 -1.20 inf inf inf inf -0.90 -1.10 -0.30 0.00 +inf inf inf inf -1.90 -1.00 -2.20 -1.50 inf inf inf inf -0.30 -0.30 -0.40 -1.10 +-0.50 -0.30 -0.60 -0.50 inf inf inf inf -0.50 -0.30 -0.60 -0.50 inf inf inf inf +-0.20 -0.10 -1.20 -0.00 inf inf inf inf -0.20 -0.10 -1.70 0.00 inf inf inf inf +-1.40 -1.20 -0.70 -0.20 inf inf inf inf -0.80 -1.20 -0.30 -0.70 inf inf inf inf +-0.30 -0.10 -0.50 -0.80 inf inf inf inf -0.60 -0.10 -0.60 -0.80 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tstacki.DAT b/gtfold-mfe/data/Turner99/tstacki.DAT new file mode 100644 index 0000000..dd7b5da --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstacki.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.00 +inf inf inf inf inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf +inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf 0.70 0.70 0.70 0.00 +0.70 0.70 -0.40 0.70 inf inf inf inf 0.70 0.70 -0.40 0.70 inf inf inf inf +0.70 0.70 0.70 0.70 inf inf inf inf 0.70 0.70 0.70 0.70 inf inf inf inf +-0.40 0.70 0.70 0.70 inf inf inf inf -0.40 0.70 0.70 0.70 inf inf inf inf +0.70 0.70 0.70 0.00 inf inf inf inf 0.70 0.70 0.70 0.00 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/tstackm.DAT b/gtfold-mfe/data/Turner99/tstackm.DAT new file mode 100644 index 0000000..b850f80 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf -1.00 inf inf inf -1.00 inf inf inf -2.20 -0.80 -1.00 -0.80 -0.90 +inf inf -1.50 inf inf inf -1.50 inf inf inf -2.70 inf -0.60 -0.70 -2.20 -0.70 +inf -1.50 inf -1.00 inf -1.50 inf -1.00 inf -2.70 inf -2.20 -0.80 -2.10 -0.80 -0.80 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -2.20 inf -2.70 inf -1.10 -0.80 -1.10 -0.80 +inf inf inf -1.00 inf inf inf -1.00 -1.70 -1.70 -1.70 -1.70 inf inf inf -1.00 +inf inf -1.50 inf inf inf -1.50 inf -1.00 -1.10 -3.30 -0.80 inf inf -1.50 inf +inf -1.50 inf -1.00 inf -1.50 inf -1.00 -1.70 -2.40 -1.70 -1.70 inf -1.50 inf -1.00 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -1.60 -1.40 -1.60 -1.20 -1.00 inf -1.50 inf +inf inf inf -2.20 -1.10 -1.50 -1.30 -1.90 inf inf inf -1.00 -0.80 -1.00 -0.80 -1.30 +inf inf -2.70 inf -1.10 -0.70 -3.40 -0.50 inf inf -1.50 inf -0.60 -0.70 -2.50 -0.70 +inf -2.70 inf -2.20 -1.60 -3.30 -1.40 -1.30 inf -1.50 inf -1.00 -0.80 -2.10 -0.80 -0.80 +-2.20 inf -2.70 inf -1.70 -1.00 -2.00 -0.70 -1.00 inf -1.50 inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf -1.00 -1.00 -0.80 -1.10 -1.00 inf inf inf -2.00 +-0.70 -0.60 -2.40 -0.50 inf inf -1.50 inf -0.70 -0.60 -1.50 -0.50 inf inf -2.50 inf +-1.10 -2.10 -1.20 -1.00 inf -1.50 inf -1.00 -0.70 -1.40 -0.80 0.30 inf -2.50 inf -2.00 +-0.90 -0.60 -1.40 -0.50 -1.00 inf -1.50 inf -0.50 -0.60 -0.50 -0.50 -2.00 inf -2.50 inf diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index 20a0708..f8fdc78 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -27,16 +27,16 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic); -int initStackValues(std::string fileName); -int initMiscloopValues(std::string fileName); -int initDangleValues(std::string fileName); -int initLoopValues(std::string fileName); -int initTstkhValues(std::string fileName); -int initTstkiValues(std::string fileName); -int initTloopValues(std::string fileName); -int initInt21Values(std::string fileName); -int initInt22Values(std::string fileName); -int initInt11Values(std::string fileName); +int initStackValues(const std::string& fileName, const std::string& dirPath); +int initMiscloopValues(const std::string& fileName, const std::string& dirPath); +int initDangleValues(const std::string& fileName, const std::string& dirPath); +int initLoopValues(const std::string& fileName, const std::string& dirPath); +int initTstkhValues(const std::string& fileName, const std::string& dirPath); +int initTstkiValues(const std::string& fileName, const std::string& dirPath); +int initTloopValues(const std::string& fileName, const std::string& dirPath); +int initInt21Values(const std::string& fileName, const std::string& dirPath); +int initInt22Values(const std::string& fileName, const std::string& dirPath); +int initInt11Values(const std::string& fileName, const std::string& dirPath); extern std::string EN_DATADIR; diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 1bfbb5a..79cb62b 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -10,18 +10,29 @@ using namespace std; extern bool ILSA; extern bool NOISOLATE; +<<<<<<< .merge_file_N36WcI extern bool USERDATA; extern bool PARAMS; +======= +//extern bool USERDATA; +//extern bool PARAMS; +extern bool LIMIT_DISTANCE; +>>>>>>> .merge_file_qTispI extern bool BPP_ENABLED; extern bool SUBOPT_ENABLED; extern bool CONS_ENABLED; extern bool VERBOSE; +<<<<<<< .merge_file_N36WcI extern bool SHAPE_ENABLED; +======= +extern bool PARAM_DIR; +>>>>>>> .merge_file_qTispI extern string seqfile; extern string constraintsFile; extern string shapeFile; extern string outputFile; +extern string paramDir; extern int suboptDelta; extern int nThreads; diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py new file mode 100755 index 0000000..e488b84 --- /dev/null +++ b/gtfold-mfe/scripts/dats2DATs.py @@ -0,0 +1,53 @@ +import os, sys, re + +# read in arguments from command line +if len(sys.argv) != 3: + print "need directory names" + print "Usage: dats2DATs.py " +source_dir_name = sys.argv[1] +target_dir_name = sys.argv[2] + +# this function opens a .dat formatted file and returns a string with .DAT file format +def dat2DAT(file_name, num_cols, num_rows): + num_data_rows_seen = 0 + DAT_content = "" + file = open(file_name,'r') + + for line in file.readlines() : + if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line + + return DAT_content + +for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]: + file_name = source_dir_name+"/"+file_prefix+".dat" + output_file_path = target_dir_name+"/"+file_prefix+".DAT" + output_file = open(output_file_path, 'w') + output_file.write(dat2DAT(file_name, 16, 16)) + #print dat2DAT(file_name, 16, 16) + +file_name = source_dir_name+"/tloop.dat" +output_file_path = target_dir_name+"/tloop.DAT" +DAT_content = "" +file = open(file_name,'r') + +for line in file.readlines() : + if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space or ACGU + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line +output_file = open(output_file_path, 'w') +output_file.write(DAT_content) + diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 59a1824..65ac5f0 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -45,12 +45,22 @@ int calculate(int len, int nThreads) { #endif for (i = 1; i <= len - b; i++) { j = i + b; +<<<<<<< .merge_file_vD135I int flag = 0, newWM = INFINITY_; if (canPair(RNA[i], RNA[j])) { flag = 1; int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack if (j-i > 6) { // Internal Loop BEGIN +======= + int newWM = INFINITY_; + + if (canPair(RNA[i], RNA[j])) { + int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin + int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack + + if (j-i > 6) { // Internal Loop BEGIN +>>>>>>> .merge_file_o95D9I int p=0, q=0; int VBIij = INFINITY_; for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { @@ -72,10 +82,17 @@ int calculate(int len, int nThreads) { int VMij, VMijd, VMidj, VMidjd; VMij = VMijd = VMidj = VMidjd = INFINITY_; for (h = i+TURN+1; h <= j-1-TURN; h++) { +<<<<<<< .merge_file_vD135I VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); +======= + VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); + VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); + VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); + VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); +>>>>>>> .merge_file_o95D9I } int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; @@ -91,10 +108,16 @@ int calculate(int len, int nThreads) { if (j-i > 4) { // WM BEGIN int h; for (h = i+TURN+1 ; h <= j-TURN-1; h++) { +<<<<<<< .merge_file_vD135I //ZS: This sum corresponds to when i,j are NOT paired with each other. //So we need to make sure only terms where i,j aren't pairing are considered. newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; } +======= + newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); + } + +>>>>>>> .merge_file_o95D9I newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index a2f1042..c8d9055 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -44,7 +44,12 @@ bool compare_bp(const std::pair& o1, static int load_constraints(const char* constr_file, int verbose=0) { +<<<<<<< .merge_file_FGxfkH +======= + fprintf(stdout, "- Running with constraints %s\n", constr_file); + std::ifstream cfcons; +>>>>>>> .merge_file_mYvNsH fprintf(stdout, "- Running with constraints\n"); @@ -106,12 +111,13 @@ static int load_constraints(const char* constr_file, int verbose=0) { pit++; } } - + /* std::vector > v_fbp; for(it=0; it< nFBP; it++) { for(int k=1;k<= FBP[it][2];k++) v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); } +<<<<<<< .merge_file_FGxfkH if(v_fbp.size()>1){ std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); @@ -126,6 +132,21 @@ static int load_constraints(const char* constr_file, int verbose=0) { } +======= + + if (v_fbp.size() > 1) { + std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); + for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { + if (v_fbp[ii].second <= v_fbp[ii+1].second) { + fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); + exit(-1); + } + + } + } +*/ + +>>>>>>> .merge_file_mYvNsH return 0; } @@ -170,6 +191,7 @@ int init_constraints(const char* constr_file,int length) { } } } +<<<<<<< .merge_file_FGxfkH //ZS: set prohibited basepairs @@ -188,6 +210,13 @@ int init_constraints(const char* constr_file,int length) { if(PBP[it][2] < 1 || PBP[it][1] == 0){ printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; +======= + if (nFBP != 0) { + for (it = 0; it < nFBP; it++) { + if (FBP[it][2] < 1) { + printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]); + continue; // TODO: report and exit here +>>>>>>> .merge_file_mYvNsH } for(k = 1; k <= PBP[it][2]; k++){ @@ -222,6 +251,7 @@ int init_constraints(const char* constr_file,int length) { for(k = 1; k<=FBP[it][2]; k++){ int i1 = FBP[it][0]+k-1; int j1 = FBP[it][1]-k+1; +<<<<<<< .merge_file_FGxfkH if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){ printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); continue; @@ -274,6 +304,18 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1; } +======= + if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) { + printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1); + continue; // TODO: report and exit here + } + if (j1-i1 < TURN) { + printf("Can't constrain (%d,%d)\n", i1, j1); + continue; // TODO: report and exit here + } + BP[FBP[it][0]+k-1] = FBP[it][1]+1-k; + BP[FBP[it][1]+1-k] = FBP[it][0]+k-1; +>>>>>>> .merge_file_mYvNsH } } } @@ -406,10 +448,23 @@ void print_constraints(int len) { } +<<<<<<< .merge_file_FGxfkH int forcePair(int i, int j) { //ZS: this function returns true if the pair i-j is forced. if (CONS_ENABLED) return BP(i,j)==1; +======= + + +int is_ss(int i, int j) { + if (CONS_ENABLED) { + int it; + for (it = i + 1; it < j; it++) { + if (BP[it] > 0) return 1; + } + return 0; + } +>>>>>>> .merge_file_mYvNsH else return 0; } diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 6d0f375..1118794 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -17,8 +17,9 @@ int *VM; int **WM; int *indx; -void create_tables(int len) -{ +int alloc_flag = 0; + +void create_tables(int len) { V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); if (V == NULL) { perror("Cannot allocate variable 'V'"); @@ -75,12 +76,13 @@ void create_tables(int len) exit(-1); } + alloc_flag = 1; + init_tables(len); } -void init_tables(int len) -{ +void init_tables(int len) { int i, j, LLL; for (i = 0; i <= len; i++) { @@ -106,21 +108,21 @@ void init_tables(int len) return; } -void free_tables(int len) -{ - free(indx); - - int i; - for (i = 0; i <= len; i++) - free(WM[i]); - free(WM); - - free(VM); - free(VBI); - free(V); - free(VV); - free(VV1); - free(W); +void free_tables(int len) { + if (alloc_flag == 1) { + free(indx); + + int i; + for (i = 0; i <= len; i++) free(WM[i]); + free(WM); + + free(VM); + free(VBI); + free(V); + free(VV); + free(VV1); + free(W); + } } @@ -217,8 +219,7 @@ inline int eL(int i, int j, int ip, int jp) { return energy; } -inline int eH(int i, int j) -{ +inline int eH(int i, int j) { /* Hairpin loop for all the bases between i and j */ /* size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */ int size; @@ -323,8 +324,7 @@ inline int eH(int i, int j) return energy; } -inline int eS(int i, int j) -{ +inline int eS(int i, int j) { int energy; /* not sure about eparam[1], come from MFold.. = 0 */ energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1] diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index f916f3c..c68ee22 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -20,6 +20,7 @@ #include #include #include +#include #include #include @@ -75,198 +76,102 @@ int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loo float prelog; void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { - -#ifndef GENBIN - if (!userdatalogic) - { + if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; EN_DATADIR += userdatadir; - } else - { + } else { EN_DATADIR.assign(userdatadir); } -#else - EN_DATADIR = "data"; -#endif //Handle the ending forward slash case if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { EN_DATADIR += "/"; } - initMiscloopValues("miscloop.dat"); - // miscloop.dat - Miscellaneous loop file - initStackValues("stack.dat"); - // stack.dat - free energies for base pair stacking - initDangleValues("dangle.dat"); - // dangle.dat - single base stacking free energies - initLoopValues("loop.dat"); - // loop.dat - entropic component for internal, bulge and hairpin loops. - initTstkhValues("tstackh.dat"); - // tstackh.dat - free energies for terminal mismatch stacking in hairpin loops - initTstkiValues("tstacki.dat"); - // tstacki.dat - free energies for terminal mismatch stacking in internal loops - initTloopValues("tloop.dat"); - // tloop.dat - free energies for distinguished tetraloops - initInt21Values("int21.dat"); - // int21.dat - free energies for 2 x 1 interior loops - initInt22Values("int22.dat"); - // int22.dat - free energies for 2 x 2 interior loops - initInt11Values("int11.dat"); - // int11.dat - free energies for 1 x 1 interior loops + initMiscloopValues("miscloop.DAT", EN_DATADIR); + initDangleValues("dangle.DAT", EN_DATADIR); + initStackValues("stack.DAT", EN_DATADIR); + initLoopValues("loop.DAT", EN_DATADIR); + initTstkhValues("tstackh.DAT", EN_DATADIR); + initTstkiValues("tstacki.DAT", EN_DATADIR); + initTloopValues("tloop.DAT", EN_DATADIR); + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); } +int initStackValues(const string& fileName, const string& dirPath) { + std::string filePath; + std::ifstream cf; - int initStackValues(string fileName) { - - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - // Initialize the array with INFINITY - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { stack[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // Read the thermodynamic parameters. - // The 24 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - stack[fourBaseIndex(ii,jj,kk,ll)] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + stack[fourBaseIndex(i,j,k,l)] = (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - /* jj = 1; */ - kk = (i % 4); - + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initMiscloopValues(string fileName) { - /* - miscloop.dat - Miscellaneous loop file. Contains : - 1. Extrapolation for large loops based on polymer theory - 2. Asymmetric internal loop correction parameters. - 3. the f(m) array (see Ninio for details) - 4. Paremeters for multibranch loops - 5. Paremeters for multibranch loops (for efn2 only) - 6. Terminal AU or GU penalty - 7. Bonus for GGG hairpin - 8,9,10. C hairpin rules: a) slope b) intercept c) value for size 3 - 11. Intermolecular initiation free energy - 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off) - */ +int initMiscloopValues(const string& fileName, const string& dirpath) { + std::string filePath; + std::ifstream cf; - char currentWord[256]; - string s; - ifstream cf; //cf = current file + filePath = dirpath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; -#if 0 - cout << "Getting miscloop values from " << fileName << endl; -#endif - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); } - s = ""; - cf >> currentWord; + char currentWord[256]; + std::string s; + for (int index = 1; index < 13; index++) { // There are total 12 values to read in. - while (strcmp(currentWord, "-->")) { - cf >> currentWord; - } if (index == 1) { cf >> currentWord; prelog = 100 * atof(currentWord); - //cout << "prelog = " << prelog << endl; } if (index == 2) { cf >> currentWord; maxpen = int(atof(currentWord) * 100.0 + .5); - //cout << "maxpen = " << maxpen << endl; } if (index == 3) { for (int count = 1; count <= 4; count++) { @@ -292,7 +197,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { s = currentWord; multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5); eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "\n multi " << multConst[count-1]; } } if (index == 5) { @@ -336,150 +240,86 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } } - cf.close(); + cf.close(); + return 0; } - int initDangleValues(string fileName) { - ifstream cf; //cf = current file - char currentLine[256]; - string currentString; - string s; - int index; - int i, j, k, l; - int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low - - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 2; l++) { +int initDangleValues(const std::string& fileName, + const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { dangle[i][j][k][l] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 8 first lines are junk - for (index = 1; index <= 8; index++) { - cf.getline(currentLine, 256); - } - - // 8 lines of useful data - i = 0; - ii = 0; - jj = 0; - kk = 0; - ll = 0; - - while (i < 8) { - - if (i != 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - kk++; - if (kk == 4) - kk = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - //if ( temp == 0 ) temp = -1; - dangle[ii][jj][kk][ll] = temp; - //cout<< "\n " << temp << " "<< ii <<" "<< jj << " "<< kk << " " << ll ; - r++; - z++; - if (r % 4 == 0) - jj++; - kk++; - if (kk == 4) - kk = 0; - + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count%4; + l = count/4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + + j = cols/4; + ss >> val; + k = cols%4; + if (!(val == "inf")) { + dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5); } - - } - - i++; - ii++; - if (ii == 4) - ii = 0; - - if (i == 4) - ll = 1; - + } + ++count; } - cf.close(); - -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initLoopValues(string fileName) { +int initLoopValues( const string& fileName, const string& dirPath) { // algorithm.c, line 2996 ifstream cf; // current file - char currentLine[256]; + std::string filePath; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + //char currentLine[256]; char currentWord[256]; string s; - int index; + int index= 0; int tempValue = 0; -#if 0 - cout << "Getting loop values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // The 4 first lines are junk we don't need - for (index = 1; index <= 4; index++) { - cf.getline(currentLine, 256); - //s = currentLine; - //cout << s << endl; - } + while (index < 30) { for (int j = 1; j <= 4; j++) { cf >> currentWord; if (j == 1) index = atoi(currentWord); if (j > 1) { - if (strcmp(currentWord, ".")) { + if (strcmp(currentWord, "inf")) { tempValue = (int) (100 * atof(currentWord) + 0.5); } else { tempValue = INFINITY_; @@ -500,228 +340,111 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initTstkhValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; +int initTstkhValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp; - - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - jj = 0; - kk = (i % 4); - + } + ++count; } - - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initTstkiValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { +int initTstkiValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { + int count = 0; - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; + while (cf.good()) { + int i, j, k, l; - int z = 0; - int r = 0; + std::string line; + std::stringstream ss; - while (s[z] != '\0') { + getline(cf, line); + ss << line; + if (line.empty()) continue; - if (s[z] == ' ') - z++; + i = count/4; + k = count%4; - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstki[fourBaseIndex(ii,jj,kk,ll)] = temp; - - //cout << "\n temp " << temp << " " <> s; + int k = 0; + int z = 0; while (s[z] != '\0') { - if (s[z] == 'A') base[k++] = BASE_A; else if (s[z] == 'C') @@ -871,22 +540,15 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base[k++] = BASE_G; else if (s[z] == 'U') base[k++] = BASE_U; - z++; } - cf.getline(currentLine, 256); - - //key iloop22[a][b][c][d][j][l][k][m] = - //a j l b - //c k m d - - for (int rowIndex = 1; rowIndex <= 16; rowIndex++) { + cf.getline(currentLine, 256); + std::stringstream ss; + ss << currentLine; for (int colIndex = 1; colIndex <= 16; colIndex++) { - cf >> currentValue; - // rowIndex = j*4+k - // colIndex = l*4+m + ss >> currentValue; j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4; k = (rowIndex - 1) % 4; @@ -894,23 +556,17 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { l = ((colIndex - 1) - (colIndex - 1) % 4) / 4; m = (colIndex - 1) % 4; - iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] - = (int) floor(100.0 * atof(currentValue) + 0.5); - //int temp = (int) floor(100.0*atof(currentValue)+0.5); - //printf("\n temp is : %d %d %d %d %d %d %d %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m ); + iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] + = (int) floor(100.0 * atof(currentValue) + 0.5); } } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initInt21Values(string fileName) { - +int initInt21Values(const std::string& fileName, const std::string& dirPath) { // 24x6 arrays of 4x4 values // c // a f @@ -921,7 +577,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { char currentLine[256]; string sre; string s, s1, s2; - int a, b, c, d, e, f, g, index; + int a, b, c, d, e, f, g; int i, j, k, r, q, t, y; int z; @@ -958,87 +614,44 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base1[6] = BASE_U + 1; base2[6] = BASE_G + 1; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // Get rid of the 18 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - i = 1; - while (i <= 6) { - j = 1; - while (j <= 4) { - k = 1; - - for (index = 1; index <= 10; index++) - cf.getline(currentLine, 256); - - s = currentLine; - while (k <= 4) { - cf.getline(currentLine, 256); - - s = currentLine; - r = 0; - z = 0; int jj = 1; d = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - d++; - if (d == 5) - d = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[i]; - b = base2[i]; - f = base1[jj]; - g = base2[jj]; - c = k; - e = j; - - iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] - = temp; - //printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g); - r++; - z++; - if (r % 4 == 0) - jj++; - d++; - if (d == 5) - d = 1; - } + + std::stringstream ss; + ss << currentLine; + + for (z = 1; z <=24 ; z++) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[i]; + b = base2[i]; + f = base1[jj]; + g = base2[jj]; + c = k; + e = j; + + iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] + = temp; + r++; + if (r % 4 == 0) jj++; + d++; + if (d == 5) d = 1; } k++; } @@ -1050,13 +663,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { return 0; } - int initInt11Values(string fileName) { - - //Read the 1x1 internal loops - //key iloop11[a][b][c][d][j][l][k][m] = - //a b c - //d e f - +int initInt11Values(const std::string& fileName, const std::string& dirPath) { int i, j, k, r, q, t; for (i = 0; i < 4; i++) @@ -1068,37 +675,20 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { iloop11[i][j][k][r][q][t] = INFINITY_; ifstream cf; - int index; char currentLine[256]; string s; int base1[7]; int base2[7]; - //int j, k, l, m; int a, b, c, d, f; -#if 0 - cout << "Getting Int11 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { cerr << "File open failed" << endl; exit(-1); } - // Get rid of the 19 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - - /* - Structure of the file: - array of 6x6 arrays - Order: - AU CG GC UA GU UG - */ - base1[1] = BASE_A + 1; base2[1] = BASE_U + 1; base1[2] = BASE_C + 1; @@ -1117,75 +707,38 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { while (k < 6) { k++; - index = 0; - for (index = 1; index <= 10; index++) { - cf.getline(currentLine, 256); - } - i = 0; b = 1; while (i < 4) { - int jj = 1; ++i; cf.getline(currentLine, 256); - s = currentLine; - j = 0; int r = 0; - int z = 0; int e = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - e++; - if (e == 5) - e = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; + std::stringstream ss; + ss << currentLine; - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[k]; - d = base2[k]; - c = base1[jj]; - f = base2[jj]; - iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - e++; - if (e == 5) - e = 1; - } + for (int z=1; z <= 24; ++z) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[k]; + d = base2[k]; + c = base1[jj]; + f = base2[jj]; + iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; + r++; + if (r % 4 == 0) jj++; + e++; + if (e == 5) e = 1; } b++; } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - - diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 9294cbf..2c56804 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -94,16 +94,14 @@ int read_sequence_file(const char* filename, std::string& seq) { ifstream fs; fs.open(filename, ios::in); - if (fs == NULL) - return FAILURE; + if (!fs.good()) return FAILURE; string line; - getline(fs, line); - while(line.length() > 0) { + while(fs.good()) { + getline(fs, line); // exclude lines starting with FASTA comment characters - if(line[0] != ';' && line[0] != '>') + if(line[0] != ';' && line[0] != '>' && line.length() > 0) seq += line; - getline(fs, line); } fs.close(); @@ -188,7 +186,7 @@ int main(int argc, char** argv) { std::string seq; int energy; double t1; - + print_header(); parse_options(argc, argv); @@ -199,7 +197,7 @@ int main(int argc, char** argv) { } // Read in thermodynamic parameters. Always use Turner99 data (for now) - readThermodynamicParameters("Turner99",false); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR); printRunConfiguration(seq); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 9ded8dd..565ca5d 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -5,8 +5,9 @@ using namespace std; bool ILSA; bool NOISOLATE; -bool USERDATA; -bool PARAMS; +//bool USERDATA; +//bool PARAMS; +bool PARAM_DIR = false; bool LIMIT_DISTANCE; bool BPP_ENABLED; bool SUBOPT_ENABLED; @@ -16,8 +17,13 @@ bool SHAPE_ENABLED = false; string seqfile = ""; string constraintsFile = ""; +<<<<<<< .merge_file_vAQXEJ string outputFile = ""; string shapeFile = ""; +======= +string outputFile = ""; +string paramDir = "Turner99"; // default value +>>>>>>> .merge_file_058DyL int suboptDelta = -1; int nThreads = -1; @@ -37,7 +43,8 @@ void help() { printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); + printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); + printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); printf(" -t, --threads num Limit number of threads used\n"); @@ -89,7 +96,15 @@ void parse_options(int argc, char** argv) { outputFile = argv[++i]; else help(); - } else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { if(i < argc) nThreads = atoi(argv[++i]); else @@ -189,7 +204,6 @@ void printRunConfiguration(string seq) { printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); printf("- input file: %s\n", seqfile.c_str()); - printf(" - sequence length: %d\n", (int)seq.length()); - printf(" - sequence contents: %s\n", seq.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); printf("- output file: %s\n", outputFile.c_str()); } From da4c291ef2289d3ac6aa134b2af16c1e5f985b1a Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Wed, 25 May 2011 15:49:53 +0200 Subject: [PATCH 038/187] Fixed merge errors, should compile now --- gtfold-mfe/include/options.h | 8 ----- gtfold-mfe/src/.deps/loader.Po | 7 +++- gtfold-mfe/src/algorithms.c | 24 +------------- gtfold-mfe/src/constraints.cc | 58 ++-------------------------------- gtfold-mfe/src/options.cc | 5 +-- gtfold-mfe/src/traceback.c | 2 +- 6 files changed, 11 insertions(+), 93 deletions(-) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 79cb62b..ec0ff7f 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -10,23 +10,15 @@ using namespace std; extern bool ILSA; extern bool NOISOLATE; -<<<<<<< .merge_file_N36WcI -extern bool USERDATA; -extern bool PARAMS; -======= //extern bool USERDATA; //extern bool PARAMS; extern bool LIMIT_DISTANCE; ->>>>>>> .merge_file_qTispI extern bool BPP_ENABLED; extern bool SUBOPT_ENABLED; extern bool CONS_ENABLED; extern bool VERBOSE; -<<<<<<< .merge_file_N36WcI extern bool SHAPE_ENABLED; -======= extern bool PARAM_DIR; ->>>>>>> .merge_file_qTispI extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po index 290868e..a00ed8b 100644 --- a/gtfold-mfe/src/.deps/loader.Po +++ b/gtfold-mfe/src/.deps/loader.Po @@ -74,7 +74,8 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/math.h \ + /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/sstream \ + /usr/include/c++/4.4/bits/sstream.tcc /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ @@ -310,6 +311,10 @@ loader.o: loader.cc /usr/include/c++/4.4/iostream \ /usr/include/c++/4.4/bits/fstream.tcc: +/usr/include/c++/4.4/sstream: + +/usr/include/c++/4.4/bits/sstream.tcc: + /usr/include/math.h: /usr/include/bits/huge_val.h: diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 65ac5f0..1950fc0 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -45,22 +45,12 @@ int calculate(int len, int nThreads) { #endif for (i = 1; i <= len - b; i++) { j = i + b; -<<<<<<< .merge_file_vD135I int flag = 0, newWM = INFINITY_; if (canPair(RNA[i], RNA[j])) { flag = 1; int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack if (j-i > 6) { // Internal Loop BEGIN -======= - int newWM = INFINITY_; - - if (canPair(RNA[i], RNA[j])) { - int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin - int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack - - if (j-i > 6) { // Internal Loop BEGIN ->>>>>>> .merge_file_o95D9I int p=0, q=0; int VBIij = INFINITY_; for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { @@ -82,17 +72,10 @@ int calculate(int len, int nThreads) { int VMij, VMijd, VMidj, VMidjd; VMij = VMijd = VMidj = VMidjd = INFINITY_; for (h = i+TURN+1; h <= j-1-TURN; h++) { -<<<<<<< .merge_file_vD135I VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); -======= - VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); - VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); - VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); - VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); ->>>>>>> .merge_file_o95D9I } int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; @@ -108,16 +91,10 @@ int calculate(int len, int nThreads) { if (j-i > 4) { // WM BEGIN int h; for (h = i+TURN+1 ; h <= j-TURN-1; h++) { -<<<<<<< .merge_file_vD135I //ZS: This sum corresponds to when i,j are NOT paired with each other. //So we need to make sure only terms where i,j aren't pairing are considered. newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; } -======= - newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); - } - ->>>>>>> .merge_file_o95D9I newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle @@ -144,3 +121,4 @@ int calculate(int len, int nThreads) { } return W[len]; } + diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index c8d9055..add3113 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -44,12 +44,7 @@ bool compare_bp(const std::pair& o1, static int load_constraints(const char* constr_file, int verbose=0) { -<<<<<<< .merge_file_FGxfkH -======= - fprintf(stdout, "- Running with constraints %s\n", constr_file); - std::ifstream cfcons; ->>>>>>> .merge_file_mYvNsH fprintf(stdout, "- Running with constraints\n"); @@ -111,13 +106,12 @@ static int load_constraints(const char* constr_file, int verbose=0) { pit++; } } - /* + std::vector > v_fbp; for(it=0; it< nFBP; it++) { for(int k=1;k<= FBP[it][2];k++) v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); } -<<<<<<< .merge_file_FGxfkH if(v_fbp.size()>1){ std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); @@ -132,21 +126,6 @@ static int load_constraints(const char* constr_file, int verbose=0) { } -======= - - if (v_fbp.size() > 1) { - std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); - for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second <= v_fbp[ii+1].second) { - fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(-1); - } - - } - } -*/ - ->>>>>>> .merge_file_mYvNsH return 0; } @@ -191,7 +170,6 @@ int init_constraints(const char* constr_file,int length) { } } } -<<<<<<< .merge_file_FGxfkH //ZS: set prohibited basepairs @@ -210,13 +188,6 @@ int init_constraints(const char* constr_file,int length) { if(PBP[it][2] < 1 || PBP[it][1] == 0){ printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; -======= - if (nFBP != 0) { - for (it = 0; it < nFBP; it++) { - if (FBP[it][2] < 1) { - printf("Invalid entry (%d %d %d)\n", FBP[it][0], FBP[it][1], FBP[it][2]); - continue; // TODO: report and exit here ->>>>>>> .merge_file_mYvNsH } for(k = 1; k <= PBP[it][2]; k++){ @@ -251,7 +222,6 @@ int init_constraints(const char* constr_file,int length) { for(k = 1; k<=FBP[it][2]; k++){ int i1 = FBP[it][0]+k-1; int j1 = FBP[it][1]-k+1; -<<<<<<< .merge_file_FGxfkH if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){ printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); continue; @@ -304,18 +274,6 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1; } -======= - if (!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])) { - printf("Can't constrain (%d,%d)\n", FBP[it][0]+k-1, FBP[it][1]-k+1); - continue; // TODO: report and exit here - } - if (j1-i1 < TURN) { - printf("Can't constrain (%d,%d)\n", i1, j1); - continue; // TODO: report and exit here - } - BP[FBP[it][0]+k-1] = FBP[it][1]+1-k; - BP[FBP[it][1]+1-k] = FBP[it][0]+k-1; ->>>>>>> .merge_file_mYvNsH } } } @@ -448,23 +406,10 @@ void print_constraints(int len) { } -<<<<<<< .merge_file_FGxfkH int forcePair(int i, int j) { //ZS: this function returns true if the pair i-j is forced. if (CONS_ENABLED) return BP(i,j)==1; -======= - - -int is_ss(int i, int j) { - if (CONS_ENABLED) { - int it; - for (it = i + 1; it < j; it++) { - if (BP[it] > 0) return 1; - } - return 0; - } ->>>>>>> .merge_file_mYvNsH else return 0; } @@ -552,3 +497,4 @@ int withinCD(int i, int j){ } else return 1; } + diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 565ca5d..76cbe44 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -17,13 +17,10 @@ bool SHAPE_ENABLED = false; string seqfile = ""; string constraintsFile = ""; -<<<<<<< .merge_file_vAQXEJ string outputFile = ""; string shapeFile = ""; -======= -string outputFile = ""; string paramDir = "Turner99"; // default value ->>>>>>> .merge_file_058DyL + int suboptDelta = -1; int nThreads = -1; diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 60ce3da..445c851 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -54,7 +54,7 @@ void trace(int len, int vbose) { } void traceW(int j) { - int done, i, Wj,Wj_temp; + int done, i, Wj; int wim1, flag, Widjd, Wijd, Widj, Wij; Wj = INFINITY_; flag = 1; From a5ebd1672b168bcdfb047186c310f1f1b0e38ed9 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Wed, 25 May 2011 16:48:05 +0200 Subject: [PATCH 039/187] replaced data Makefiles with Prashant's version --- gtfold-mfe/Makefile | 2 +- gtfold-mfe/src/Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile index 75480ce..8bba63d 100644 --- a/gtfold-mfe/Makefile +++ b/gtfold-mfe/Makefile @@ -214,7 +214,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /usr/local +prefix = /home/zs/gtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile index 0f50f74..c79eea5 100644 --- a/gtfold-mfe/src/Makefile +++ b/gtfold-mfe/src/Makefile @@ -162,7 +162,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /usr/local +prefix = /home/zs/gtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin From b4b005510bf27baba412743718d80077793da46c Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Wed, 25 May 2011 16:51:01 +0200 Subject: [PATCH 040/187] trying to commit data Makefiles again --- gtfold-mfe/test.txt | 1 - 1 file changed, 1 deletion(-) delete mode 100644 gtfold-mfe/test.txt diff --git a/gtfold-mfe/test.txt b/gtfold-mfe/test.txt deleted file mode 100644 index 229c9b9..0000000 --- a/gtfold-mfe/test.txt +++ /dev/null @@ -1 +0,0 @@ -this is to test how my Git setup works - Zs \ No newline at end of file From ecf119af1c35f4f5b7e2718744e30955e26c5625 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Wed, 25 May 2011 16:53:21 +0200 Subject: [PATCH 041/187] ...and once more..? --- gtfold-mfe/data/Andronescu/Makefile | 399 +++++++++++++++++++++ gtfold-mfe/data/Makefile | 536 ++++++++++++++++++++++++++++ gtfold-mfe/data/Turner04/Makefile | 405 +++++++++++++++++++++ gtfold-mfe/data/Turner99/Makefile | 420 ++++++++++++++++++++++ gtfold-mfe/include/Makefile | 388 ++++++++++++++++++++ 5 files changed, 2148 insertions(+) create mode 100644 gtfold-mfe/data/Andronescu/Makefile create mode 100644 gtfold-mfe/data/Makefile create mode 100644 gtfold-mfe/data/Turner04/Makefile create mode 100644 gtfold-mfe/data/Turner99/Makefile create mode 100644 gtfold-mfe/include/Makefile diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile new file mode 100644 index 0000000..ece5bb2 --- /dev/null +++ b/gtfold-mfe/data/Andronescu/Makefile @@ -0,0 +1,399 @@ +# Makefile.in generated by automake 1.11.1 from Makefile.am. +# data/Andronescu/Makefile. Generated from Makefile.in by configure. + +# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, +# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, +# Inc. +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + + + + +pkgdatadir = $(datadir)/gtfold +pkgincludedir = $(includedir)/gtfold +pkglibdir = $(libdir)/gtfold +pkglibexecdir = $(libexecdir)/gtfold +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +build_triplet = x86_64-unknown-linux-gnu +host_triplet = x86_64-unknown-linux-gnu +target_triplet = x86_64-unknown-linux-gnu +subdir = data/Andronescu +DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.in +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/gtfold_config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +SOURCES = +DIST_SOURCES = +am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; 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install-exec install-exec-am install-html install-html-am \ + install-info install-info-am install-man install-pdf \ + install-pdf-am install-ps install-ps-am install-strip \ + installcheck installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am tags uninstall uninstall-am + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: From 7227e162d9e6f8d2c42b110749e252b61227f8a6 Mon Sep 17 00:00:00 2001 From: Zsuzsanna Sukosd Date: Wed, 25 May 2011 18:17:37 +0200 Subject: [PATCH 042/187] fixed lost support for contact distance --- gtfold-mfe/Makefile | 2 +- gtfold-mfe/data/Andronescu/Makefile | 2 +- gtfold-mfe/data/Makefile | 2 +- gtfold-mfe/data/Turner04/Makefile | 2 +- gtfold-mfe/data/Turner99/Makefile | 2 +- gtfold-mfe/include/Makefile | 2 +- gtfold-mfe/src/.deps/global.Po | 5 ++++- gtfold-mfe/src/Makefile | 2 +- gtfold-mfe/src/algorithms.c | 2 ++ gtfold-mfe/src/constraints.cc | 12 ++++++------ gtfold-mfe/src/global.c | 1 + 11 files changed, 20 insertions(+), 14 deletions(-) diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile index 8bba63d..608a49b 100644 --- a/gtfold-mfe/Makefile +++ b/gtfold-mfe/Makefile @@ -214,7 +214,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile index ece5bb2..b2fd9ef 100644 --- a/gtfold-mfe/data/Andronescu/Makefile +++ b/gtfold-mfe/data/Andronescu/Makefile @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile index 90fd188..0331574 100644 --- a/gtfold-mfe/data/Makefile +++ b/gtfold-mfe/data/Makefile @@ -175,7 +175,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile index d64ce66..382eac6 100644 --- a/gtfold-mfe/data/Turner04/Makefile +++ b/gtfold-mfe/data/Turner04/Makefile @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile index 413b605..0fee0e5 100644 --- a/gtfold-mfe/data/Turner99/Makefile +++ b/gtfold-mfe/data/Turner99/Makefile @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile index 6318aff..ced6c10 100644 --- a/gtfold-mfe/include/Makefile +++ b/gtfold-mfe/include/Makefile @@ -140,7 +140,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po index e2d1748..a407344 100644 --- a/gtfold-mfe/src/.deps/global.Po +++ b/gtfold-mfe/src/.deps/global.Po @@ -14,7 +14,8 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ /usr/include/bits/select.h /usr/include/bits/sigset.h \ /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h + /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h \ + ../include/constraints.h /usr/include/stdio.h: @@ -83,3 +84,5 @@ global.o: global.c /usr/include/stdio.h /usr/include/features.h \ ../include/global.h: ../include/constants.h: + +../include/constraints.h: diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile index c79eea5..6385554 100644 --- a/gtfold-mfe/src/Makefile +++ b/gtfold-mfe/src/Makefile @@ -162,7 +162,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/gtfold +prefix = /home/zs/dsgtfold program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 1950fc0..3262322 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -39,6 +39,8 @@ int calculate(int len, int nThreads) { #pragma omp master fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif + + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index add3113..45d6280 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -443,7 +443,7 @@ int canILoop(int i, int j, int p, int q) { return canStack(i,j) && canStack(p,q) && canSSregion(i,p) && canSSregion(q,j); } else - return 1; + return withinCD(i,j) && withinCD(p,q); } int canHairpin(int i, int j) { @@ -452,7 +452,7 @@ int canHairpin(int i, int j) { //Need to check if pair is allowed and if anything pairs between them return canStack(i,j) && canSSregion(i,j); } - else return 1; + else return withinCD(i,j); } int canSSregion(int i, int j){ @@ -485,15 +485,15 @@ int canStack(int i, int j) { if(BP(i,j)==2||BP(i,i)==3||BP(j,j)==3) return 0; //can't pair if i or j are forced to pair with something other than each other if((BP(i,i)==4||BP(j,j)==4)&&BP(i,j)!=1) return 0; - else return 1; + else return withinCD(i,j); } - else return 1; + else return withinCD(i,j); } int withinCD(int i, int j){ //ZS: This function returns 1 if i and j are within the required contact distance from each other. - if (LIMIT_DISTANCE){ - return j-i+1>contactDistance; + if (LIMIT_DISTANCE){ + return (j-i>=contactDistance); } else return 1; } diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c index 5197c1e..a83c475 100644 --- a/gtfold-mfe/src/global.c +++ b/gtfold-mfe/src/global.c @@ -2,6 +2,7 @@ #include #include "global.h" +#include "constraints.h" unsigned char *RNA; int *structure; From 71de763ded642d0c33a60c7bb66590e888c3ed32 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 7 Jun 2011 17:53:53 -0400 Subject: [PATCH 043/187] testing --- gtfold-mfe/src/algorithms.c | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 3262322..91191dc 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -12,7 +12,8 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . -*/ +*/ + #include #include #include From f3fdde6ada0a7aff0e7cbfcd3191c7bdd9567294 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 7 Jun 2011 17:58:26 -0400 Subject: [PATCH 044/187] change to speedup multiloop calculations --- gtfold-mfe/include/energy.h | 8 ++----- gtfold-mfe/src/algorithms.c | 44 ++++++++++++++++++------------------- gtfold-mfe/src/energy.c | 41 +++++++++++++++++----------------- 3 files changed, 44 insertions(+), 49 deletions(-) diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index c5fdb1f..5b7b5cc 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -4,24 +4,20 @@ #include "data.h" extern int *V; -extern int *VV; -extern int *VV1; extern int *W; extern int *VBI; extern int *VM; extern int **WM; -extern int *WMu; -extern int *WMl; +extern int **WMPrime; extern int *indx; #define V(i,j) V[indx[j]+i] #define VM(i,j) VM[indx[j]+i] #define WM(i,j) WM[i][j] +#define WMPrime(i,j) WMPrime[i][j] #define WMU(i,j) WM[i][j] #define WML(i,j) WM[j][i] -//#define WMU(i,j) WMu[indx[j]+i] -//#define WML(i,j) WMl[indx[j]+i] #define VBI(i,j) VBI[indx[j]+i] #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 91191dc..0fd0c72 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -12,8 +12,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . -*/ - +*/ #include #include #include @@ -41,19 +40,19 @@ int calculate(int len, int nThreads) { fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif - for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) #endif for (i = 1; i <= len - b; i++) { j = i + b; - int flag = 0, newWM = INFINITY_; + int newWM = INFINITY_; if (canPair(RNA[i], RNA[j])) { - flag = 1; int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack - if (j-i > 6) { // Internal Loop BEGIN + + int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack + + if (j-i > 6) { // Internal Loop BEGIN int p=0, q=0; int VBIij = INFINITY_; for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { @@ -68,18 +67,14 @@ int calculate(int len, int nThreads) { } VBI(i,j) = VBIij; V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); - } // Internal Loop END - if (j-i > 10) { // Multi Loop BEGIN - int h; - int VMij, VMijd, VMidj, VMidjd; - VMij = VMijd = VMidj = VMidjd = INFINITY_; - for (h = i+TURN+1; h <= j-1-TURN; h++) { - VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); - VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); - VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); - VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); - } + + if (j-i > 10) { // Multi Loop BEGIN + int VMij = WMPrime[i+1][j-1]; + int VMidj = WMPrime[i+2][j-1]; + int VMijd = WMPrime[i+1][j-2]; + int VMidjd = WMPrime[i+2][j-2]; + int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; VMij = MIN(VMij, (VMidj + d5 +Ec)) ; @@ -88,16 +83,21 @@ int calculate(int len, int nThreads) { VMij = VMij + Ea + Eb + auPenalty(i,j); VM(i,j) = canStack(i,j)?VMij:INFINITY_; } // Multi Loop END - V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); + + V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); } else V(i,j) = INFINITY_; - if (j-i > 4) { // WM BEGIN + + if (j-i > 4) { // WM BEGIN int h; for (h = i+TURN+1 ; h <= j-TURN-1; h++) { //ZS: This sum corresponds to when i,j are NOT paired with each other. //So we need to make sure only terms where i,j aren't pairing are considered. - newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; + // Added auxillary storage WMPrime to speedup multiloop calculations + WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); + //newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; } + newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle @@ -108,6 +108,7 @@ int calculate(int len, int nThreads) { } // WM END } } + for (j = TURN+2; j <= len; j++) { int i, Wj, Widjd, Wijd, Widj, Wij, Wim1; Wj = INFINITY_; @@ -124,4 +125,3 @@ int calculate(int len, int nThreads) { } return W[len]; } - diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 1118794..9450f92 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -9,12 +9,11 @@ #include "shapereader.h" int *V; -int *VV; -int *VV1; int *W; int *VBI; int *VM; int **WM; +int **WMPrime; int *indx; int alloc_flag = 0; @@ -26,18 +25,6 @@ void create_tables(int len) { exit(-1); } - VV1 = (int *) malloc((len+ 1)*sizeof(int)); - if (VV1 == NULL) { - perror("Cannot allocate variable 'V'"); - exit(-1); - } - - VV = (int *) malloc((len+ 1)*sizeof(int)); - if (VV == NULL) { - perror("Cannot allocate variable 'V'"); - exit(-1); - } - int i; WM = (int **) malloc((len+1)* sizeof(int *)); if (WM == NULL) { @@ -50,7 +37,20 @@ void create_tables(int len) { perror("Cannot allocate variable 'WM[i]'"); exit(-1); } + } + + WMPrime = (int **) malloc((len+1)* sizeof(int *)); + if (WMPrime == NULL) { + perror("Cannot allocate variable 'WM'"); + exit(-1); } + for (i = 0; i <= len; i++) { + WMPrime[i] = (int *)malloc((len+1)* sizeof(int)); + if (WMPrime[i] == NULL) { + perror("Cannot allocate variable 'WM[i]'"); + exit(-1); + } + } VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); if (VM == NULL) { @@ -87,15 +87,13 @@ void init_tables(int len) { for (i = 0; i <= len; i++) { W[i] = INFINITY_; - VV[i] = INFINITY_; - VV1[i] = INFINITY_; - for (j = 0; j <= len; j++) + for (j = 0; j <= len; j++) { WM[i][j] = INFINITY_; + WMPrime[i][j] = INFINITY_; + } } - LLL = (len)*(len+1)/2 + 1; - for (i = 0; i < LLL; i++) { V[i] = INFINITY_; VM[i] = INFINITY_; @@ -116,11 +114,12 @@ void free_tables(int len) { for (i = 0; i <= len; i++) free(WM[i]); free(WM); + for (i = 0; i <= len; i++) free(WMPrime[i]); + free(WMPrime); + free(VM); free(VBI); free(V); - free(VV); - free(VV1); free(W); } } From 7b9fe56de9247ae20d5d9c6a8a078dcb170b6bcc Mon Sep 17 00:00:00 2001 From: Janderson Date: Sat, 11 Jun 2011 18:52:01 -0400 Subject: [PATCH 045/187] Bugfix in partition. Random sample now compiles, links --- gtfold-mfe/include/Makefile.am | 2 +- gtfold-mfe/include/Makefile.in | 2 +- gtfold-mfe/include/energy.h | 1 + gtfold-mfe/include/partition-dangle.h | 19 ++ gtfold-mfe/include/random-sample.h | 15 + gtfold-mfe/src/Makefile | 7 +- gtfold-mfe/src/Makefile.am | 2 + gtfold-mfe/src/Makefile.in | 7 +- gtfold-mfe/src/algorithms-partition.c | 23 +- gtfold-mfe/src/partition-dangle.c | 197 +++++++++++++ gtfold-mfe/src/random-sample.cc | 394 +++++++++++++++++++++++++- 11 files changed, 642 insertions(+), 27 deletions(-) create mode 100644 gtfold-mfe/include/partition-dangle.h create mode 100644 gtfold-mfe/include/random-sample.h create mode 100644 gtfold-mfe/src/partition-dangle.c diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index b73b2f6..ee1eb98 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,3 @@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index a0bf52b..3565a69 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -155,7 +155,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h CLEANFILES = *~ all: all-am diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index c5fdb1f..f8d7c77 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -23,6 +23,7 @@ extern int *indx; //#define WMU(i,j) WMu[indx[j]+i] //#define WML(i,j) WMl[indx[j]+i] #define VBI(i,j) VBI[indx[j]+i] +#define RT ((0.00198721 * 310.15)/100.00) #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h new file mode 100644 index 0000000..e483aa1 --- /dev/null +++ b/gtfold-mfe/include/partition-dangle.h @@ -0,0 +1,19 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + + +typedef struct partition_d{ + double ** u; + double ** up; + double ** upm; + double ** s1; + double ** s2; + double ** s3; + double ** u1; + int length; +}dangle_struct; + +double cond_dangle(int j, int h, int l); +void fill_partition_arrays_d(dangle_struct part_struct); + +#endif diff --git a/gtfold-mfe/include/random-sample.h b/gtfold-mfe/include/random-sample.h new file mode 100644 index 0000000..4a68889 --- /dev/null +++ b/gtfold-mfe/include/random-sample.h @@ -0,0 +1,15 @@ +#ifndef _RANDOM_SAMPLE_H +#define _RANDOM_SAMPLE_H + +#include + +using namespace std; + +typedef struct sub_seq_t{ + int start; + int end; + int paired; +}sub_seq; + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack); +#endif diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile index 53081de..8d533f1 100644 --- a/gtfold-mfe/src/Makefile +++ b/gtfold-mfe/src/Makefile @@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS) am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \ + subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ + partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \ shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = @@ -192,7 +193,9 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + algorithms-partition.c\ partition-dangle.c\ + random-sample.cc\ shapereader.cc gtfold_LDFLAGS = @@ -279,6 +282,7 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c +include ./$(DEPDIR)/algorithms-partition.Po include ./$(DEPDIR)/algorithms.Po include ./$(DEPDIR)/constraints.Po include ./$(DEPDIR)/energy.Po @@ -287,6 +291,7 @@ include ./$(DEPDIR)/loader.Po include ./$(DEPDIR)/main.Po include ./$(DEPDIR)/options.Po include ./$(DEPDIR)/partition-dangle.Po +include ./$(DEPDIR)/random-sample.Po include ./$(DEPDIR)/shapereader.Po include ./$(DEPDIR)/subopt_traceback.Po include ./$(DEPDIR)/traceback.Po diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 797391e..aaa9481 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -16,7 +16,9 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + algorithms-partition.c\ partition-dangle.c\ + random-sample.cc\ shapereader.cc gtfold_LDFLAGS = diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index 0de321f..8b6d90d 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -51,7 +51,8 @@ PROGRAMS = $(bin_PROGRAMS) am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) partition-dangle.$(OBJEXT) \ + subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ + partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \ shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = @@ -192,7 +193,9 @@ gtfold_SOURCES = \ algorithms.c \ traceback.c \ subopt_traceback.cc\ + algorithms-partition.c\ partition-dangle.c\ + random-sample.cc\ shapereader.cc gtfold_LDFLAGS = @@ -279,6 +282,7 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@ @@ -287,6 +291,7 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index c39128e..1ed7895 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -16,7 +16,6 @@ // Boltzmann constant (R) * Standard 37C temperature (T in Kelvin) -double RT = 0.00198721 * 310.15; // Based on pseudocode in figure 6 in // @@ -67,18 +66,18 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { // NOTE: eH returns an integer encoded as fixed point. So a // return value of 115 represents raw value 115/100 = 1.15 - QB[i][j] = exp(-eH(i,j)/100.0/RT); + QB[i][j] = exp(-eH(i,j)/RT); for(d=i+1; d<=j-4; ++d) { for(e=d+4; e<=j-1; ++e) { if(d == i + 1 && e == j -1) - QB[i][j] += exp(-eS(i,j)/100.0/RT)*QB[d][e]; + QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; else - QB[i][j] += exp(-eL(i,j,d,e)/100.0/RT)*QB[d][e]; + QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; QB[i][j] += QM[i+1][d-1]*QB[d][e] * - exp(-(a + b + c*(j-e-1))/100.0/RT); + exp(-(a + b + c*(j-e-1))/RT); } } } @@ -88,8 +87,8 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { for(d=i; d<=j-4; ++d) { for(e=d+4; e<=j; ++e) { Q[i][j] += Q[i][d-1]*QB[d][e]; - QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/100.0) * QB[d][e]; - QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/100.0/RT); + QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/RT) * QB[d][e]; + QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/RT); } } } @@ -137,22 +136,22 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double ** tempBuffer = P[i][j]*QB[h][l]/QB[i][j]; if(i == h-1 && j == l+1) //of which stacked pairs are a special case - tempBuffer *= exp(-eS(i,j)/100.0/RT); + tempBuffer *= exp(-eS(i,j)/RT); else - tempBuffer *= exp(-eL(i,j,h,l)/100.0/RT); + tempBuffer *= exp(-eL(i,j,h,l)/RT); P[h][l] += tempBuffer; // third term tempBuffer = 0; // Start over for multiloops if(j - l > 3) - tempBuffer += exp(-((h-i-1)*c/100.0/RT)) * QM[l+1][j-1]; + tempBuffer += exp(-((h-i-1)*c/RT)) * QM[l+1][j-1]; if(h - i > 3) - tempBuffer += exp(-((j-l-1)*c/100.0/RT)) * QM[i+1][h-1]; + tempBuffer += exp(-((j-l-1)*c/RT)) * QM[i+1][h-1]; if(j - l > 3 && h - i > 3) tempBuffer += QM[i+1][h-1] * QM[l+1][j-1]; - tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/100.0/RT); + tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/RT); P[h][l] += tempBuffer; } diff --git a/gtfold-mfe/src/partition-dangle.c b/gtfold-mfe/src/partition-dangle.c new file mode 100644 index 0000000..df677fc --- /dev/null +++ b/gtfold-mfe/src/partition-dangle.c @@ -0,0 +1,197 @@ +//Attempting to follow Ding and Lawrence as closely as possible + +/**s1 -> partial_external +* s2 -> partial_multi +* s3 -> partial_multi2 +* u1 -> u_multi +* f -> cond_dangle (conditional) +* ebi -> eL +**/ + +#include +#include + +#include "energy.h" +#include "utils.h" +#include "global.h" +#include "data.h" +#include "algorithms-partition.h" +#include "partition-dangle.h" + +#define MIN_TURN 4 +#define MAX_LOOP 30 + +//double RT = (0.00198721 * 310.15)/100.00; + +double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +} + +dangle_struct malloc_partition_arrays_d(int length){ + dangle_struct ret_struct; + ret_struct.length = length; + + //Add 1 since we're not zero indexed + ret_struct.u = mallocTwoD(length + 1, length + 1); + ret_struct.up = mallocTwoD(length + 1, length + 1); + ret_struct.upm = mallocTwoD(length + 1, length + 1); + ret_struct.u1 = mallocTwoD(length + 1, length + 1); + ret_struct.s1 = mallocTwoD(length + 1, length + 1); + ret_struct.s2 = mallocTwoD(length + 1, length + 1); + ret_struct.s3 = mallocTwoD(length + 1, length + 1); + + int i,j; + + for(i = 0; i < length + 1; i++){ + for(j = 0; j < length + 1; j++){ + ret_struct.u[i][j] = 1; + ret_struct.up[i][j] = 0; + ret_struct.upm[i][j] = 0; + ret_struct.u1[i][j] = 0; + ret_struct.s1[i][j] = 0; + ret_struct.s2[i][j] = 0; + ret_struct.s3[i][j] = 0; + } + } + return ret_struct; +} + +void free_partition_arrays_d(struct partition_d part) +{ + freeTwoD(part.u, part.length, part.length); + freeTwoD(part.up, part.length, part.length); + freeTwoD(part.upm, part.length, part.length); + freeTwoD(part.u1, part.length, part.length); + freeTwoD(part.s1, part.length, part.length); + freeTwoD(part.s2, part.length, part.length); + freeTwoD(part.s3, part.length, part.length); +} + +void fill_partition_arrays_d(dangle_struct part_struct){ + //So that we don't have the /100 in every exponent + //Seeing as we missed some last time + + double ** partial_external = part_struct.s1; + double ** partial_multi = part_struct.s2; + double ** partial_multi2 = part_struct.s3; + double ** u_multi = part_struct.u1; + double ** u = part_struct.u; + double ** up = part_struct.up; + double ** upm = part_struct.upm; + int len = part_struct.length; + + int seg_length; + int i,j; + + for(seg_length = MIN_TURN; seg_length <= len; len++){ + //Insert parallelism here. + for(i = 1; i < len - seg_length; i++){ + j = i + seg_length - 1; + + int l; + if(canPair(i,j)){ + for(l = i+2; l < j; l++){ + upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) * + (exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + if(l != i+2){ //goes from i + 2 < l < j + upm[i][j] += up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) * + (exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + if(l != j - 1){ + upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * + partial_multi[l][j]; + //Changed h in the paper to l it makes no difference + //other than unifying loops + } + } + } + + + up[i][j] += exp(-eH(i,j)/RT) + exp(-eS(i,j)/RT) * up[i + 1][j - 1] + upm[i][j]; + for(l = j - 1; l > i + 1; l--){ + if((j - l) - 2> MAX_LOOP){ + break; + } + int h; + for(h = i + 1 ; h < l; h++){ + if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack + up[i][j] += exp(-eL(i,j,h,l)/RT); + } + if((j - l) + (h - i) - 2 > MAX_LOOP){ + break; + } + } + } + }//End checkpair conditional + + for(l = i + 1; l <= j ; l++){ + u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) * + (cond_dangle(j + 1,i,l) * exp(-(j - l) * Eb/RT) + + exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != i+1){ + u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)* + (cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + + exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != j){ + u_multi[i][j] += exp(-(Ec + (l - i) * Eb)/RT) * partial_multi2[l][j]; + + } + } + } + + + int h = i; //To stay consistant with the notation in the paper. + + for(l = h+1; l < j; l++){ + partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u[l + 2][j - 1] + + u[l + 1][j] - + u[l + 2][j]); + + partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + } + /** partial_multi2 goes up to j **/ + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + //Finally we do the u matrix + u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT); + + for(l = i + 1; l < j; l++){ + //Replaced l with h in the next line to unify loops + u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT); + + u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] + + u[l + 1][j] - u[l + 2][j]); + if(l != j - 1) { + u[i][j] += partial_external[l][j]; + } + } + }//end of minor (paralellizeable) for loop + }//End of major for loop +} diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc index 3290e38..ff53afa 100644 --- a/gtfold-mfe/src/random-sample.cc +++ b/gtfold-mfe/src/random-sample.cc @@ -1,10 +1,29 @@ #include #include +#include -#include "parition-dangle.h" +#include "partition-dangle.h" +#include "algorithms-partition.h" #include "energy.h" +#include "random-sample.h" -double RT=(0.00198721 * 310.15)/100.00; +using namespace std; + +#define MIN_TURN 4 + +//double RT=(0.00198721 * 310.15)/100.00; + + +//I don't know why not having this function +//gives me a link error it should get this function +//from partition-dangle + +double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +} double randdouble(){ return rand()/(double(RAND_MAX)+1); @@ -25,14 +44,14 @@ double prob_h_pairs_with_5_end (int i, int h, int j, dangle_struct d_struct){ return d_struct.up[h][j] * - exp(-(ed5(h,j,h - 1) + + exp(-(Ed5(h,j,h - 1) + auPenalty(h,j))/RT) / d_struct.u[i][j]; } //P_{il} double prob_l_pairs_with_3_end - (int i, int l, int j dangle_struct d_struct){ + (int i, int l, int j, dangle_struct d_struct){ return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) * (exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] + @@ -96,7 +115,7 @@ double first_multi_prob_pair_next_base double first_multi_prob_pair_after_base (int i, int l, int j, dangle_struct d_struct){ - return d_struct[i + 2][l] * + return d_struct.up[i + 2][l] * exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) * (exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + d_struct.u1[l + 1][j - 1] - @@ -106,7 +125,7 @@ double first_multi_prob_pair_after_base //P_{ijs2h) double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){ - return exp(-(Ea + 2 * Ec + (h - i - 1) * b + Ed3(j,i,i+1))/RT) * + return exp(-(Ea + 2 * Ec + (h - i - 1) * Eb + Ed3(j,i,i+1))/RT) * d_struct.s2[h][j] / d_struct.upm[i][j]; } //P_{ijhl} @@ -120,10 +139,9 @@ double first_multi_prob_base_rest } //Q_{(l1 + 1)(j -1)(l1 +1)} -double rest_multi_prob_next_base_pairs - (int l1, int l, int j, dangle_struct d_struct){ +double rest_multi_prob_next_base_pairs (int l1, int l, int j, dangle_struct d_struct){ - return d_struct.up[l1 +1][l] * exp( - (Ec + auPenalty(l1 + 1, l))/RT) + return d_struct.up[l1 +1][l] * exp(-(Ec + auPenalty(l1 + 1, l))/RT) * (cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) + exp(-(j - 1 - l) * Eb) / RT + exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] + @@ -166,9 +184,10 @@ double rest_multi_prob_h_pairs_with_l d_struct.s3[h][j - 1]; } +//P_{Bh2l2} int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){ double counter = randdouble(); - double coin-flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) / + double coin_flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) / (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] + d_struct.u1[l2 + 1][j - 1] - @@ -178,10 +197,363 @@ int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){ //return counter > coin-flip - if(counter <= coin-flip){ + if(counter <= coin_flip){ return 0; } else{ return 1; } } + +void single_stranded(int i, int j, int * structure){ + for(;i <= j; i++) + { + structure[i] = 0; + } +} + +void unknown_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ +//Unknown strand from i,j + double counter = randdouble(); + counter -= single_stranded_prob(i, j, d_struct); + if (counter <= 0){ + single_stranded(i,j, structure); + return; + } + counter -= ends_pair_prob(i, j, d_struct); + if(counter <= 0){ + sub_seq seq; + seq.start = i; + seq.end = j; + seq.paired = 1; + //put i j on paired and push i j on stack as paired + + structure[i] = j; + structure[j] = i; + stack->push_front(seq); + return; + } + for (int h = i + MIN_TURN; h < j; h++){ + counter -= prob_h_pairs_with_5_end(i,h,j,d_struct); + if(counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = i; + seq1.end = h; + seq1.paired = 1; + + seq2.start = h + 1; + seq2.end = j; + seq2.paired = 0; + + //Push i h as paired and h + 1 to j as unknown + structure[i] = h; + structure[h] = i; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + + for(int l = i + 1; l <= j - MIN_TURN; l++){ + counter -= prob_l_pairs_with_3_end(i,l,j,d_struct); + if (counter < 0){ + + sub_seq seq; + seq.start = l; + seq.end = j; + seq.paired = 1; + + //put from i to l - 1 as unpaired and push l and j as paired + single_stranded(i, l - 1, structure); + structure[l] = j; + structure[j] = l; + stack->push_front(seq); + return; + } + } + int h; //The loop is just to find h we need it later + for(h = i + 1; i <= j - MIN_TURN - 1; h++){ + counter -= prob_h_pairs_in_ij(i,h,j,d_struct); + if(counter < 0) + { + break; + } + } + + //Now to find l + counter = randdouble(); //reset counter, this is a seperate case + for(int l = h + MIN_TURN; l <= j - MIN_TURN; l++){ + counter -= prob_h_pairs_with_l(h,l,j,d_struct); + if (counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = h; + seq1.end = l; + seq1.paired = 1; + + seq2.start = l + 1; + seq2.end = j; + seq2.paired = 0; + + //set from i to h - 1 as single stranded + //Push h l as paired and l + 1 to j + //as unknown. + + single_stranded(i, h - 1, structure); + structure[h] = l; + structure[l] = h; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + //If we hit here, that's bad +} + +void paired_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + double cumulative_prob = 0; + + + cumulative_prob = prob_ij_pair_is_hairpin(i,j,d_struct); + if(counter - cumulative_prob < 0){ + //i + 1, j - 1 is single stranded + single_stranded(i + 1, j - 1, structure); + return; + } + + cumulative_prob += prob_ij_pair_is_stack(i,j,d_struct); + if(counter - cumulative_prob < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = j - 1; + seq.paired = 1; + + //i + 1, j - 1 is pushed as stack + stack->push_front(seq); + structure[i + 1] = j - 1; + structure[j - 1] = i + 1; + return; + } + + cumulative_prob += prob_ij_pair_is_multiloop(i,j,d_struct); + if(counter - cumulative_prob < 0){ + multi_loop_strand(i,j,d_struct,structure,stack); + return; + } + + //else we know we have an internal loop. + //The probabilities should work out so that + //we never get more than 30 base internal loops. + //Might need to put guards in here. + counter = randdouble(); + for(int h = i + 1; h < j; h++){ + for(int l = h + MIN_TURN; l < j; l++){ + if(!(h == i + 1 && l == j - 1)) //Don't want a stack + counter -= exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / (1 - cumulative_prob); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //hl goes on the stack as a pair and the rest of the internal loop + //gets put on a single stranded + + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + single_stranded(i + 1, h - 1,structure); + single_stranded(l + 1, j - 1,structure); + } + } + } +} + +//It returns where it stops. +int multi_first_loop(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + for(int l= i + MIN_TURN + 1; l < j - 1; l++){ + counter -= first_multi_prob_pair_next_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[i + 1] = l; + structure[l] = i + 1; + return l + 1; + } + } + for(int l = i + MIN_TURN + 2; l < j - 1; l++){ + counter -= first_multi_prob_pair_after_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[i + 1] = 0; + structure[i + 2] = l; + structure[l] = i + 2; + return l + 1; + } + } + + //We need h after this loop so we declare it here. + int h; + for(h = i + 3; h < j - 1; h ++){ + counter -= first_multi_prob_pair_rest_base(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= first_multi_prob_base_rest(i,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(i + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + return l + 1; + } + } + + return -1; //We have an underflow or calculation error. +} + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + int l1 = multi_first_loop(i,j,d_struct, structure,stack);//l1 is the name of the closing base of the first loop + int h1 = i; + int notdone = 1; + int breakflag = 0; + + while(notdone){ + double counter = randdouble(); + for(int l = l1 + MIN_TURN + 1; l < j - 1; l++){ + counter -= rest_multi_prob_next_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[l1 + 1] = l; + structure[l] = i + 1; + h1 = l1 + 1; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + for(int l = l1 + MIN_TURN + 2; l < j - 1; l++){ + counter -= rest_multi_prob_after_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[l1 + 1] = 0; + structure[l1 + 2] = l; + structure[l] = l1 + 2; + h1 = l1 + 2; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + //We need h after this loop so we declare it here. + int h; + for(h = l1 + 3; h < j - 1; h ++){ + counter -= rest_multi_prob_rest_base_pairs(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= rest_multi_prob_h_pairs_with_l(l1,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(l1 + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + l1 = l + 1; + h1 = h; + } + } + notdone = there_is_another_helix(h1, l1, j, d_struct); + }//End while +}//End function + + +void sample_structure(int * structure, dangle_struct d_struct){ + sub_seq seq; + seq.start = 1; + seq.end = d_struct.length; + seq.paired = 0; + + list da_stack; + da_stack.push_front(seq); + while(!da_stack.empty()){ + sub_seq cur_seq = da_stack.front(); + if(cur_seq.paired) + { + paired_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + else + { + unknown_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + da_stack.pop_front(); + } + +} From 142e6c6580b6e0d733eefd4d10c1b697ff1f6e5b Mon Sep 17 00:00:00 2001 From: Janderson Date: Thu, 16 Jun 2011 11:55:09 -0400 Subject: [PATCH 046/187] I believe my automake is broken, but bpp theoretically re-integrated --- gtfold-mfe/INSTALL | 228 ++++++++++++++++---- gtfold-mfe/aclocal.m4 | 12 -- gtfold-mfe/config.guess | 248 ++++++++++------------ gtfold-mfe/config.sub | 102 +++++++-- gtfold-mfe/configure | 1 - gtfold-mfe/configure.in | 34 ++- gtfold-mfe/depcomp | 87 ++++++-- gtfold-mfe/include/Makefile.am | 2 +- gtfold-mfe/include/Makefile.in | 2 +- gtfold-mfe/include/algorithms-partition.h | 18 +- gtfold-mfe/include/partition-dangle.h | 1 + gtfold-mfe/install-sh | 5 +- gtfold-mfe/missing | 49 +++-- gtfold-mfe/src/.deps/main.Po | 15 +- gtfold-mfe/src/Makefile | 4 +- gtfold-mfe/src/Makefile.am | 4 +- gtfold-mfe/src/Makefile.in | 4 +- gtfold-mfe/src/algorithms-partition.c | 4 +- gtfold-mfe/src/main.cc | 25 +++ gtfold-mfe/src/random-sample.cc | 4 +- 20 files changed, 540 insertions(+), 309 deletions(-) mode change 100644 => 100755 gtfold-mfe/config.guess mode change 100644 => 100755 gtfold-mfe/config.sub mode change 100644 => 100755 gtfold-mfe/depcomp mode change 100644 => 100755 gtfold-mfe/missing diff --git a/gtfold-mfe/INSTALL b/gtfold-mfe/INSTALL index 54caf7c..7d1c323 100644 --- a/gtfold-mfe/INSTALL +++ b/gtfold-mfe/INSTALL @@ -1,13 +1,25 @@ -Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software -Foundation, Inc. +Installation Instructions +************************* - This file is free documentation; the Free Software Foundation gives -unlimited permission to copy, distribute and modify it. +Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005, +2006, 2007, 2008, 2009 Free Software Foundation, Inc. + + Copying and distribution of this file, with or without modification, +are permitted in any medium without royalty provided the copyright +notice and this notice are preserved. This file is offered as-is, +without warranty of any kind. Basic Installation ================== - These are generic installation instructions. + Briefly, the shell commands `./configure; make; make install' should +configure, build, and install this package. The following +more-detailed instructions are generic; see the `README' file for +instructions specific to this package. Some packages provide this +`INSTALL' file but do not implement all of the features documented +below. The lack of an optional feature in a given package is not +necessarily a bug. More recommendations for GNU packages can be found +in *note Makefile Conventions: (standards)Makefile Conventions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses @@ -20,9 +32,9 @@ debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves -the results of its tests to speed up reconfiguring. (Caching is +the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale -cache files.) +cache files. If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail @@ -32,30 +44,37 @@ some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You only need -`configure.ac' if you want to change it or regenerate `configure' using -a newer version of `autoconf'. +`configure' by a program called `autoconf'. You need `configure.ac' if +you want to change it or regenerate `configure' using a newer version +of `autoconf'. -The simplest way to compile this package is: + The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type - `./configure' to configure the package for your system. If you're - using `csh' on an old version of System V, you might need to type - `sh ./configure' instead to prevent `csh' from trying to execute - `configure' itself. + `./configure' to configure the package for your system. - Running `configure' takes awhile. While running, it prints some - messages telling which features it is checking for. + Running `configure' might take a while. While running, it prints + some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with - the package. + the package, generally using the just-built uninstalled binaries. 4. Type `make install' to install the programs and any data files and - documentation. - - 5. You can remove the program binaries and object files from the + documentation. When installing into a prefix owned by root, it is + recommended that the package be configured and built as a regular + user, and only the `make install' phase executed with root + privileges. + + 5. Optionally, type `make installcheck' to repeat any self-tests, but + this time using the binaries in their final installed location. + This target does not install anything. Running this target as a + regular user, particularly if the prior `make install' required + root privileges, verifies that the installation completed + correctly. + + 6. You can remove the program binaries and object files from the source code directory by typing `make clean'. To also remove the files that `configure' created (so you can compile the package for a different kind of computer), type `make distclean'. There is @@ -64,6 +83,16 @@ The simplest way to compile this package is: all sorts of other programs in order to regenerate files that came with the distribution. + 7. Often, you can also type `make uninstall' to remove the installed + files again. In practice, not all packages have tested that + uninstallation works correctly, even though it is required by the + GNU Coding Standards. + + 8. Some packages, particularly those that use Automake, provide `make + distcheck', which can by used by developers to test that all other + targets like `make install' and `make uninstall' work correctly. + This target is generally not run by end users. + Compilers and Options ===================== @@ -75,7 +104,7 @@ for details on some of the pertinent environment variables. by setting variables in the command line or in the environment. Here is an example: - ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix + ./configure CC=c99 CFLAGS=-g LIBS=-lposix *Note Defining Variables::, for more details. @@ -84,44 +113,89 @@ Compiling For Multiple Architectures You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their -own directory. To do this, you must use a version of `make' that -supports the `VPATH' variable, such as GNU `make'. `cd' to the +own directory. To do this, you can use GNU `make'. `cd' to the directory where you want the object files and executables to go and run the `configure' script. `configure' automatically checks for the -source code in the directory that `configure' is in and in `..'. +source code in the directory that `configure' is in and in `..'. This +is known as a "VPATH" build. - If you have to use a `make' that does not support the `VPATH' -variable, you have to compile the package for one architecture at a -time in the source code directory. After you have installed the -package for one architecture, use `make distclean' before reconfiguring -for another architecture. + With a non-GNU `make', it is safer to compile the package for one +architecture at a time in the source code directory. After you have +installed the package for one architecture, use `make distclean' before +reconfiguring for another architecture. + + On MacOS X 10.5 and later systems, you can create libraries and +executables that work on multiple system types--known as "fat" or +"universal" binaries--by specifying multiple `-arch' options to the +compiler but only a single `-arch' option to the preprocessor. Like +this: + + ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CPP="gcc -E" CXXCPP="g++ -E" + + This is not guaranteed to produce working output in all cases, you +may have to build one architecture at a time and combine the results +using the `lipo' tool if you have problems. Installation Names ================== - By default, `make install' will install the package's files in -`/usr/local/bin', `/usr/local/man', etc. You can specify an -installation prefix other than `/usr/local' by giving `configure' the -option `--prefix=PATH'. + By default, `make install' installs the package's commands under +`/usr/local/bin', include files under `/usr/local/include', etc. You +can specify an installation prefix other than `/usr/local' by giving +`configure' the option `--prefix=PREFIX', where PREFIX must be an +absolute file name. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you -give `configure' the option `--exec-prefix=PATH', the package will use -PATH as the prefix for installing programs and libraries. -Documentation and other data files will still use the regular prefix. +pass the option `--exec-prefix=PREFIX' to `configure', the package uses +PREFIX as the prefix for installing programs and libraries. +Documentation and other data files still use the regular prefix. In addition, if you use an unusual directory layout you can give -options like `--bindir=PATH' to specify different values for particular +options like `--bindir=DIR' to specify different values for particular kinds of files. Run `configure --help' for a list of the directories -you can set and what kinds of files go in them. +you can set and what kinds of files go in them. In general, the +default for these options is expressed in terms of `${prefix}', so that +specifying just `--prefix' will affect all of the other directory +specifications that were not explicitly provided. + + The most portable way to affect installation locations is to pass the +correct locations to `configure'; however, many packages provide one or +both of the following shortcuts of passing variable assignments to the +`make install' command line to change installation locations without +having to reconfigure or recompile. + + The first method involves providing an override variable for each +affected directory. For example, `make install +prefix=/alternate/directory' will choose an alternate location for all +directory configuration variables that were expressed in terms of +`${prefix}'. Any directories that were specified during `configure', +but not in terms of `${prefix}', must each be overridden at install +time for the entire installation to be relocated. The approach of +makefile variable overrides for each directory variable is required by +the GNU Coding Standards, and ideally causes no recompilation. +However, some platforms have known limitations with the semantics of +shared libraries that end up requiring recompilation when using this +method, particularly noticeable in packages that use GNU Libtool. + + The second method involves providing the `DESTDIR' variable. For +example, `make install DESTDIR=/alternate/directory' will prepend +`/alternate/directory' before all installation names. The approach of +`DESTDIR' overrides is not required by the GNU Coding Standards, and +does not work on platforms that have drive letters. On the other hand, +it does better at avoiding recompilation issues, and works well even +when some directory options were not specified in terms of `${prefix}' +at `configure' time. + +Optional Features +================= If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving `configure' the option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. -Optional Features -================= - Some packages pay attention to `--enable-FEATURE' options to `configure', where FEATURE indicates an optional part of the package. They may also pay attention to `--with-PACKAGE' options, where PACKAGE @@ -134,6 +208,45 @@ find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. + Some packages offer the ability to configure how verbose the +execution of `make' will be. For these packages, running `./configure +--enable-silent-rules' sets the default to minimal output, which can be +overridden with `make V=1'; while running `./configure +--disable-silent-rules' sets the default to verbose, which can be +overridden with `make V=0'. + +Particular systems +================== + + On HP-UX, the default C compiler is not ANSI C compatible. If GNU +CC is not installed, it is recommended to use the following options in +order to use an ANSI C compiler: + + ./configure CC="cc -Ae -D_XOPEN_SOURCE=500" + +and if that doesn't work, install pre-built binaries of GCC for HP-UX. + + On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot +parse its `' header file. The option `-nodtk' can be used as +a workaround. If GNU CC is not installed, it is therefore recommended +to try + + ./configure CC="cc" + +and if that doesn't work, try + + ./configure CC="cc -nodtk" + + On Solaris, don't put `/usr/ucb' early in your `PATH'. This +directory contains several dysfunctional programs; working variants of +these programs are available in `/usr/bin'. So, if you need `/usr/ucb' +in your `PATH', put it _after_ `/usr/bin'. + + On Haiku, software installed for all users goes in `/boot/common', +not `/usr/local'. It is recommended to use the following options: + + ./configure --prefix=/boot/common + Specifying the System Type ========================== @@ -149,14 +262,15 @@ type, such as `sun4', or a canonical name which has the form: where SYSTEM can have one of these forms: - OS KERNEL-OS + OS + KERNEL-OS See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the machine type. If you are _building_ compiler tools for cross-compiling, you should -use the `--target=TYPE' option to select the type of system they will +use the option `--target=TYPE' to select the type of system they will produce code for. If you want to _use_ a cross compiler, that generates code for a @@ -186,9 +300,14 @@ them in the `configure' command line, using `VAR=value'. For example: ./configure CC=/usr/local2/bin/gcc -will cause the specified gcc to be used as the C compiler (unless it is +causes the specified `gcc' to be used as the C compiler (unless it is overridden in the site shell script). +Unfortunately, this technique does not work for `CONFIG_SHELL' due to +an Autoconf bug. Until the bug is fixed you can use this workaround: + + CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash + `configure' Invocation ====================== @@ -197,7 +316,14 @@ operates. `--help' `-h' - Print a summary of the options to `configure', and exit. + Print a summary of all of the options to `configure', and exit. + +`--help=short' +`--help=recursive' + Print a summary of the options unique to this package's + `configure', and exit. The `short' variant lists options used + only in the top level, while the `recursive' variant lists options + also present in any nested packages. `--version' `-V' @@ -224,6 +350,16 @@ operates. Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. +`--prefix=DIR' + Use DIR as the installation prefix. *note Installation Names:: + for more details, including other options available for fine-tuning + the installation locations. + +`--no-create' +`-n' + Run the configure checks, but stop before creating any output + files. + `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4 index f5a02ce..eba341b 100644 --- a/gtfold-mfe/aclocal.m4 +++ b/gtfold-mfe/aclocal.m4 @@ -406,18 +406,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"]) ]) -# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005 -# Free Software Foundation, Inc. -# -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# serial 8 - -# AM_CONFIG_HEADER is obsolete. It has been replaced by AC_CONFIG_HEADERS. -AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)]) - # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, diff --git a/gtfold-mfe/config.guess b/gtfold-mfe/config.guess old mode 100644 new mode 100755 index ca2a03c..c2246a4 --- a/gtfold-mfe/config.guess +++ b/gtfold-mfe/config.guess @@ -1,10 +1,10 @@ #! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-08' +timestamp='2009-12-30' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by @@ -27,16 +27,16 @@ timestamp='2008-01-08' # the same distribution terms that you use for the rest of that program. -# Originally written by Per Bothner . -# Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# Originally written by Per Bothner. Please send patches (context +# diff format) to and include a ChangeLog +# entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # -# The plan is that this can be called by configure scripts if you -# don't specify an explicit build system type. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD me=`echo "$0" | sed -e 's,.*/,,'` @@ -56,8 +56,9 @@ version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -170,7 +171,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep __ELF__ >/dev/null + | grep -q __ELF__ then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? @@ -324,14 +325,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; + s390x:SunOS:*:*) + echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux${UNAME_RELEASE} + exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) - echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + eval $set_cc_for_build + SUN_ARCH="i386" + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH="x86_64" + fi + fi + echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize @@ -640,7 +660,7 @@ EOF # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | - grep __LP64__ >/dev/null + grep -q __LP64__ then HP_ARCH="hppa2.0w" else @@ -791,12 +811,12 @@ EOF i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; - *:Interix*:[3456]*) + *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; - EM64T | authenticamd) + authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) @@ -806,6 +826,9 @@ EOF [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; + 8664:Windows_NT:*) + echo x86_64-pc-mks + exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we @@ -835,6 +858,20 @@ EOF i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ @@ -857,6 +894,17 @@ EOF frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; + i*86:Linux:*:*) + LIBC=gnu + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` + echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; @@ -866,74 +914,33 @@ EOF m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - mips:Linux:*:*) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #undef CPU - #undef mips - #undef mipsel - #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mipsel - #else - #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips - #else - CPU= - #endif - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" - test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } - ;; - mips64:Linux:*:*) + mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU - #undef mips64 - #undef mips64el + #undef ${UNAME_MACHINE} + #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mips64el + CPU=${UNAME_MACHINE}el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips64 + CPU=${UNAME_MACHINE} #else CPU= #endif #endif EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; - ppc:Linux:*:*) - echo powerpc-unknown-linux-gnu - exit ;; - ppc64:Linux:*:*) - echo powerpc64-unknown-linux-gnu + padre:Linux:*:*) + echo sparc-unknown-linux-gnu exit ;; - alpha:Linux:*:*) - case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in - EV5) UNAME_MACHINE=alphaev5 ;; - EV56) UNAME_MACHINE=alphaev56 ;; - PCA56) UNAME_MACHINE=alphapca56 ;; - PCA57) UNAME_MACHINE=alphapca56 ;; - EV6) UNAME_MACHINE=alphaev6 ;; - EV67) UNAME_MACHINE=alphaev67 ;; - EV68*) UNAME_MACHINE=alphaev68 ;; - esac - objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null - if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi - echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level @@ -943,8 +950,11 @@ EOF *) echo hppa-unknown-linux-gnu ;; esac exit ;; - parisc64:Linux:*:* | hppa64:Linux:*:*) - echo hppa64-unknown-linux-gnu + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux @@ -967,69 +977,6 @@ EOF xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - i*86:Linux:*:*) - # The BFD linker knows what the default object file format is, so - # first see if it will tell us. cd to the root directory to prevent - # problems with other programs or directories called `ld' in the path. - # Set LC_ALL=C to ensure ld outputs messages in English. - ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ - | sed -ne '/supported targets:/!d - s/[ ][ ]*/ /g - s/.*supported targets: *// - s/ .*// - p'` - case "$ld_supported_targets" in - elf32-i386) - TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" - ;; - a.out-i386-linux) - echo "${UNAME_MACHINE}-pc-linux-gnuaout" - exit ;; - coff-i386) - echo "${UNAME_MACHINE}-pc-linux-gnucoff" - exit ;; - "") - # Either a pre-BFD a.out linker (linux-gnuoldld) or - # one that does not give us useful --help. - echo "${UNAME_MACHINE}-pc-linux-gnuoldld" - exit ;; - esac - # Determine whether the default compiler is a.out or elf - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #include - #ifdef __ELF__ - # ifdef __GLIBC__ - # if __GLIBC__ >= 2 - LIBC=gnu - # else - LIBC=gnulibc1 - # endif - # else - LIBC=gnulibc1 - # endif - #else - #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) - LIBC=gnu - #else - LIBC=gnuaout - #endif - #endif - #ifdef __dietlibc__ - LIBC=dietlibc - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^LIBC/{ - s: ::g - p - }'`" - test x"${LIBC}" != x && { - echo "${UNAME_MACHINE}-pc-linux-${LIBC}" - exit - } - test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } - ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both @@ -1058,7 +1005,7 @@ EOF i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; - i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) @@ -1102,8 +1049,11 @@ EOF pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about - # the processor, so we play safe by assuming i386. - echo i386-pc-msdosdjgpp + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configury will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 @@ -1141,6 +1091,16 @@ EOF 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; @@ -1153,7 +1113,7 @@ EOF rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; - PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) @@ -1216,6 +1176,9 @@ EOF BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; @@ -1243,6 +1206,16 @@ EOF *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in + i386) + eval $set_cc_for_build + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + UNAME_PROCESSOR="x86_64" + fi + fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} @@ -1324,6 +1297,9 @@ EOF i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; + i*86:AROS:*:*) + echo ${UNAME_MACHINE}-pc-aros + exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 @@ -1484,9 +1460,9 @@ This script, last modified $timestamp, has failed to recognize the operating system you are using. It is advised that you download the most up to date version of the config scripts from - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD and - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD If the version you run ($0) is already up to date, please send the following data and any information you think might be diff --git a/gtfold-mfe/config.sub b/gtfold-mfe/config.sub old mode 100644 new mode 100755 index 6759825..c2d1257 --- a/gtfold-mfe/config.sub +++ b/gtfold-mfe/config.sub @@ -1,10 +1,10 @@ #! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-16' +timestamp='2010-01-22' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software @@ -32,13 +32,16 @@ timestamp='2008-01-16' # Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# diff and a properly formatted GNU ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD + # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. @@ -72,8 +75,9 @@ Report bugs and patches to ." version="\ GNU config.sub ($timestamp) -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -122,6 +126,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` @@ -148,10 +153,13 @@ case $os in -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ - -apple | -axis | -knuth | -cray) + -apple | -axis | -knuth | -cray | -microblaze) os= basic_machine=$1 ;; + -bluegene*) + os=-cnk + ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 @@ -249,13 +257,16 @@ case $basic_machine in | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ + | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep \ + | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ - | mips64vr | mips64vrel \ + | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ @@ -268,6 +279,7 @@ case $basic_machine in | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ + | moxie \ | mt \ | msp430 \ | nios | nios2 \ @@ -276,20 +288,22 @@ case $basic_machine in | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ + | rx \ | score \ - | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ + | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ + | ubicom32 \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ - | z8k) + | z8k | z80) basic_machine=$basic_machine-unknown ;; - m6811 | m68hc11 | m6812 | m68hc12) + m6811 | m68hc11 | m6812 | m68hc12 | picochip) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none @@ -329,14 +343,17 @@ case $basic_machine in | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ + | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ - | mips64vr-* | mips64vrel-* \ + | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ + | mips64r5900-* | mips64r5900el-* \ + | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ @@ -357,21 +374,23 @@ case $basic_machine in | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ - | romp-* | rs6000-* \ - | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | romp-* | rs6000-* | rx-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tile-* | tilegx-* \ | tron-* \ + | ubicom32-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ - | z8k-*) + | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) @@ -439,6 +458,10 @@ case $basic_machine in basic_machine=m68k-apollo os=-bsd ;; + aros) + basic_machine=i386-pc + os=-aros + ;; aux) basic_machine=m68k-apple os=-aux @@ -455,10 +478,18 @@ case $basic_machine in basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; + bluegene*) + basic_machine=powerpc-ibm + os=-cnk + ;; c90) basic_machine=c90-cray os=-unicos ;; + cegcc) + basic_machine=arm-unknown + os=-cegcc + ;; convex-c1) basic_machine=c1-convex os=-bsd @@ -526,6 +557,10 @@ case $basic_machine in basic_machine=m88k-motorola os=-sysv3 ;; + dicos) + basic_machine=i686-pc + os=-dicos + ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp @@ -699,6 +734,9 @@ case $basic_machine in basic_machine=ns32k-utek os=-sysv ;; + microblaze) + basic_machine=microblaze-xilinx + ;; mingw32) basic_machine=i386-pc os=-mingw32 @@ -1049,6 +1087,11 @@ case $basic_machine in basic_machine=tic6x-unknown os=-coff ;; + # This must be matched before tile*. + tilegx*) + basic_machine=tilegx-unknown + os=-linux-gnu + ;; tile*) basic_machine=tile-unknown os=-linux-gnu @@ -1128,6 +1171,10 @@ case $basic_machine in basic_machine=z8k-unknown os=-sim ;; + z80-*-coff) + basic_machine=z80-unknown + os=-sim + ;; none) basic_machine=none-none os=-none @@ -1166,7 +1213,7 @@ case $basic_machine in we32k) basic_machine=we32k-att ;; - sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) @@ -1216,6 +1263,9 @@ case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. + -auroraux) + os=-auroraux + ;; -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; @@ -1236,10 +1286,11 @@ case $os in # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ - | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ - | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \ + | -sym* | -kopensolaris* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ - | -aos* \ + | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ @@ -1248,7 +1299,7 @@ case $os in | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ - | -chorusos* | -chorusrdb* \ + | -chorusos* | -chorusrdb* | -cegcc* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ @@ -1258,7 +1309,7 @@ case $os in | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ - | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) + | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*) # Remember, each alternative MUST END IN *, to match a version number. ;; -qnx*) @@ -1388,6 +1439,11 @@ case $os in -zvmoe) os=-zvmoe ;; + -dicos*) + os=-dicos + ;; + -nacl*) + ;; -none) ;; *) @@ -1585,7 +1641,7 @@ case $basic_machine in -sunos*) vendor=sun ;; - -aix*) + -cnk*|-aix*) vendor=ibm ;; -beos*) diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index c5acafe..679f8a1 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -2372,7 +2372,6 @@ test -n "$target_alias" && NONENONEs,x,x, && program_prefix=${target_alias}- - am__api_version='1.11' # Find a good install program. We prefer a C program (faster), diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index b5b456b..ef1ddde 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -1,8 +1,8 @@ dnl Process this file with autoconf to produce a configure script. -dnl AC_PREREQ(1.8) +dnl AC_PREREQ([2.67]) dnl AC 2.62 needed for OpenMP -AC_PREREQ(2.62) +AC_PREREQ([2.67]) dnl AC_INIT (package, version, [bug-report-email], [tarname]) AC_INIT([gtfold],[1.18]) @@ -12,11 +12,11 @@ dnl specified by --srcdir is the right one AC_CONFIG_SRCDIR([README]) dnl Specify a header configuration file -AM_CONFIG_HEADER(gtfold_config.h) +AC_CONFIG_HEADERS([gtfold_config.h]) dnl Compute the canonical host-system type variable, host, and its dnl three individual parts host_cpu, host_vendor, and host_os. -AC_CANONICAL_SYSTEM +AC_CANONICAL_TARGET dnl Initialize Automake AM_INIT_AUTOMAKE @@ -62,7 +62,7 @@ dnl Check for libraries AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present])) dnl Check for header files -AC_STDC_HEADERS +AC_HEADER_STDC #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) AC_CHECK_HEADERS([stdlib.h string.h sys/time.h]) @@ -101,25 +101,21 @@ dnl are not a part of the standard Autoconf tests: If Sun cc is present, define appropriate compiler flags AC_MSG_CHECKING(for Sun C compiler) -AC_TRY_COMPILE([], [#ifndef __SUNPRO_C +AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C #include "error: this is not a Sun C compiler." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sunpro_cc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sunpro_cc=no]) if test "$gtfold_cv_check_sunpro_cc" == "yes"; then AC_MSG_CHECKING(for Sun C compiler architecture target) - AC_TRY_COMPILE([], [#ifndef __sparc + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc #include "error: this is not a Sun Sparc processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparc=no]) fi @@ -128,13 +124,11 @@ then if test "$gtfold_cv_check_sun_sparc" == "yes"; then AC_MSG_CHECKING(for Sun sparc v9 architecture) - AC_TRY_COMPILE([], [#ifndef __sparcv9 + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9 #include "error: this is not a Sun Sparc V9 processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparcv9=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparcv9=no]) fi fi diff --git a/gtfold-mfe/depcomp b/gtfold-mfe/depcomp old mode 100644 new mode 100755 index e5f9736..df8eea7 --- a/gtfold-mfe/depcomp +++ b/gtfold-mfe/depcomp @@ -1,10 +1,10 @@ #! /bin/sh # depcomp - compile a program generating dependencies as side-effects -scriptversion=2007-03-29.01 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software -# Foundation, Inc. +# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free +# Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -17,9 +17,7 @@ scriptversion=2007-03-29.01 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then depmode=dashmstdout fi +cygpath_u="cygpath -u -f -" +if test "$depmode" = msvcmsys; then + # This is just like msvisualcpp but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u="sed s,\\\\\\\\,/,g" + depmode=msvisualcpp +fi + case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what @@ -192,14 +199,14 @@ sgi) ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' -' ' ' >> $depfile - echo >> $depfile +' ' ' >> "$depfile" + echo >> "$depfile" # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ - >> $depfile + >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile @@ -328,7 +335,12 @@ hp2) if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" # Add `dependent.h:' lines. - sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile" + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi @@ -404,7 +416,7 @@ dashmstdout) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -455,32 +467,39 @@ makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift fi # X makedepend shift - cleared=no - for arg in "$@"; do + cleared=no eat=no + for arg + do case $cleared in no) set ""; shift cleared=yes ;; esac + if test $eat = yes; then + eat=no + continue + fi case "$arg" in -D*|-I*) set fnord "$@" "$arg"; shift ;; # Strip any option that makedepend may not understand. Remove # the object too, otherwise makedepend will parse it as a source file. + -arch) + eat=yes ;; -*|$object) ;; *) set fnord "$@" "$arg"; shift ;; esac done - obj_suffix="`echo $object | sed 's/^.*\././'`" + obj_suffix=`echo "$object" | sed 's/^.*\././'` touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" @@ -500,7 +519,7 @@ cpp) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -538,13 +557,27 @@ cpp) msvisualcpp) # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o, - # because we must use -o when running libtool. + # always write the preprocessed file to stdout. "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + IFS=" " for arg do case "$arg" in + -o) + shift + ;; + $object) + shift + ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift @@ -557,16 +590,23 @@ msvisualcpp) ;; esac done - "$@" -E | - sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + none) exec "$@" ;; @@ -585,5 +625,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index ee1eb98..a03865e 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,3 @@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index 3565a69..44a1859 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -155,7 +155,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-paritition.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h CLEANFILES = *~ all: all-am diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h index b45d656..77c2377 100644 --- a/gtfold-mfe/include/algorithms-partition.h +++ b/gtfold-mfe/include/algorithms-partition.h @@ -5,8 +5,14 @@ #ifdef __cplusplus extern "C" { #endif - - +/* +typedef struct _pFuncData { + int len; + double** QB; + double** Q; + double** QM; +} p_func_data; +*/ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM); void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P); void printBasePairProbabilities(int n, int *structure, double **P); @@ -16,14 +22,6 @@ double probabilityUnpaired(int length, int i, double **P); double **mallocTwoD(int r, int c); void freeTwoD(double** arr, int r, int c); -typedef struct _pFuncData { - int len; - double** QB; - double** Q; - double** QM; - - // TODO: probability function stuff here -} pFuncData; #ifdef __cplusplus diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h index e483aa1..1fb8a3b 100644 --- a/gtfold-mfe/include/partition-dangle.h +++ b/gtfold-mfe/include/partition-dangle.h @@ -14,6 +14,7 @@ typedef struct partition_d{ }dangle_struct; double cond_dangle(int j, int h, int l); +dangle_struct malloc_partition_arrays_d(int len); void fill_partition_arrays_d(dangle_struct part_struct); #endif diff --git a/gtfold-mfe/install-sh b/gtfold-mfe/install-sh index a5897de..6781b98 100755 --- a/gtfold-mfe/install-sh +++ b/gtfold-mfe/install-sh @@ -1,7 +1,7 @@ #!/bin/sh # install - install a program, script, or datafile -scriptversion=2006-12-25.00 +scriptversion=2009-04-28.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the @@ -515,5 +515,6 @@ done # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/missing b/gtfold-mfe/missing old mode 100644 new mode 100755 index 1c8ff70..28055d2 --- a/gtfold-mfe/missing +++ b/gtfold-mfe/missing @@ -1,10 +1,10 @@ #! /bin/sh # Common stub for a few missing GNU programs while installing. -scriptversion=2006-05-10.23 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006 -# Free Software Foundation, Inc. +# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006, +# 2008, 2009 Free Software Foundation, Inc. # Originally by Fran,cois Pinard , 1996. # This program is free software; you can redistribute it and/or modify @@ -18,9 +18,7 @@ scriptversion=2006-05-10.23 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -89,6 +87,9 @@ Supported PROGRAM values: tar try tar, gnutar, gtar, then tar without non-portable flags yacc create \`y.tab.[ch]', if possible, from existing .[ch] +Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and +\`g' are ignored when checking the name. + Send bug reports to ." exit $? ;; @@ -106,15 +107,22 @@ Send bug reports to ." esac +# normalize program name to check for. +program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + # Now exit if we have it, but it failed. Also exit now if we # don't have it and --version was passed (most likely to detect -# the program). +# the program). This is about non-GNU programs, so use $1 not +# $program. case $1 in - lex|yacc) + lex*|yacc*) # Not GNU programs, they don't have --version. ;; - tar) + tar*) if test -n "$run"; then echo 1>&2 "ERROR: \`tar' requires --run" exit 1 @@ -138,7 +146,7 @@ esac # If it does not exist, or fails to run (possibly an outdated version), # try to emulate it. -case $1 in +case $program in aclocal*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if @@ -148,7 +156,7 @@ WARNING: \`$1' is $msg. You should only need it if touch aclocal.m4 ;; - autoconf) + autoconf*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`${configure_ac}'. You might want to install the @@ -157,7 +165,7 @@ WARNING: \`$1' is $msg. You should only need it if touch configure ;; - autoheader) + autoheader*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`acconfig.h' or \`${configure_ac}'. You might want @@ -187,7 +195,7 @@ WARNING: \`$1' is $msg. You should only need it if while read f; do touch "$f"; done ;; - autom4te) + autom4te*) echo 1>&2 "\ WARNING: \`$1' is needed, but is $msg. You might have modified some files without having the @@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg. fi ;; - bison|yacc) + bison*|yacc*) echo 1>&2 "\ WARNING: \`$1' $msg. You should only need it if you modified a \`.y' file. You may need the \`Bison' package @@ -240,7 +248,7 @@ WARNING: \`$1' $msg. You should only need it if fi ;; - lex|flex) + lex*|flex*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.l' file. You may need the \`Flex' package @@ -263,7 +271,7 @@ WARNING: \`$1' is $msg. You should only need it if fi ;; - help2man) + help2man*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a dependency of a manual page. You may need the @@ -277,11 +285,11 @@ WARNING: \`$1' is $msg. You should only need it if else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" - exit 1 + exit $? fi ;; - makeinfo) + makeinfo*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file @@ -310,7 +318,7 @@ WARNING: \`$1' is $msg. You should only need it if touch $file ;; - tar) + tar*) shift # We have already tried tar in the generic part. @@ -363,5 +371,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po index 73ec5ce..64c9b68 100644 --- a/gtfold-mfe/src/.deps/main.Po +++ b/gtfold-mfe/src/.deps/main.Po @@ -94,11 +94,12 @@ main.o: main.cc /usr/include/c++/4.5/iostream \ /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \ ../include/utils.h ../include/loader.h ../include/data.h \ ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \ - ../include/energy.h ../include/algorithms.h ../include/constraints.h \ - ../include/traceback.h ../include/subopt_traceback.h \ - /usr/include/c++/4.5/cassert /usr/include/assert.h \ - /usr/include/c++/4.5/stack /usr/include/c++/4.5/deque \ - /usr/include/c++/4.5/bits/stl_deque.h \ + ../include/energy.h ../include/algorithms.h \ + ../include/algorithms-partition.h ../include/partition-dangle.h \ + ../include/constraints.h ../include/traceback.h \ + ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \ + /usr/include/assert.h /usr/include/c++/4.5/stack \ + /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_deque.h \ /usr/include/c++/4.5/bits/deque.tcc \ /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \ /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \ @@ -404,6 +405,10 @@ main.o: main.cc /usr/include/c++/4.5/iostream \ ../include/algorithms.h: +../include/algorithms-partition.h: + +../include/partition-dangle.h: + ../include/constraints.h: ../include/traceback.h: diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile index 8d533f1..e7c9193 100644 --- a/gtfold-mfe/src/Makefile +++ b/gtfold-mfe/src/Makefile @@ -190,8 +190,8 @@ gtfold_SOURCES = \ constraints.cc\ global.c\ energy.c\ - algorithms.c \ - traceback.c \ + algorithms.c\ + traceback.c\ subopt_traceback.cc\ algorithms-partition.c\ partition-dangle.c\ diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index aaa9481..428951a 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -13,8 +13,8 @@ gtfold_SOURCES = \ constraints.cc\ global.c\ energy.c\ - algorithms.c \ - traceback.c \ + algorithms.c\ + traceback.c\ subopt_traceback.cc\ algorithms-partition.c\ partition-dangle.c\ diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index 8b6d90d..e8e0471 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -190,8 +190,8 @@ gtfold_SOURCES = \ constraints.cc\ global.c\ energy.c\ - algorithms.c \ - traceback.c \ + algorithms.c\ + traceback.c\ subopt_traceback.cc\ algorithms-partition.c\ partition-dangle.c\ diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index 1ed7895..77e4fdf 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -30,7 +30,9 @@ * @param QM Matrix * */ -void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { + + +void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { // multiConst[3] is a global variable with 3 values: a, b, c for the // experimental constants diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 6394068..c970d59 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -36,6 +36,8 @@ #include "global.h" #include "energy.h" #include "algorithms.h" +#include "algorithms-partition.h" +#include "partition-dangle.h" #include "constraints.h" #include "traceback.h" #include "subopt_traceback.h" @@ -259,5 +261,28 @@ int main(int argc, char** argv) { // release the malloc'd arrays free_fold(seq.length()); + if(BPP_ENABLED){ + printf("Calculating partition function\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + fillBasePairProbabilities(seq.length(), structure, Q, QB, QM, P); + printBasePairProbabilities(seq.length(), structure, P); + + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } +/* + dangle_struct partition; + partition = malloc_partition_arrays_d(seq.length()); + fill_partition_arrays_d(partition); + printf("Done with the partition functioni.\n"); +*/ return EXIT_SUCCESS; } diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc index ff53afa..c336b68 100644 --- a/gtfold-mfe/src/random-sample.cc +++ b/gtfold-mfe/src/random-sample.cc @@ -18,12 +18,12 @@ using namespace std; //gives me a link error it should get this function //from partition-dangle -double cond_dangle(int j, int h, int l){ +/*double cond_dangle(int j, int h, int l){ if(j - 1 == l) return 1; else return exp(-Ed3(h,l,l+1)/RT); -} +}*/ double randdouble(){ return rand()/(double(RAND_MAX)+1); From b491b38e5c5095c46bd2acf0b10dcbd0e15b3211 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:09:56 -0400 Subject: [PATCH 047/187] added new macro --- gtfold-mfe/include/utils.h | 1 + 1 file changed, 1 insertion(+) diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h index dbe0fa7..8b33655 100644 --- a/gtfold-mfe/include/utils.h +++ b/gtfold-mfe/include/utils.h @@ -7,6 +7,7 @@ #define MIN(X,Y) ((X) < (Y) ? (X) : (Y)) #define MAX(X,Y) ((X) > (Y) ? (X) : (Y)) #define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z)) +#define MIN3(W,X,Y) MIN(MIN(W,X),Y) char baseToDigit(const char* base) ; unsigned char encode(char base); From 265ac33c2db2f6255ccb6db848faadf3ebed3e8f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:14:28 -0400 Subject: [PATCH 048/187] added new macro --- gtfold-mfe/include/data.h | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/gtfold-mfe/include/data.h b/gtfold-mfe/include/data.h index d88382f..c0875eb 100644 --- a/gtfold-mfe/include/data.h +++ b/gtfold-mfe/include/data.h @@ -59,6 +59,11 @@ extern int init; extern int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ extern float prelog; +extern int tstackm[5][5][6][6]; +extern int tstacke[5][5][6][6]; +extern int tstacki23[5][5][5][5]; + + #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d)) #endif From f192620c4fa87055a4576b4d0498ee7f95d2d42d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:17:05 -0400 Subject: [PATCH 049/187] added -m option --- gtfold-mfe/include/options.h | 1 + gtfold-mfe/src/options.cc | 4 ++++ 2 files changed, 5 insertions(+) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index ec0ff7f..0862b03 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -19,6 +19,7 @@ extern bool CONS_ENABLED; extern bool VERBOSE; extern bool SHAPE_ENABLED; extern bool PARAM_DIR; +extern bool T_MISMATCH; extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 76cbe44..1545f60 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -14,6 +14,7 @@ bool SUBOPT_ENABLED; bool CONS_ENABLED = false; bool VERBOSE = false; bool SHAPE_ENABLED = false; +bool T_MISMATCH = false; string seqfile = ""; string constraintsFile = ""; @@ -41,6 +42,7 @@ void help() { printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); + printf(" -m enable terminal mismatch calculations\n"); printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); printf(" -t, --threads num Limit number of threads used\n"); @@ -100,6 +102,8 @@ void parse_options(int argc, char** argv) { } else help(); + } else if (strcmp(argv[i], "-m") == 0) { + T_MISMATCH = true; } else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { if(i < argc) From 4c9b019122d63aa205119c5ffa42fabfc0bbac70 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:18:40 -0400 Subject: [PATCH 050/187] added energy functions to support unafold mode --- gtfold-mfe/include/energy.h | 5 +- gtfold-mfe/src/energy.c | 151 ++++++++++++++++++++++++++---------- 2 files changed, 113 insertions(+), 43 deletions(-) diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index 5b7b5cc..7ccf999 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -10,7 +10,7 @@ extern int *VM; extern int **WM; extern int **WMPrime; extern int *indx; - +extern int **PP; #define V(i,j) V[indx[j]+i] #define VM(i,j) VM[indx[j]+i] @@ -36,6 +36,9 @@ int auPenalty(int i, int j); int eS(int i, int j); int eH(int i, int j); int eL(int i, int j, int ip, int jp); +int eL1(int i, int j, int ip, int jp); +int Estackm(int i, int j); +int Estacke(int i, int j); void create_tables(int len); void init_tables(int len); diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 9450f92..985d47a 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -15,6 +15,7 @@ int *VM; int **WM; int **WMPrime; int *indx; +int **PP; int alloc_flag = 0; @@ -39,7 +40,20 @@ void create_tables(int len) { } } - WMPrime = (int **) malloc((len+1)* sizeof(int *)); + PP = (int **) malloc((len+1)* sizeof(int *)); + if (PP == NULL) { + perror("Cannot allocate variable 'WM'"); + exit(-1); + } + for (i = 0; i <= len; i++) { + PP[i] = (int *)malloc((len+1)* sizeof(int)); + if (PP[i] == NULL) { + perror("Cannot allocate variable 'WM[i]'"); + exit(-1); + } + } + + WMPrime = (int **) malloc((len+1)* sizeof(int *)); if (WMPrime == NULL) { perror("Cannot allocate variable 'WM'"); exit(-1); @@ -90,7 +104,8 @@ void init_tables(int len) { for (j = 0; j <= len; j++) { WM[i][j] = INFINITY_; WMPrime[i][j] = INFINITY_; - } + PP[i][j] = 0; + } } LLL = (len)*(len+1)/2 + 1; @@ -129,6 +144,67 @@ inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];} inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; } inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);} +inline int eL1(int i, int j, int ii, int jj) { + int loopSize1, loopSize2; + int loopEnergy, asPenalty; + + loopSize1 = ii - i - 1; + loopSize2 = j - jj - 1; + if (loopSize1 + loopSize2 > MAXLOOP) + return INFINITY_; + + if (loopSize1 == 0) { + if (loopSize2 == 1) + return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])]; + else if (loopSize2 <= 30) + return bulge[loopSize2] + auPenalty(i, j) + auPenalty(ii, jj); + else + return bulge[30] + (int)floor(prelog*log((double) loopSize2 / 30)) + auPenalty(i, j) + auPenalty(ii, jj); + } + else if (loopSize2 == 0) { + if (loopSize1 == 1) + return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])]; + else if (loopSize1 <= 30) + return bulge[loopSize1] + auPenalty(i, j) + auPenalty(ii, jj); + else + return bulge[30] + (int)floor(prelog* log((double) loopSize1 / 30)) + auPenalty(i, j) + auPenalty(ii, jj); + } + else if (loopSize1 == 1 && loopSize2 == 1) + return iloop11[RNA[i]][RNA[i + 1]][RNA[ii]][RNA[j]][RNA[j - 1]][RNA[jj]]; + else if (loopSize1 == 1 && loopSize2 == 2) + return iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ii]][RNA[jj]]; + else if (loopSize1 == 2 && loopSize2 == 1) + return iloop21[RNA[jj]][RNA[ii]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + else if (loopSize1 == 2 && loopSize2 == 2) + return iloop22[RNA[i]][RNA[ii]][RNA[j]][RNA[jj]][RNA[i+1]][RNA[i+2]][RNA[j-1]][RNA[j-2]]; + else if ((loopSize1 == 2 && loopSize2 == 3) || + (loopSize1 == 3 && loopSize2 == 2)) { + return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + tstacki23[RNA[jj]][RNA[ii]][RNA[jj + 1]][RNA[ii - 1]]; + } + else { + if (loopSize1 + loopSize2 <= 30) + loopEnergy = inter[loopSize1 + loopSize2]; + else + loopEnergy = inter[30] + (int)floor(prelog* log((double) (loopSize1 + loopSize2) / 30)); + + if (gail && (loopSize1 == 1 || loopSize2 == 1)) { + loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]; + loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], BASE_A, BASE_A)]; + } + else { + loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]; + loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], RNA[jj + 1], RNA[ii - 1])]; + } + asPenalty = abs(loopSize1 - loopSize2)*poppen[MIN3(2, loopSize1, loopSize2) - 1]; + asPenalty = MIN(asPenalty, maxpen); + + loopEnergy += asPenalty; + + return loopEnergy; + } +} + inline int eL(int i, int j, int ip, int jp) { int energy; int size1, size2, size; @@ -165,53 +241,36 @@ inline int eL(int i, int j, int ip, int jp) { if (size > 30) { loginc = (int) floor(prelog * log((double) size / 30.0)); - /* Please check what should be the difference in the following two options. Is it correct?*/ if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ - energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp - + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3] - + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, - size2))])); + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, - BASE_A)] + inter[30] + loginc - + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } } - /* if size is not > 30, we have a looooot of cases... */ - else if (size1 == 2 && size2 == 2) { - /* 2x2 internal loop */ - energy - = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i - + 2]][RNA[j - 1]][RNA[j - 2]]; + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; + if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy); } else if (size1 == 1 && size2 == 2) { - energy - = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; - } else if (size1 == 2 && size2 == 1) { - /* 1x2 internal loop */ - energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i - + 1]][RNA[j]][RNA[i]]; - } else if (size == 2) { - /* 1*1 internal loops */ - energy - = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; - } else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ - energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] - + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + } + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } else { /* General Internal loops */ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], - RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], - RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] - + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */ - + MIN(maxpen, - (lopsided * poppen[MIN(2, MIN(size1, size2))])); /* */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } } @@ -331,3 +390,11 @@ inline int eS(int i, int j) { return energy; } + +inline int Estackm(int i, int j) { + return tstackm[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} + +inline int Estacke(int i, int j) { + return tstacke[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} From 7ff348f3cc6fe9eee24f7b7d00a77b6467b7aa95 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:22:08 -0400 Subject: [PATCH 051/187] added function to load tstacke tstackm tstacki23 enegery values --- gtfold-mfe/include/loader.h | 5 +- gtfold-mfe/src/loader.cc | 182 +++++++++++++++++++++++++++++++----- 2 files changed, 163 insertions(+), 24 deletions(-) diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index f8fdc78..c7eff12 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -25,7 +25,7 @@ #include "constants.h" #include "data.h" -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic); +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch); int initStackValues(const std::string& fileName, const std::string& dirPath); int initMiscloopValues(const std::string& fileName, const std::string& dirPath); @@ -37,6 +37,9 @@ int initTloopValues(const std::string& fileName, const std::string& dirPath); int initInt21Values(const std::string& fileName, const std::string& dirPath); int initInt22Values(const std::string& fileName, const std::string& dirPath); int initInt11Values(const std::string& fileName, const std::string& dirPath); +int initTstkmValues(const std::string& fileName, const std::string& dirPath); +int initTstkeValues(const std::string& fileName, const std::string& dirPath); +int initTstk23Values(const std::string& fileName, const std::string& dirPath); extern std::string EN_DATADIR; diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index c68ee22..66e0ff0 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -34,7 +34,6 @@ #define xstr(s) str(s) #define str(s) #s -//#define GENBIN 1 using namespace std; @@ -53,14 +52,20 @@ int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */ int tloop[maxtloop + 1][2]; int numoftloops; -int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */ +int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */ -int coax[6][6][6][6]; -int tstackcoax[6][6][6][6]; -int coaxstack[6][6][6][6]; -int tstack[6][6][6][6]; -int tstkm[6][6][6][6]; + +//int coax[6][6][6][6]; +//int tstackcoax[6][6][6][6]; +//int coaxstack[6][6][6][6]; +//int tstack[6][6][6][6]; +//int tstkm[6][6][6][6]; + +int tstackm[5][5][6][6]; +int tstacke[5][5][6][6]; +int tstacki23[5][5][5][5]; + int auend; int gubonus; int cint; /* cint, cslope, c3 are used for poly C hairpin loops */ @@ -75,7 +80,7 @@ int init; int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ float prelog; -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch=0) { if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; @@ -96,9 +101,19 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { initTstkhValues("tstackh.DAT", EN_DATADIR); initTstkiValues("tstacki.DAT", EN_DATADIR); initTloopValues("tloop.DAT", EN_DATADIR); - initInt21Values("int21.DAT", EN_DATADIR); - initInt22Values("int22.DAT", EN_DATADIR); - initInt11Values("int11.DAT", EN_DATADIR); + + if (t_mismatch) { + initInt21Values("asint1x2.DAT", EN_DATADIR); + initInt22Values("sint4.DAT", EN_DATADIR); + initInt11Values("sint2.DAT", EN_DATADIR); + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initTstk23Values("tstacki23.DAT", EN_DATADIR); + } else { + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + } } int initStackValues(const string& fileName, const string& dirPath) { @@ -111,7 +126,7 @@ int initStackValues(const string& fileName, const string& dirPath) { for (int i = 0; i < 4; i++) { for (int j = 0; j < 4; j++) { for (int k = 0; k < 4; k++) { - for (int l = 0; l < 2; l++) { + for (int l = 0; l < 4; l++) { stack[fourBaseIndex(i,j,k,l)] = INFINITY_; } } @@ -309,7 +324,7 @@ int initLoopValues( const string& fileName, const string& dirPath) { int tempValue = 0; if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } @@ -343,6 +358,119 @@ int initLoopValues( const string& fileName, const string& dirPath) { return 0; } +int initTstk23Values(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + if (cf.fail()) { + cerr << "File open failed " << filePath << endl; + exit(-1); + } + + for (i1 = 0; i1 < 5; ++i1) + for (i2 = 0; i2 < 5; ++i2) + for (j1 = 0; j1 < 5; ++j1) + for (j2 = 0; j2 < 5; ++j2) + if (i1 == 4 || j1 == 4) + tstacki23[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacki23[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacki23[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + cf.close(); + + return 0; +} + + + + +int initTstkeValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + if (cf.fail()) { + cerr << "File open failed " << filePath << endl; + exit(-1); + } + + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacke[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacke[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + } + } + } + } + + cf.close(); + + return 0; +} + +int initTstkmValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + if (cf.fail()) { + cerr << "File open failed " << filePath << endl; + exit(-1); + } + + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstackm[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstackm[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + } + } + } + } + + cf.close(); + + return 0; +} + int initTstkhValues(const std::string& fileName, const std::string& dirPath) { std::string filePath; std::ifstream cf; @@ -476,9 +604,11 @@ int initTloopValues(const std::string& fileName, const std::string& dirPath) { currentValue[count] = currentLine[count + clindex]; count++; } - + tloop[numoftloops][0] = (int) atoi(currentSeqNumbers); - tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); + + if (!(strcmp(currentValue,"inf")==0)) + tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); } cf.close(); return 0; @@ -510,7 +640,7 @@ int initInt22Values(const std::string& fileName, const std::string& dirPath) { string filePath = dirPath + fileName; cf.open(filePath.c_str(), ios::in); if (!cf.good()) { - cerr << "File open failed " << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } @@ -556,8 +686,9 @@ int initInt22Values(const std::string& fileName, const std::string& dirPath) { l = ((colIndex - 1) - (colIndex - 1) % 4) / 4; m = (colIndex - 1) % 4; - iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] - = (int) floor(100.0 * atof(currentValue) + 0.5); + if (!(strcmp(currentValue,"inf")==0)) + iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] + = (int) floor(100.0 * atof(currentValue) + 0.5); } } } @@ -617,7 +748,7 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) { std::string filePath = dirPath + fileName; cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed" << filePath << endl; exit(-1); } @@ -646,8 +777,8 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) { c = k; e = j; - iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] - = temp; + if (!(strcmp(value,"inf")==0)) + iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] = temp; r++; if (r % 4 == 0) jj++; d++; @@ -663,6 +794,7 @@ int initInt21Values(const std::string& fileName, const std::string& dirPath) { return 0; } + int initInt11Values(const std::string& fileName, const std::string& dirPath) { int i, j, k, r, q, t; @@ -685,7 +817,7 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) { std::string filePath = dirPath + fileName; cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } @@ -729,7 +861,10 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) { d = base2[k]; c = base1[jj]; f = base2[jj]; - iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; + + if (!(strcmp(value,"inf")==0)) + iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; + r++; if (r % 4 == 0) jj++; e++; @@ -740,5 +875,6 @@ int initInt11Values(const std::string& fileName, const std::string& dirPath) { } cf.close(); + return 0; } From e0ab3434577a985c29871cca3fe9248374a74e9b Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:26:55 -0400 Subject: [PATCH 052/187] added change to handle unafold mode --- gtfold-mfe/src/main.cc | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 2c56804..18489d1 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -169,11 +169,18 @@ void print_header() { * @param outputFile The file to save to * @param energy The MFE energy (multiplied by 100) */ -void save_ct_file(string outputFile, string seq, int energy) { +void save_ct_file(string outputFile, string seq, int energy, string seqfile) { + if(seqfile.find("/") != string::npos) { + size_t pos = seqfile.find_last_of("/"); + seqfile.erase(0,pos+1); + } + if(seqfile.find(".") != string::npos) + seqfile.erase(seqfile.rfind(".")); ofstream outfile; outfile.open(outputFile.c_str()); outfile << seq.length() << "\t dG = " << energy/100.0 << endl; + //outfile << seq.length() << "\tdG = " << energy/100.0 << "\t" << seqfile << endl; unsigned int i = 1; for(i=1; i <= seq.length(); i++) @@ -197,7 +204,7 @@ int main(int argc, char** argv) { } // Read in thermodynamic parameters. Always use Turner99 data (for now) - readThermodynamicParameters(paramDir.c_str(), PARAM_DIR); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, T_MISMATCH); printRunConfiguration(seq); @@ -207,7 +214,7 @@ int main(int argc, char** argv) { fflush(stdout); t1 = get_seconds(); - energy = calculate(seq.length(), nThreads); + energy = calculate(seq.length(), nThreads, T_MISMATCH); t1 = get_seconds() - t1; printf("Done.\n\n"); @@ -227,7 +234,7 @@ int main(int argc, char** argv) { } t1 = get_seconds(); - trace(seq.length(), VERBOSE); + trace(seq.length(), VERBOSE, T_MISMATCH); t1 = get_seconds() - t1; printf("\n"); @@ -241,7 +248,7 @@ int main(int argc, char** argv) { print_shapeArray(seq.length()); - save_ct_file(outputFile, seq, energy); + save_ct_file(outputFile, seq, energy,seqfile); printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); From 2ed0a6459b6d4b903687a5f0164ab01957d74ae9 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:29:29 -0400 Subject: [PATCH 053/187] added changes to handle unafold mode --- gtfold-mfe/include/algorithms.h | 2 +- gtfold-mfe/include/traceback.h | 2 +- gtfold-mfe/src/algorithms.c | 215 ++++++++++++++++++++++++-------- gtfold-mfe/src/traceback.c | 213 +++++++++++++++++-------------- 4 files changed, 283 insertions(+), 149 deletions(-) diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h index 336e443..9b3dee0 100644 --- a/gtfold-mfe/include/algorithms.h +++ b/gtfold-mfe/include/algorithms.h @@ -23,7 +23,7 @@ #ifdef __cplusplus extern "C" { #endif - int calculate(int len, int nThreads); + int calculate(int len, int nThreads, int t_mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h index a8bd6c4..47a4f19 100644 --- a/gtfold-mfe/include/traceback.h +++ b/gtfold-mfe/include/traceback.h @@ -26,7 +26,7 @@ #ifdef __cplusplus extern "C" { #endif - void trace(int len, int vbose); + void trace(int len, int vbose, int t_mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 0fd0c72..4bf8cc0 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -29,7 +29,79 @@ along with this program. If not, see . #ifdef _OPENMP #include "omp.h" #endif -int calculate(int len, int nThreads) { + +//#define DEBUG 1 + +void initializeMatrix(int len) { + int i, j; + + for (i = 1; i <= len; ++i) + for (j = len; j >= i; --j) + if (canPair(RNA[i],RNA[j]) && j-i >= TURN) + PP[i][j] = 1; +} + +void prefilter(int len, int prefilter1, int prefilter2) { + char** in; + int i, j, k, count; + + in = (char**)malloc(len*sizeof(char*)); + for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char)); + + for (i = 1; i <= len - prefilter2 + 1; ++i) + for (j = len; j >= prefilter2 && j >= i; --j) { + count = 0; + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + if (PP[i + k][j - k] == 1) ++count; + if (count >= prefilter1) + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + ++in[i + k - 1][j - k - 1]; + } + + for (i = 1; i <= len; ++i) { + for (j = len; j >= i; --j) + if (!in[i - 1][j - 1]) PP[i][j] = 0; + free(in[i - 1]); + } + + free(in); +} + +int calcVBI(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; +} + +int calcVBI2(int i, int j, int len) { + int d, ii, jj; + int energy = INFINITY_; + + for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) + for (ii = i + 1; ii < j - d && ii <= len; ++ii) + { + jj = d + ii; + if (PP[ii][jj]==1) + energy = MIN(energy, eL(i, j, ii, jj) + V(ii, jj)); + } + + return energy; +} + +int calculate(int len, int nThreads, int t_mismatch) { int b, i, j; #ifdef _OPENMP if (nThreads>0) omp_set_num_threads(nThreads); @@ -40,6 +112,11 @@ int calculate(int len, int nThreads) { fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif + initializeMatrix(len); + if (t_mismatch) { + prefilter(len,2,2); + } + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) @@ -47,65 +124,67 @@ int calculate(int len, int nThreads) { for (i = 1; i <= len - b; i++) { j = i + b; int newWM = INFINITY_; - if (canPair(RNA[i], RNA[j])) { + + if (PP[i][j]==1) { int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - - int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack - - if (j-i > 6) { // Internal Loop BEGIN - int p=0, q=0; - int VBIij = INFINITY_; - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==i+1)?(j-2):(j-1); - for (q = minq; q <= maxq; q++) { - if (!canPair(RNA[p], RNA[q])) continue; - if (!canILoop(i,j,p,q)) continue; - VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); - } - } - VBI(i,j) = VBIij; - V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); - } // Internal Loop END - - if (j-i > 10) { // Multi Loop BEGIN - int VMij = WMPrime[i+1][j-1]; - int VMidj = WMPrime[i+2][j-1]; - int VMijd = WMPrime[i+1][j-2]; - int VMidjd = WMPrime[i+2][j-2]; - - int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; - int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; - VMij = MIN(VMij, (VMidj + d5 +Ec)) ; - VMij = MIN(VMij, (VMijd + d3 +Ec)); + int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack + + // Internal Loop BEGIN + VBI(i,j) = calcVBI(i,j); + V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); + // Internal Loop END + + // Multi Loop BEGIN + int VMij = WMPrime[i+1][j-1]; + int VMidj = WMPrime[i+2][j-1]; + int VMijd = WMPrime[i+1][j-2]; + int VMidjd = WMPrime[i+2][j-2]; + + int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; + int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; + VMij = MIN(VMij, (VMidj + d5 +Ec)) ; + VMij = MIN(VMij, (VMijd + d3 +Ec)); + + if (t_mismatch) { + VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec)); + } else { VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); - VMij = VMij + Ea + Eb + auPenalty(i,j); - VM(i,j) = canStack(i,j)?VMij:INFINITY_; - } // Multi Loop END - - V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); + } + + VMij = VMij + Ea + Eb + auPenalty(i,j); + VM(i,j) = canStack(i,j)?VMij:INFINITY_; + // Multi Loop END + + V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); } else V(i,j) = INFINITY_; + + int h; + for (h = i+TURN+1 ; h <= j-TURN-2; h++) { + // Added auxillary storage WMPrime to speedup multiloop calculations + WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); + //newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; + } - if (j-i > 4) { // WM BEGIN - int h; - for (h = i+TURN+1 ; h <= j-TURN-1; h++) { - //ZS: This sum corresponds to when i,j are NOT paired with each other. - //So we need to make sure only terms where i,j aren't pairing are considered. - // Added auxillary storage WMPrime to speedup multiloop calculations - WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); - //newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; - } - newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; - newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle - newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle + //ZS: This sum corresponds to when i,j are NOT paired with each other. + //So we need to make sure only terms where i,j aren't pairing are considered. + newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; + + newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); + newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle + newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle + + if (t_mismatch) { + if (i Date: Thu, 16 Jun 2011 16:31:22 -0400 Subject: [PATCH 054/187] merged ZS bug fix on constraints --- gtfold-mfe/src/constraints.cc | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 45d6280..c491068 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -205,8 +205,9 @@ int init_constraints(const char* constr_file,int length) { if(nFBP != 0){ int temp; + //Make sure smallest one is first, UNLESS forcing single-stranded for(it = 0; it < nFBP; it++){ - if(FBP[it][0] > FBP[it][1]){ + if(FBP[it][0] > FBP[it][1] && FBP[it][1]!=0){ temp = FBP[it][0]; FBP[it][0] = FBP[it][1]; FBP[it][1] = temp; @@ -223,11 +224,11 @@ int init_constraints(const char* constr_file,int length) { int i1 = FBP[it][0]+k-1; int j1 = FBP[it][1]-k+1; if(FBP[it][1]!=0&&!canPair(RNA[FBP[it][0]+k-1], RNA[FBP[it][1]-k+1])){ - printf("Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); + fprintf(stderr,"Can't force (%d, %d) to pair (non-canonical) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); continue; } if(FBP[it][1]!=0&&(j1-i1 < TURN)){ - printf("Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); + fprintf(stderr,"Can't force (%d, %d) to pair (turn too tight) \n", FBP[it][0]+k-1, FBP[it][1]-k+1); continue; } if(FBP[it][1] == 0){ From 9cb4ef7ef64aa956a9505d6c3bde5467af58fc8f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:39:56 -0400 Subject: [PATCH 055/187] merged ZS changes with SHAPE --- gtfold-mfe/src/algorithms.c | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 4bf8cc0..c22da33 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -127,11 +127,10 @@ int calculate(int len, int nThreads, int t_mismatch) { if (PP[i][j]==1) { int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - int es = canStack(i,j)?eS(i,j)+getShapeEnergy(i)+getShapeEnergy(j)+V(i+1,j-1):INFINITY_; // stack + int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack // Internal Loop BEGIN VBI(i,j) = calcVBI(i,j); - V(i,j) = V(i,j) + getShapeEnergy(i) + getShapeEnergy(j); // Internal Loop END // Multi Loop BEGIN From 25b03068c2d50d282a01062de89685221c30fa5c Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 16 Jun 2011 16:40:47 -0400 Subject: [PATCH 056/187] merged ZS changes with SHAPE --- gtfold-mfe/src/shapereader.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc index 43083ab..fcbcbc5 100644 --- a/gtfold-mfe/src/shapereader.cc +++ b/gtfold-mfe/src/shapereader.cc @@ -42,7 +42,7 @@ void readSHAPEarray(const char* filename, int seqlength){ while(getline(infile,line)>0){ if(sscanf(line.c_str(), "%d %lf", &position, &SHAPEnumber)==2){ - if(position < seqlength){ + if(position <= seqlength){ SHAPEarray[position] = SHAPEnumber; SHAPEenergies[position] = calcShapeEnergy(SHAPEnumber); } From 69de0414f0d551bd4e2b22616057e4239eb25068 Mon Sep 17 00:00:00 2001 From: Andrew Ash Date: Thu, 16 Jun 2011 23:29:19 -0700 Subject: [PATCH 057/187] Accessing C declarations from C++ requires the "C" extern --- gtfold-mfe/include/partition-dangle.h | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h index 1fb8a3b..2843a60 100644 --- a/gtfold-mfe/include/partition-dangle.h +++ b/gtfold-mfe/include/partition-dangle.h @@ -1,6 +1,9 @@ #ifndef _PARTITION_DANGLE_H #define _PARTITION_DANGLE_H +#ifdef __cplusplus +extern "C" { +#endif typedef struct partition_d{ double ** u; @@ -17,4 +20,8 @@ double cond_dangle(int j, int h, int l); dangle_struct malloc_partition_arrays_d(int len); void fill_partition_arrays_d(dangle_struct part_struct); +#ifdef __cplusplus +} +#endif + #endif From 2223754819754809dbab5be0a9add615d34a625d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 17 Jun 2011 13:00:06 -0400 Subject: [PATCH 058/187] removed Makefile --- gtfold-mfe/src/Makefile | 522 ---------------------------------------- 1 file changed, 522 deletions(-) delete mode 100644 gtfold-mfe/src/Makefile diff --git a/gtfold-mfe/src/Makefile b/gtfold-mfe/src/Makefile deleted file mode 100644 index 6385554..0000000 --- a/gtfold-mfe/src/Makefile +++ /dev/null @@ -1,522 +0,0 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. -# src/Makefile. 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mostlyclean-compile \ - mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \ - uninstall-am uninstall-binPROGRAMS - - -# Tell versions [3.59,3.63) of GNU make to not export all variables. -# Otherwise a system limit (for SysV at least) may be exceeded. -.NOEXPORT: From 92625685f8f946e3b15095bca9ba597a3b18e14f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 17 Jun 2011 15:10:42 -0400 Subject: [PATCH 059/187] seperate functions eL1(), eL() to handle 2x3 internal loop --- gtfold-mfe/src/algorithms.c | 26 +++++++- gtfold-mfe/src/energy.c | 126 ++++++++++++++++++++---------------- 2 files changed, 93 insertions(+), 59 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index c22da33..6f4a314 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -86,6 +86,25 @@ int calcVBI(int i, int j) { return VBIij; } +int calcVBI1(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; +} + int calcVBI2(int i, int j, int len) { int d, ii, jj; int energy = INFINITY_; @@ -95,7 +114,7 @@ int calcVBI2(int i, int j, int len) { { jj = d + ii; if (PP[ii][jj]==1) - energy = MIN(energy, eL(i, j, ii, jj) + V(ii, jj)); + energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj)); } return energy; @@ -130,7 +149,10 @@ int calculate(int len, int nThreads, int t_mismatch) { int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack // Internal Loop BEGIN - VBI(i,j) = calcVBI(i,j); + if (t_mismatch) + VBI(i,j) = calcVBI1(i,j); + else + VBI(i,j) = calcVBI(i,j); // Internal Loop END // Multi Loop BEGIN diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 985d47a..616ad48 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -144,65 +144,76 @@ inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];} inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; } inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);} -inline int eL1(int i, int j, int ii, int jj) { - int loopSize1, loopSize2; - int loopEnergy, asPenalty; +inline int eL1(int i, int j, int ip, int jp) { + int energy; + int size1, size2, size; + int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */ + int lopsided; /* define the asymmetry of an interior loop */ - loopSize1 = ii - i - 1; - loopSize2 = j - jj - 1; - if (loopSize1 + loopSize2 > MAXLOOP) - return INFINITY_; + energy = INFINITY_; + loginc = 0; - if (loopSize1 == 0) { - if (loopSize2 == 1) - return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])]; - else if (loopSize2 <= 30) - return bulge[loopSize2] + auPenalty(i, j) + auPenalty(ii, jj); - else - return bulge[30] + (int)floor(prelog*log((double) loopSize2 / 30)) + auPenalty(i, j) + auPenalty(ii, jj); - } - else if (loopSize2 == 0) { - if (loopSize1 == 1) - return bulge[1] + stack[fourBaseIndex(RNA[i], RNA[j], RNA[ii], RNA[jj])]; - else if (loopSize1 <= 30) - return bulge[loopSize1] + auPenalty(i, j) + auPenalty(ii, jj); - else - return bulge[30] + (int)floor(prelog* log((double) loopSize1 / 30)) + auPenalty(i, j) + auPenalty(ii, jj); - } - else if (loopSize1 == 1 && loopSize2 == 1) - return iloop11[RNA[i]][RNA[i + 1]][RNA[ii]][RNA[j]][RNA[j - 1]][RNA[jj]]; - else if (loopSize1 == 1 && loopSize2 == 2) - return iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ii]][RNA[jj]]; - else if (loopSize1 == 2 && loopSize2 == 1) - return iloop21[RNA[jj]][RNA[ii]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; - else if (loopSize1 == 2 && loopSize2 == 2) - return iloop22[RNA[i]][RNA[ii]][RNA[j]][RNA[jj]][RNA[i+1]][RNA[i+2]][RNA[j-1]][RNA[j-2]]; - else if ((loopSize1 == 2 && loopSize2 == 3) || - (loopSize1 == 3 && loopSize2 == 2)) { - return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + - tstacki23[RNA[jj]][RNA[ii]][RNA[jj + 1]][RNA[ii - 1]]; - } - else { - if (loopSize1 + loopSize2 <= 30) - loopEnergy = inter[loopSize1 + loopSize2]; - else - loopEnergy = inter[30] + (int)floor(prelog* log((double) (loopSize1 + loopSize2) / 30)); - - if (gail && (loopSize1 == 1 || loopSize2 == 1)) { - loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)]; - loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], BASE_A, BASE_A)]; - } - else { - loopEnergy += tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])]; - loopEnergy += tstki[fourBaseIndex(RNA[jj], RNA[ii], RNA[jj + 1], RNA[ii - 1])]; + /*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */ + size1 = ip - i - 1; + size2 = j - jp - 1; + size = size1 + size2; + + if (size1 == 0 || size2 == 0) { + if (size > 30) { + /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */ + loginc = (int) floor(prelog * log((double) size / 30.0)); + energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j]) + + auPen(RNA[ip], RNA[jp]); + } else if (size <= 30 && size != 1) { + /* Does not depend upon i and j and ip and jp - Stacking Energies */ + energy = bulge[size] + eparam[2]; + energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); + } else if (size == 1) { + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] + + bulge[size] + eparam[2] + + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp); } - asPenalty = abs(loopSize1 - loopSize2)*poppen[MIN3(2, loopSize1, loopSize2) - 1]; - asPenalty = MIN(asPenalty, maxpen); + } else { + /* Internal loop */ + lopsided = abs(size1 - size2); - loopEnergy += asPenalty; + if (size > 30) { + loginc = (int) floor(prelog * log((double) size / 30.0)); - return loopEnergy; + if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ + + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } + } + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; + if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy); + } else if (size1 == 1 && size2 == 2) { + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + } + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* General Internal loops */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + + } } + + return energy; } inline int eL(int i, int j, int ip, int jp) { @@ -260,10 +271,11 @@ inline int eL(int i, int j, int ip, int jp) { energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; } else if (size == 2) { /* 1*1 internal loops */ energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; - } else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { - return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + - tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; - } + } + //else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + // return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + // tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + //} else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); From 92191276d372d3927a1485cb7980a0c58d73b2c0 Mon Sep 17 00:00:00 2001 From: Janderson Date: Sun, 19 Jun 2011 15:27:44 -0400 Subject: [PATCH 060/187] Pull from gtfold master --- gtfold-mfe/src/algorithms-partition.c | 30 ++++++++++++++++++++------- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index 77e4fdf..83d1a4d 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -10,6 +10,13 @@ #include "algorithms-partition.h" #include "data.h" +#ifdef _OPENMP +#include "omp.h" +#endif + + +#define DANGLE_DEBUG + // double[][] QB; // double[][] Q; // double[][] QM; @@ -58,6 +65,12 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { // fill in values in the array for(l=1; l<=len; ++l) { + //Parrallelize + #ifndef DANGLE_DEBUG + #ifdef _OPENMP + #pragma omp parallel for private (i,j) schedule(guided) + #endif + #endif for(i=1; i<= len-l+1; ++i) { int j = i+l-1; @@ -73,13 +86,16 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { for(d=i+1; d<=j-4; ++d) { for(e=d+4; e<=j-1; ++e) { - if(d == i + 1 && e == j -1) - QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; - else - QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; - - QB[i][j] += QM[i+1][d-1]*QB[d][e] * - exp(-(a + b + c*(j-e-1))/RT); + if(d == i + 1 && e == j -1){ + QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; + } + else{ + printf("i: %d j: %d d: %d e: %d\n", i,j,d,e); + QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; + } + + QB[i][j] += QM[i+1][d-1]*QB[d][e] * + exp(-(a + b + c*(j-e-1))/RT); } } } From 12b006bc6387cc2b60a0937d71fe6df0609466f0 Mon Sep 17 00:00:00 2001 From: Janderson Date: Sun, 19 Jun 2011 23:22:45 -0400 Subject: [PATCH 061/187] --bpp option re-integrated. --- gtfold-mfe/Makefile | 2 +- gtfold-mfe/data/Andronescu/Makefile | 26 ++-- gtfold-mfe/data/Makefile | 26 ++-- gtfold-mfe/data/Turner04/Makefile | 26 ++-- gtfold-mfe/data/Turner99/Makefile | 26 ++-- gtfold-mfe/include/Makefile | 162 +--------------------- gtfold-mfe/include/algorithms-partition.h | 2 +- gtfold-mfe/include/energy.h | 2 +- gtfold-mfe/src/.deps/loader.Po | 12 +- gtfold-mfe/src/algorithms-partition.c | 51 ++++--- gtfold-mfe/src/main.cc | 8 +- 11 files changed, 100 insertions(+), 243 deletions(-) diff --git a/gtfold-mfe/Makefile b/gtfold-mfe/Makefile index f791022..cdd52e6 100644 --- a/gtfold-mfe/Makefile +++ b/gtfold-mfe/Makefile @@ -214,7 +214,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile index b2fd9ef..8dc0b5c 100644 --- a/gtfold-mfe/data/Andronescu/Makefile +++ b/gtfold-mfe/data/Andronescu/Makefile @@ -71,12 +71,12 @@ am__base_list = \ am__installdirs = "$(DESTDIR)$(gtfold_datadir)" DATA = $(gtfold_data_DATA) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -103,7 +103,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -119,10 +119,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Andronescu -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Andronescu +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -150,7 +150,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Makefile b/gtfold-mfe/data/Makefile index 0331574..654058c 100644 --- a/gtfold-mfe/data/Makefile +++ b/gtfold-mfe/data/Makefile @@ -87,12 +87,12 @@ am__relativize = \ dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \ done; \ reldir="$$dir2" -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -119,7 +119,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -135,10 +135,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -166,7 +166,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -175,7 +175,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Turner04/Makefile b/gtfold-mfe/data/Turner04/Makefile index 382eac6..65f56b2 100644 --- a/gtfold-mfe/data/Turner04/Makefile +++ b/gtfold-mfe/data/Turner04/Makefile @@ -71,12 +71,12 @@ am__base_list = \ am__installdirs = "$(DESTDIR)$(gtfold_datadir)" DATA = $(gtfold_data_DATA) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -103,7 +103,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -119,10 +119,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04 -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner04 -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04 +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner04 +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -150,7 +150,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/data/Turner99/Makefile b/gtfold-mfe/data/Turner99/Makefile index 0fee0e5..abc7da4 100644 --- a/gtfold-mfe/data/Turner99/Makefile +++ b/gtfold-mfe/data/Turner99/Makefile @@ -71,12 +71,12 @@ am__base_list = \ am__installdirs = "$(DESTDIR)$(gtfold_datadir)" DATA = $(gtfold_data_DATA) DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) -ACLOCAL = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run aclocal-1.11 -AMTAR = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run tar -AUTOCONF = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoconf -AUTOHEADER = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run autoheader -AUTOMAKE = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run automake-1.11 -AWK = gawk +ACLOCAL = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run aclocal-1.11 +AMTAR = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run tar +AUTOCONF = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoconf +AUTOHEADER = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run autoheader +AUTOMAKE = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run automake-1.11 +AWK = mawk CC = gcc CCDEPMODE = depmode=gcc3 CFLAGS = -g -O2 -Wall @@ -103,7 +103,7 @@ LDFLAGS = LIBOBJS = LIBS = -lgomp LTLIBOBJS = -MAKEINFO = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/missing --run makeinfo +MAKEINFO = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/missing --run makeinfo MKDIR_P = /bin/mkdir -p OBJEXT = o OPENMP_CFLAGS = -fopenmp @@ -119,10 +119,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99 -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/data/Turner99 -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99 +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/data/Turner99 +abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe +abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -150,7 +150,7 @@ host_vendor = unknown htmldir = ${docdir} includedir = ${prefix}/include infodir = ${datarootdir}/info -install_sh = ${SHELL} /home/zs/git/gtfold/gtfold-mfe/install-sh +install_sh = ${SHELL} /home/josh/Projects/gtfold/gtfold-mfe/install-sh libdir = ${exec_prefix}/lib libexecdir = ${exec_prefix}/libexec localedir = ${datarootdir}/locale @@ -159,7 +159,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin diff --git a/gtfold-mfe/include/Makefile b/gtfold-mfe/include/Makefile index 8b19e61..596ed80 100644 --- a/gtfold-mfe/include/Makefile +++ b/gtfold-mfe/include/Makefile @@ -46,39 +46,9 @@ mkinstalldirs = $(install_sh) -d CONFIG_HEADER = $(top_builddir)/gtfold_config.h CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = -<<<<<<< HEAD -am__installdirs = "$(DESTDIR)$(bindir)" -PROGRAMS = $(bin_PROGRAMS) -am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ - options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ - energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ - partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \ - shapereader.$(OBJEXT) -gtfold_OBJECTS = $(am_gtfold_OBJECTS) -gtfold_DEPENDENCIES = -gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ - $(LDFLAGS) -o $@ -DEFAULT_INCLUDES = -I. -I$(top_builddir) -depcomp = $(SHELL) $(top_srcdir)/depcomp -am__depfiles_maybe = depfiles -am__mv = mv -f -COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) -CCLD = $(CC) -LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ -CXXCOMPILE = $(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) \ - $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CXXFLAGS) $(CXXFLAGS) -CXXLD = $(CXX) -CXXLINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(AM_LDFLAGS) $(LDFLAGS) \ - -o $@ -SOURCES = $(gtfold_SOURCES) -DIST_SOURCES = $(gtfold_SOURCES) -======= SOURCES = DIST_SOURCES = HEADERS = $(noinst_HEADERS) ->>>>>>> gtfold/master ETAGS = etags CTAGS = ctags DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST) @@ -130,17 +100,10 @@ SET_MAKE = SHELL = /bin/bash STRIP = VERSION = 1.18 -<<<<<<< HEAD -abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/src -abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/src +abs_builddir = /home/josh/Projects/gtfold/gtfold-mfe/include +abs_srcdir = /home/josh/Projects/gtfold/gtfold-mfe/include abs_top_builddir = /home/josh/Projects/gtfold/gtfold-mfe abs_top_srcdir = /home/josh/Projects/gtfold/gtfold-mfe -======= -abs_builddir = /home/zs/git/gtfold/gtfold-mfe/include -abs_srcdir = /home/zs/git/gtfold/gtfold-mfe/include -abs_top_builddir = /home/zs/git/gtfold/gtfold-mfe -abs_top_srcdir = /home/zs/git/gtfold/gtfold-mfe ->>>>>>> gtfold/master ac_ct_CC = gcc ac_ct_CXX = g++ am__include = include @@ -177,7 +140,7 @@ mandir = ${datarootdir}/man mkdir_p = /bin/mkdir -p oldincludedir = /usr/include pdfdir = ${docdir} -prefix = /home/zs/dsgtfold +prefix = /usr/local program_transform_name = s,x,x, psdir = ${docdir} sbindir = ${exec_prefix}/sbin @@ -192,33 +155,8 @@ target_vendor = unknown top_build_prefix = ../ top_builddir = .. top_srcdir = .. -<<<<<<< HEAD -INCLUDES = -I$(top_srcdir) -I$(top_srcdir)/include -AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/gtfold' -AM_CXXFLAGS = -DDATADIR='$(datadir)/gtfold' -gtfold_SOURCES = \ - main.cc\ - loader.cc\ - utils.cc\ - options.cc\ - constraints.cc\ - global.c\ - energy.c\ - algorithms.c\ - traceback.c\ - subopt_traceback.cc\ - algorithms-partition.c\ - partition-dangle.c\ - random-sample.cc\ - shapereader.cc - -gtfold_LDFLAGS = -gtfold_LDADD = -lm -CLEANFILES = *~ *.o -======= -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h CLEANFILES = *~ ->>>>>>> gtfold/master all: all-am .SUFFIXES: @@ -252,98 +190,6 @@ $(top_srcdir)/configure: $(am__configure_deps) $(ACLOCAL_M4): $(am__aclocal_m4_deps) cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh $(am__aclocal_m4_deps): -<<<<<<< HEAD -install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) - test -z "$(bindir)" || $(MKDIR_P) "$(DESTDIR)$(bindir)" - @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ - for p in $$list; do echo "$$p $$p"; done | \ - sed 's/$(EXEEXT)$$//' | \ - while read p p1; do if test -f $$p; \ - then echo "$$p"; echo "$$p"; else :; fi; \ - done | \ - sed -e 'p;s,.*/,,;n;h' -e 's|.*|.|' \ - -e 'p;x;s,.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/' | \ - sed 'N;N;N;s,\n, ,g' | \ - $(AWK) 'BEGIN { files["."] = ""; dirs["."] = 1 } \ - { d=$$3; if (dirs[d] != 1) { print "d", d; dirs[d] = 1 } \ - if ($$2 == $$4) files[d] = files[d] " " $$1; \ - else { print "f", $$3 "/" $$4, $$1; } } \ - END { for (d in files) print "f", d, files[d] }' | \ - while read type dir files; do \ - if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ - test -z "$$files" || { \ - echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ - $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ - } \ - ; done - -uninstall-binPROGRAMS: - @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; test -n "$(bindir)" || list=; \ - files=`for p in $$list; do echo "$$p"; done | \ - sed -e 'h;s,^.*/,,;s/$(EXEEXT)$$//;$(transform)' \ - -e 's/$$/$(EXEEXT)/' `; \ - test -n "$$list" || exit 0; \ - echo " ( cd '$(DESTDIR)$(bindir)' && rm -f" $$files ")"; \ - cd "$(DESTDIR)$(bindir)" && rm -f $$files - -clean-binPROGRAMS: - -test -z "$(bin_PROGRAMS)" || rm -f $(bin_PROGRAMS) -gtfold$(EXEEXT): $(gtfold_OBJECTS) $(gtfold_DEPENDENCIES) - @rm -f gtfold$(EXEEXT) - $(gtfold_LINK) $(gtfold_OBJECTS) $(gtfold_LDADD) $(LIBS) - -mostlyclean-compile: - -rm -f *.$(OBJEXT) - -distclean-compile: - -rm -f *.tab.c - -include ./$(DEPDIR)/algorithms-partition.Po -include ./$(DEPDIR)/algorithms.Po -include ./$(DEPDIR)/constraints.Po -include ./$(DEPDIR)/energy.Po -include ./$(DEPDIR)/global.Po -include ./$(DEPDIR)/loader.Po -include ./$(DEPDIR)/main.Po -include ./$(DEPDIR)/options.Po -include ./$(DEPDIR)/partition-dangle.Po -include ./$(DEPDIR)/random-sample.Po -include ./$(DEPDIR)/shapereader.Po -include ./$(DEPDIR)/subopt_traceback.Po -include ./$(DEPDIR)/traceback.Po -include ./$(DEPDIR)/utils.Po - -.c.o: - $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< - $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po -# source='$<' object='$@' libtool=no \ -# DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \ -# $(COMPILE) -c $< - -.c.obj: - $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` - $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po -# source='$<' object='$@' libtool=no \ -# DEPDIR=$(DEPDIR) $(CCDEPMODE) $(depcomp) \ -# $(COMPILE) -c `$(CYGPATH_W) '$<'` - -.cc.o: - $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< - $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po -# source='$<' object='$@' libtool=no \ -# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ -# $(CXXCOMPILE) -c -o $@ $< - -.cc.obj: - $(CXXCOMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ `$(CYGPATH_W) '$<'` - $(am__mv) $(DEPDIR)/$*.Tpo $(DEPDIR)/$*.Po -# source='$<' object='$@' libtool=no \ -# DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) \ -# $(CXXCOMPILE) -c -o $@ `$(CYGPATH_W) '$<'` -======= ->>>>>>> gtfold/master ID: $(HEADERS) $(SOURCES) $(LISP) $(TAGS_FILES) list='$(SOURCES) $(HEADERS) $(LISP) $(TAGS_FILES)'; \ diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h index 77c2377..ef55266 100644 --- a/gtfold-mfe/include/algorithms-partition.h +++ b/gtfold-mfe/include/algorithms-partition.h @@ -14,7 +14,7 @@ typedef struct _pFuncData { } p_func_data; */ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM); -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P); +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P); void printBasePairProbabilities(int n, int *structure, double **P); double probabilityUnpaired(int length, int i, double **P); diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index 026a26a..f742042 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -19,7 +19,7 @@ extern int **PP; #define WMU(i,j) WM[i][j] #define WML(i,j) WM[j][i] #define VBI(i,j) VBI[indx[j]+i] -#define RT ((0.00198721 * 310.15)/100.00) +#define RT ((0.00198721 * 310.15) * 100.00) #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po index 80d3963..926b316 100644 --- a/gtfold-mfe/src/.deps/loader.Po +++ b/gtfold-mfe/src/.deps/loader.Po @@ -71,10 +71,10 @@ loader.o: loader.cc /usr/include/c++/4.5/iostream \ /usr/include/libio.h /usr/include/_G_config.h \ /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.4/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.4/bits/fstream.tcc /usr/include/c++/4.4/sstream \ - /usr/include/c++/4.4/bits/sstream.tcc /usr/include/math.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ + /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ + /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/sstream \ + /usr/include/c++/4.5/bits/sstream.tcc /usr/include/math.h \ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ @@ -307,9 +307,9 @@ loader.o: loader.cc /usr/include/c++/4.5/iostream \ /usr/include/c++/4.5/bits/fstream.tcc: -/usr/include/c++/4.4/sstream: +/usr/include/c++/4.5/sstream: -/usr/include/c++/4.4/bits/sstream.tcc: +/usr/include/c++/4.5/bits/sstream.tcc: /usr/include/math.h: diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index 83d1a4d..1492a8e 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -15,7 +15,7 @@ #endif -#define DANGLE_DEBUG +#define MAX_LOOP 30 // double[][] QB; // double[][] Q; @@ -66,36 +66,44 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { // fill in values in the array for(l=1; l<=len; ++l) { //Parrallelize - #ifndef DANGLE_DEBUG - #ifdef _OPENMP - #pragma omp parallel for private (i,j) schedule(guided) - #endif - #endif - for(i=1; i<= len-l+1; ++i) { + //#ifdef _OPENMP + //#pragma omp parallel for private (i,j) schedule(guided) + //#endif + for(i=1; i<= len - l + 1; i++) { - int j = i+l-1; + int j = i + l - 1; // QB recursion // Only calculate if i and j actually pair - if(checkPair(i,j)) { + if(canPair(RNA[i],RNA[j])) { // NOTE: eH returns an integer encoded as fixed point. So a // return value of 115 represents raw value 115/100 = 1.15 QB[i][j] = exp(-eH(i,j)/RT); - + for(d=i+1; d<=j-4; ++d) { + //if(d - i - 1 > MAX_LOOP) + // break; for(e=d+4; e<=j-1; ++e) { - - if(d == i + 1 && e == j -1){ - QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; - } - else{ - printf("i: %d j: %d d: %d e: %d\n", i,j,d,e); - QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; - } - QB[i][j] += QM[i+1][d-1]*QB[d][e] * - exp(-(a + b + c*(j-e-1))/RT); + // if(d - i - 1 + j - e - 1 > MAX_LOOP) + // break; + + if(QB[d][e] != 0){ + //more general than chkpair + //if we cant pair, move on + + if(d == i + 1 && e == j -1){ + QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; + } + else{ + //printf("i: %d j: %d d: %d e: %d\n", i,j,d,e); + QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; + } + + QB[i][j] += QM[i+1][d-1]*QB[d][e] * + exp(-(a + b + c*(j-e-1))/RT); + } } } } @@ -111,6 +119,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { } } } + printf("Total partition number: %f", Q[1][len]); } /** @@ -120,7 +129,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { * index j. structure[i] = 0 means the nucleotide is * unpaired. */ -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P) { +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P) { int d, l, h, i, j; double tempBuffer; diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index ddcd987..a4cfe32 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -266,8 +266,6 @@ int main(int argc, char** argv) { fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); } } - // release the malloc'd arrays - free_fold(seq.length()); if(BPP_ENABLED){ printf("Calculating partition function\n"); @@ -277,8 +275,9 @@ int main(int argc, char** argv) { QB = mallocTwoD(seq.length() + 1, seq.length() + 1); P = mallocTwoD(seq.length() + 1, seq.length() + 1); + fill_partition_fn_arrays(seq.length(), Q, QB, QM); - fillBasePairProbabilities(seq.length(), structure, Q, QB, QM, P); + fillBasePairProbabilities(seq.length(), Q, QB, QM, P); printBasePairProbabilities(seq.length(), structure, P); freeTwoD(Q, seq.length() + 1, seq.length() + 1); @@ -286,6 +285,9 @@ int main(int argc, char** argv) { freeTwoD(QB, seq.length() + 1, seq.length() + 1); freeTwoD(P, seq.length() + 1, seq.length() + 1); } + + // release the malloc'd arrays + free_fold(seq.length()); /* dangle_struct partition; partition = malloc_partition_arrays_d(seq.length()); From 7d7dadb6c06bfca7cee48b61aa4bd877b588497e Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:11:50 -0400 Subject: [PATCH 062/187] subopt related changes --- gtfold-mfe/src/main.cc | 37 +++++++++++++++++++------ gtfold-mfe/src/subopt_traceback.cc | 44 +++++++++++++++--------------- 2 files changed, 50 insertions(+), 31 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 18489d1..7f2ceba 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -163,19 +163,27 @@ void print_header() { printf("Georgia Institute of Technology\n\n"); } +void save_subopt_file(string outputFile, ss_map_t& ss_data) +{ + ofstream outfile; + outfile.open(outputFile.c_str()); + + for (ss_map_t::iterator it = ss_data.begin(); + it != ss_data.end(); ++it) { + outfile << it->first << '\t' << it->second/100.0 << std::endl; + } + + outfile.close(); +} + /** * Save the output to a ct file * * @param outputFile The file to save to * @param energy The MFE energy (multiplied by 100) */ -void save_ct_file(string outputFile, string seq, int energy, string seqfile) { - if(seqfile.find("/") != string::npos) { - size_t pos = seqfile.find_last_of("/"); - seqfile.erase(0,pos+1); - } - if(seqfile.find(".") != string::npos) - seqfile.erase(seqfile.rfind(".")); +void save_ct_file(string outputFile, string seq, int energy) { + ofstream outfile; outfile.open(outputFile.c_str()); @@ -225,10 +233,21 @@ int main(int argc, char** argv) { if (SUBOPT_ENABLED) { t1 = get_seconds(); - subopt_traceback(seq.length(), suboptDelta); + ss_map_t subopt_data = subopt_traceback(seq.length(), suboptDelta); t1 = get_seconds() - t1; printf("Subopt traceback running time: %9.6f seconds\n\n", t1); + + string suboptfile; + suboptfile += seqfile; + if(suboptfile.find("/") != string::npos) { + size_t pos = suboptfile.find_last_of("/"); + suboptfile.erase(0,pos+1); + } + if(suboptfile.find(".") != string::npos) + suboptfile.erase(suboptfile.rfind(".")); + suboptfile += ".ss"; + save_subopt_file(suboptfile, subopt_data); free_fold(seq.length()); exit(0); } @@ -248,7 +267,7 @@ int main(int argc, char** argv) { print_shapeArray(seq.length()); - save_ct_file(outputFile, seq, energy,seqfile); + save_ct_file(outputFile, seq, energy); printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 45c72d9..6375f2e 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -84,7 +84,7 @@ void process(ss_map_t& subopt_data, int energy, int len) (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy); } - if (gstack.size() == s1 && ps.total() <= energy) + if (gstack.size() == s1 && ps.total() == energy) { ps_t ps1(ps); gstack.push(ps1); @@ -115,7 +115,7 @@ ss_map_t subopt_traceback(int len, int delta) void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) { // Hairpin Loop - if (eH(i,j) + ps.total() <= energy ) + if (eH(i,j) + ps.total() == energy ) { // std::cout << "Hairpin " << i << ' ' << j << std::endl; ps_t ps1(ps); @@ -125,7 +125,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy) + if (eS(i, j) + V(i+1, j-1) + ps.total() == energy) { // std::cout << "Stack " << i << ' ' << j << std::endl; ps_t ps1(ps); @@ -136,7 +136,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } // Internal Loop - if (VBI(i,j) + ps.total() <= energy ) + if (VBI(i,j) + ps.total() == energy ) { //std::cout << "Internal " << i << ' ' << j << std::endl; ps_t ps1(ps); @@ -146,7 +146,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } // Multiloop - if ( VM(i,j) + ps.total() <= energy ) + if ( VM(i,j) + ps.total() == energy ) { // std::cout << "Multi " << i << ' ' << j << std::endl; ps_t ps1(ps); @@ -167,7 +167,7 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) for (q = minq; q < j; q++) { - if (V(p, q) + eL(i, j, p, q) + ps.total() <= energy ) + if (V(p, q) + eL(i, j, p, q) + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(p, q, lV, V(p, q))); @@ -187,7 +187,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) int wim1 = MIN(0, W[i-1]); int wij = V(i,j) + auPenalty(i, j) + wim1; - if (wij + ps.total() <= energy ) + if (wij + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(i, j, lV, V(i,j))); @@ -197,7 +197,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - if (wijd + ps.total() <= energy ) + if (wijd + ps.total() == energy ) { ps_t ps3(ps); ps3.push(segment(i, j-1, lV, V(i, j-1))); @@ -207,7 +207,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - if (widj + ps.total() <= energy ) + if (widj + ps.total() == energy ) { ps_t ps4(ps); ps4.push(segment(i+1, j, lV, V(i+1,j))); @@ -217,7 +217,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1; - if (widjd + ps.total() <= energy ) + if (widjd + ps.total() == energy ) { ps_t ps2(ps); ps2.push(segment(i+1, j-1, lV, V(i+1,j-1))); @@ -227,7 +227,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } } - if (W[j-1] + ps.total() <= energy ) + if (W[j-1] + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(1, j-1, lW, W[j-1])); @@ -276,7 +276,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) int h = i1; int k = j1; int wmij = V(h,k) + auPenalty(h,k) + Eb; - if (pss.total() + wmij <= energy ) + if (pss.total() + wmij == energy ) { ps_t ps1(pss); ps1.push_v(segment(h,k,lV, V(h,k))); @@ -285,7 +285,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ; - if (pss.total() + wmijd <= energy ) + if (pss.total() + wmijd == energy ) { ps_t ps1(pss); ps1.push_v(segment(h,k-1,lV, V(h,k-1))); @@ -294,7 +294,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ; - if (pss.total() + wmidj <= energy ) + if (pss.total() + wmidj == energy ) { ps_t ps1(pss); ps1.push_v(segment(h+1, k, lV, V(h+1,k))); @@ -303,7 +303,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec ; - if (pss.total() + wmidjd <= energy ) + if (pss.total() + wmidjd == energy ) { ps_t ps1(pss); ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1))); @@ -312,7 +312,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } - if (pss.total() + WM(i1,j1-1) + Ec <= energy ) + if (pss.total() + WM(i1,j1-1) + Ec == energy ) { ps_t ps1(pss); ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1))); @@ -320,7 +320,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) wm_stack.push(ps1); } - if (pss.total() + WM[i1+1][j1] + Ec <= energy ) + if (pss.total() + WM[i1+1][j1] + Ec == energy ) { ps_t ps1(pss); ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1))); @@ -330,7 +330,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) for (int h = i1+1; h <= j1-1; ++h) { - if (WM(i1,h) + WM(h+1,j1) + pss.total() <= energy ) + if (WM(i1,h) + WM(h+1,j1) + pss.total() == energy ) { ps_t ps1(pss); ps1.push(segment(i1, h, lWM, WM(i1,h))); @@ -354,7 +354,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) int common = auPenalty(i,j) + Ea + Eb; dG = common + WM[i+1][h-1] + WM[h][j-1]; - if (dG + ps.total() <= energy ) + if (dG + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); @@ -364,7 +364,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } dG = common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec; - if (dG + ps.total() <= energy ) + if (dG + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); @@ -374,7 +374,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec; - if (dG + ps.total() <= energy ) + if (dG + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); @@ -384,7 +384,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec; - if (dG + ps.total() <= energy ) + if (dG + ps.total() == energy ) { ps_t ps1(ps); ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); From 0c9f170140be04511ff9e63b7672b470da2f9df3 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:17:13 -0400 Subject: [PATCH 063/187] added print message --- gtfold-mfe/src/main.cc | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 7f2ceba..a5c5083 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -246,7 +246,8 @@ int main(int argc, char** argv) { if(suboptfile.find(".") != string::npos) suboptfile.erase(suboptfile.rfind(".")); suboptfile += ".ss"; - + + printf("Suboptimal structures saved in %s\n", suboptfile.c_str()); save_subopt_file(suboptfile, subopt_data); free_fold(seq.length()); exit(0); From f33cfc986cdcad53b2630e937e5dd0c8efa4e3e7 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:19:50 -0400 Subject: [PATCH 064/187] added .dat files to base_data dir --- .../data/Turner99/base_data/asint1x2.dat | 353 +++++++ .../data/Turner99/base_data/coaxial.dat | 63 ++ .../data/Turner99/base_data/coaxstack.dat | 63 ++ gtfold-mfe/data/Turner99/base_data/dangle.dat | 72 ++ gtfold-mfe/data/Turner99/base_data/int11.dat | 101 ++ gtfold-mfe/data/Turner99/base_data/int21.dat | 353 +++++++ gtfold-mfe/data/Turner99/base_data/int22.dat | 928 ++++++++++++++++++ gtfold-mfe/data/Turner99/base_data/loop.dat | 34 + .../data/Turner99/base_data/miscloop.dat | 42 + gtfold-mfe/data/Turner99/base_data/sint2.dat | 101 ++ gtfold-mfe/data/Turner99/base_data/sint4.dat | 928 ++++++++++++++++++ gtfold-mfe/data/Turner99/base_data/stack.dat | 63 ++ gtfold-mfe/data/Turner99/base_data/tloop.dat | 32 + .../data/Turner99/base_data/triloop.dat | 2 + gtfold-mfe/data/Turner99/base_data/tstack.dat | 63 ++ .../data/Turner99/base_data/tstackcoax.dat | 63 ++ .../data/Turner99/base_data/tstackh.dat | 63 ++ .../data/Turner99/base_data/tstacki.dat | 63 ++ .../data/Turner99/base_data/tstackm.dat | 63 ++ 19 files changed, 3450 insertions(+) create mode 100644 gtfold-mfe/data/Turner99/base_data/asint1x2.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/coaxial.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/coaxstack.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/dangle.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/int11.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/int21.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/int22.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/loop.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/miscloop.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/sint2.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/sint4.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/stack.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tloop.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/triloop.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tstack.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackcoax.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackh.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tstacki.dat create mode 100644 gtfold-mfe/data/Turner99/base_data/tstackm.dat diff --git a/gtfold-mfe/data/Turner99/base_data/asint1x2.dat b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat new file mode 100644 index 0000000..d17afd2 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat @@ -0,0 +1,353 @@ +Data tables for asymmetric interior loops of size 3 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + YA + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.20 3.00 2.40 4.80 2.30 2.20 1.10 4.00 2.40 2.20 1.60 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 + 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 + 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 + 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.50 4.00 2.20 4.00 1.30 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.80 1.40 1.20 4.80 0.80 0.60 0.40 4.00 1.00 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.20 3.00 2.40 4.80 2.40 2.20 1.60 4.00 2.50 2.20 2.10 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 + 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 + 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 + 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.30 4.00 2.20 4.00 1.20 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.80 1.40 1.20 4.80 1.00 0.60 0.40 4.00 1.20 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 diff --git a/gtfold-mfe/data/Turner99/base_data/coaxial.dat b/gtfold-mfe/data/Turner99/base_data/coaxial.dat new file mode 100644 index 0000000..9987fef --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/coaxial.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . . . . -0.90 + . . . . . . . . . . . . . . -2.20 . + . . . . . . . . . . . . . -2.10 . -0.60 + . . . . . . . . . . . . -1.10 . -1.40 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . -2.10 . . . . + . . . . . . . . . . -3.30 . . . . . + . . . . . . . . . -2.40 . -1.40 . . . . + . . . . . . . . -2.10 . -2.10 . . . . . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . -2.40 . . . . . . . -1.30 + . . . . . . -3.40 . . . . . . . -2.50 . + . . . . . -3.30 . -1.50 . . . . . -2.10 . -0.50 + . . . . -2.20 . -2.50 . . . . . -1.40 . 1.30 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.30 . . . . . . . -1.00 . . . . + . . -2.40 . . . . . . . -1.50 . . . . . + . -2.10 . -1.00 . . . . . -1.40 . 0.30 . . . . + -0.90 . -1.30 . . . . . -0.60 . -0.50 . . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/coaxstack.dat b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat new file mode 100644 index 0000000..7125756 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : COAXIAL STACKING ENERGIES + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . -2.10 -2.10 -2.10 -2.50 + . . . . . . . . . . . . -2.10 -2.10 -2.50 -2.10 + . . . . . . . . . . . . -2.10 -2.50 -2.10 -2.30 + . . . . . . . . . . . . -2.50 -2.10 -2.30 -2.10 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . -2.10 -2.10 -2.10 -2.50 . . . . + . . . . . . . . -2.10 -2.10 -2.50 -2.10 . . . . + . . . . . . . . -2.10 -2.50 -2.10 -2.30 . . . . + . . . . . . . . -2.50 -2.10 -2.30 -2.10 . . . . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . -2.10 -2.10 -2.10 -2.50 . . . . -2.10 -2.10 -2.10 -2.50 + . . . . -2.10 -2.10 -2.50 -2.10 . . . . -2.10 -2.10 -2.50 -2.10 + . . . . -2.10 -2.50 -2.10 -2.30 . . . . -2.10 -2.50 -2.10 -2.30 + . . . . -2.50 -2.10 -2.30 -2.10 . . . . -2.50 -2.10 -2.30 -2.10 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + -2.10 -2.10 -2.10 -2.50 . . . . -2.10 -2.10 -2.10 -2.50 . . . . + -2.10 -2.10 -2.50 -2.10 . . . . -2.10 -2.10 -2.50 -2.10 . . . . + -2.10 -2.50 -2.10 -2.30 . . . . -2.10 -2.50 -2.10 -2.30 . . . . + -2.50 -2.10 -2.30 -2.10 . . . . -2.50 -2.10 -2.30 -2.10 . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/dangle.dat b/gtfold-mfe/data/Turner99/base_data/dangle.dat new file mode 100644 index 0000000..2f2d2da --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/dangle.dat @@ -0,0 +1,72 @@ + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . -0.80 -0.50 -0.80 -0.60 + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . -1.70 -0.80 -1.70 -1.20 . . . . + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . -1.10 -0.40 -1.30 -0.60 . . . . -0.80 -0.50 -0.80 -0.60 + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +-0.70 -0.10 -0.70 -0.10 . . . . -0.70 -0.10 -0.70 -0.10 . . . . + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + A A A A + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . -0.30 -0.10 -0.20 -0.20 + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + C C C C + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . -0.20 -0.30 -0.0 -0.0 . . . . + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + G G G G + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . -0.50 -0.30 -0.20 -0.10 . . . . -0.30 -0.10 -0.20 -0.20 + X X X X + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + U U U U + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +-0.30 -0.30 -0.40 -0.20 . . . . -0.30 -0.30 -0.40 -0.20 . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/int11.dat b/gtfold-mfe/data/Turner99/base_data/int11.dat new file mode 100644 index 0000000..3e0f630 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/int11.dat @@ -0,0 +1,101 @@ +Data table for symetric interior loops of size 2 +Free energies at 37 degrees for RNA +Data Arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + Y + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 + 1.10 1.10 1.10 1.10 0.40 0.00 0.40 -0.30 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.10 1.10 1.10 1.10 0.80 0.40 0.40 0.40 0.40 0.30 -0.10 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 1.10 1.10 0.40 0.40 0.40 0.40 -0.40 0.50 0.40 0.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 -1.00 1.10 0.40 0.40 -2.10 0.40 0.40 0.40 -1.70 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 + 1.10 1.10 1.10 1.10 0.40 0.40 0.40 -0.70 0.40 0.50 0.40 -0.30 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/Turner99/base_data/int21.dat b/gtfold-mfe/data/Turner99/base_data/int21.dat new file mode 100644 index 0000000..d17afd2 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/int21.dat @@ -0,0 +1,353 @@ +Data tables for asymmetric interior loops of size 3 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + YA + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.20 3.00 2.40 4.80 2.30 2.20 1.10 4.00 2.40 2.20 1.60 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 + 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 + 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 + 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.50 4.00 2.20 4.00 1.30 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.80 1.40 1.20 4.80 0.80 0.60 0.40 4.00 1.00 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.20 3.00 2.40 4.80 2.40 2.20 1.60 4.00 2.50 2.20 2.10 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 + 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 + 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 + 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.30 4.00 2.20 4.00 1.20 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YG YG YG YG YG YG + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.80 1.40 1.20 4.80 1.00 0.60 0.40 4.00 1.20 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + YU YU YU YU YU YU + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 + 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 + 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 + 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 + 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 + 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + YC YC YC YC YC YC + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 + 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 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2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 + 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 + 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 + 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 + Y + --------------------------------------------------------------------------------------------- + A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + --------------------------------------------------------------------------------------------- + 5' ------> 3' + U \/ \_/ U + G /\ | G + 3' <------ 5' + 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 + 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/Turner99/base_data/loop.dat b/gtfold-mfe/data/Turner99/base_data/loop.dat new file mode 100644 index 0000000..927fbbd --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/loop.dat @@ -0,0 +1,34 @@ +DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) +hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges +SIZE INTERNAL BULGE HAIRPIN +------------------------------------------------------- +1 . 3.80 . +2 . 2.80 . +3 . 3.20 5.70 +4 1.70 3.60 5.60 +5 1.80 4.00 5.60 +6 2.00 4.40 5.40 +7 2.20 4.60 5.90 +8 2.30 4.70 5.60 +9 2.40 4.80 6.40 +10 2.50 4.90 6.50 +11 2.60 5.00 6.60 +12 2.70 5.10 6.70 +13 2.80 5.20 6.80 +14 2.90 5.30 6.90 +15 3.00 5.40 6.90 +16 3.00 5.40 7.00 +17 3.10 5.50 7.10 +18 3.10 5.50 7.10 +19 3.20 5.60 7.20 +20 3.30 5.70 7.20 +21 3.30 5.70 7.30 +22 3.40 5.80 7.30 +23 3.40 5.80 7.40 +24 3.40 5.80 7.40 +25 3.50 5.90 7.50 +26 3.50 5.90 7.50 +27 3.60 6.00 7.50 +28 3.60 6.00 7.60 +29 3.60 6.00 7.60 +30 3.70 6.10 7.70 diff --git a/gtfold-mfe/data/Turner99/base_data/miscloop.dat b/gtfold-mfe/data/Turner99/base_data/miscloop.dat new file mode 100644 index 0000000..cd585c1 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/miscloop.dat @@ -0,0 +1,42 @@ +Miscellaneous free energy rules +------------------------------- +Extrapolation for large loops based on polymer theory +internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) +--> +1.079 +asymmetric internal loops: the ninio equation +the maximum correction +--> +3.00 +the f(m) array (see Ninio for details) +--> + .50 .50 .50 .50 +multibranched loops + offset, free base penalty, helix penalty +--> + 3.40 .00 .40 +efn2 multibranched loops + offset, free base penalty, helix penalty +--> + 10.10 -0.30 -0.30 +terminal AU penalty +--> + 0.50 +bonus for GGG hairpin +--> +-2.20 +c hairpin slope +--> +0.30 +c hairpin intercept +--> +1.60 +c hairpin of 3 +--> +1.40 +Intermolecular initiation free energy +--> +4.10 +GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) +--> +1 diff --git a/gtfold-mfe/data/Turner99/base_data/sint2.dat b/gtfold-mfe/data/Turner99/base_data/sint2.dat new file mode 100644 index 0000000..3e0f630 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/sint2.dat @@ -0,0 +1,101 @@ +Data table for symetric interior loops of size 2 +Free energies at 37 degrees for RNA +Data Arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + Y + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 + 1.10 1.10 1.10 1.10 0.40 0.00 0.40 -0.30 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.10 1.10 1.10 1.10 0.80 0.40 0.40 0.40 0.40 0.30 -0.10 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 1.10 1.10 0.40 0.40 0.40 0.40 -0.40 0.50 0.40 0.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + 1.10 1.10 -1.00 1.10 0.40 0.40 -2.10 0.40 0.40 0.40 -1.70 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 + 1.10 1.10 1.10 1.10 0.40 0.40 0.40 -0.70 0.40 0.50 0.40 -0.30 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 + 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 + 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/Turner99/base_data/sint4.dat b/gtfold-mfe/data/Turner99/base_data/sint4.dat new file mode 100644 index 0000000..1939411 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/sint4.dat @@ -0,0 +1,928 @@ +Data tables for symetric interior loops of size 4 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ---------------------------------------------------------------- +(X) A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + ---------------------------------------------------------------- + 5' ------> 3' + A \/ \_/ A + U /\ | U + 3' <------ 5' +(AA) . . . . . . . . . . . . . . . . +(AC) . . . . . . . . . . . . . . . . +(AG) . . . . . . . . . . . . . . . . +(AU) . . . . . . . . . . . . . . . . +(CA) . . . . . . . . . . . . . . . . +(CC) . . . . . . . . . . . . . . . . +(CG) . . . . . . . . . . . . . . . . +(CU) . . . . . . . . . . . . . . . . +(GA) . . . . . . . . . . . . . . . . +(GC) . . . . . . . . . . . . . . . . +(GG) . . . . . . . . . . . . . . . . +(GU) . . . . . . . . . . . . . . . . +(UA) . . . . . . . . . . . . . . . . +(UC) . . . . . . . . . . . . . . . . +(UG) . . . . . . . . . . . . . . . . +(UU) . . . . . . . . . . . . . . . . + Y + --------------------------------------------------------------------------------------------- + A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + --------------------------------------------------------------------------------------------- + 5' ------> 3' + A \/ \_/ A + U /\ | U + 3' <------ 5' + 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 + 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 + 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 + 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 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--------------------------------------------------------------------------------------------- + A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + --------------------------------------------------------------------------------------------- + 5' ------> 3' + U \/ \_/ U + G /\ | A + 3' <------ 5' + 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 + 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 + Y + --------------------------------------------------------------------------------------------- + A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + --------------------------------------------------------------------------------------------- + 5' ------> 3' + U \/ \_/ G + G /\ | U + 3' <------ 5' + 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 + 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 + 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 1.90 1.30 2.00 2.30 2.30 2.00 2.30 1.30 2.00 1.70 -0.50 2.00 2.00 0.80 1.50 + 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 + 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 + 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 + 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 + 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 + Y + --------------------------------------------------------------------------------------------- + A A A A C C C C G G G G U U U U + A C G U A C G U A C G U A C G U + --------------------------------------------------------------------------------------------- + 5' ------> 3' + U \/ \_/ U + G /\ | G + 3' <------ 5' + 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 + 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/Turner99/base_data/stack.dat b/gtfold-mfe/data/Turner99/base_data/stack.dat new file mode 100644 index 0000000..ba2d3f5 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/stack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . . . . -0.90 + . . . . . . . . . . . . . . -2.20 . + . . . . . . . . . . . . . -2.10 . -0.60 + . . . . . . . . . . . . -1.10 . -1.40 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . -2.10 . . . . + . . . . . . . . . . -3.30 . . . . . + . . . . . . . . . -2.40 . -1.40 . . . . + . . . . . . . . -2.10 . -2.10 . . . . . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . -2.40 . . . . . . . -1.30 + . . . . . . -3.40 . . . . . . . -2.50 . + . . . . . -3.30 . -1.50 . . . . . -2.10 . -0.50 + . . . . -2.20 . -2.50 . . . . . -1.40 . 1.30 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.30 . . . . . . . -1.00 . . . . + . . -2.40 . . . . . . . -1.50 . . . . . + . -2.10 . -1.00 . . . . . -1.40 . 0.30 . . . . + -0.90 . -1.30 . . . . . -0.60 . -0.50 . . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/tloop.dat b/gtfold-mfe/data/Turner99/base_data/tloop.dat new file mode 100644 index 0000000..ad64bf4 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tloop.dat @@ -0,0 +1,32 @@ + Seq Energy + ------------- + GGGGAC -3.00 + GGUGAC -3.00 + CGAAAG -3.00 + GGAGAC -3.00 + CGCAAG -3.00 + GGAAAC -3.00 + CGGAAG -3.00 + CUUCGG -3.00 + CGUGAG -3.00 + CGAAGG -2.50 + CUACGG -2.50 + GGCAAC -2.50 + CGCGAG -2.50 + UGAGAG -2.50 + CGAGAG -2.00 + AGAAAU -2.00 + CGUAAG -2.00 + CUAACG -2.00 + UGAAAG -2.00 + GGAAGC -1.50 + GGGAAC -1.50 + UGAAAA -1.50 + AGCAAU -1.50 + AGUAAU -1.50 + CGGGAG -1.50 + AGUGAU -1.50 + GGCGAC -1.50 + GGGAGC -1.50 + GUGAAC -1.50 + UGGAAA -1.50 diff --git a/gtfold-mfe/data/Turner99/base_data/triloop.dat b/gtfold-mfe/data/Turner99/base_data/triloop.dat new file mode 100644 index 0000000..75c3bfc --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/triloop.dat @@ -0,0 +1,2 @@ + Seq Energy + ------------- diff --git a/gtfold-mfe/data/Turner99/base_data/tstack.dat b/gtfold-mfe/data/Turner99/base_data/tstack.dat new file mode 100644 index 0000000..97a4115 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.00 . . . -1.00 . . . -2.20 -0.80 -1.00 -0.80 . + . . -1.50 . . . -1.50 . . . -2.70 . -0.60 -0.70 . -0.70 + . -1.50 . -1.00 . -1.50 . -1.00 . -2.70 . -2.20 -0.80 . -0.80 . + -1.00 . -1.50 . -1.00 . -1.50 . -2.20 . -2.70 . . -0.80 . -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.00 . . . -1.00 -1.50 -1.50 -1.40 . . . . -1.00 + . . -1.50 . . . -1.50 . -1.00 -1.10 . -0.80 . . -1.50 . + . -1.50 . -1.00 . -1.50 . -1.00 -1.40 . -1.60 . . -1.50 . -1.00 + -1.00 . -1.50 . -1.00 . -1.50 . . -1.40 . -1.20 -1.00 . -1.50 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -2.20 -1.10 -1.50 -1.30 . . . . -1.00 -0.30 -1.00 -0.80 . + . . -2.70 . -1.10 -0.70 . -0.50 . . -1.50 . -0.60 -0.70 . -0.70 + . -2.70 . -2.20 -1.60 . -1.40 . . -1.50 . -1.00 -0.60 . -0.80 . + -2.20 . -2.70 . . -1.00 . -0.70 -1.00 . -1.50 . . -0.80 . -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + -1.00 -0.80 -1.10 . . . . -1.00 -1.00 -0.80 -1.10 . . . . -2.00 + -0.70 -0.60 . -0.50 . . -1.50 . -0.70 -0.60 . -0.50 . . -2.50 . + -1.10 . -1.20 . . -1.50 . -1.00 -0.50 . -0.80 -0.80 . -2.50 . -2.00 + . -0.60 . -0.50 -1.00 . -1.50 . . -0.60 -1.10 -0.50 -2.00 . -2.50 . diff --git a/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat new file mode 100644 index 0000000..b90d0bc --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : COAXIAL STACKING + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.00 . . . -0.70 . . . -1.10 -0.80 -1.00 -0.80 -0.40 + . . -1.10 . . . -1.10 . . . -1.60 . -0.60 -0.70 -1.70 -0.70 + . -1.50 . -1.00 . -1.00 . -0.70 . -1.40 . -0.50 -0.80 -1.60 -0.80 -0.10 + -0.80 . -0.30 . -0.60 . -0.60 . -0.80 . -0.60 . -0.60 -0.80 -0.90 -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -0.80 . . . -0.60 -1.50 -1.50 -1.40 -1.60 . . . -0.60 + . . -1.50 . . . -0.70 . -1.00 -1.10 -2.80 -0.80 . . -1.00 . + . -1.50 . -0.80 . -1.10 . -0.60 -1.40 -1.90 -1.60 -0.90 . -1.40 . -0.60 + -1.00 . -1.00 . -0.70 . -0.70 . -1.60 -1.40 -1.60 -1.20 -0.80 . -0.80 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.10 -1.10 -1.50 -1.30 -1.90 . . . -1.20 -0.30 -1.00 -0.80 -0.80 + . . -1.30 . -1.10 -0.70 -2.90 -0.50 . . -1.40 . -0.60 -0.70 -2.00 -0.70 + . -1.40 . -1.10 -1.60 -2.80 -1.40 -1.00 . -1.60 . -0.80 -0.60 -1.60 -0.80 0.00 + -0.80 . -0.80 . -1.70 -1.00 -2.00 -0.70 -0.80 . -0.80 . -0.90 -0.80 1.80 -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + -1.00 -0.80 -1.10 -0.80 . . . -0.50 -1.00 -0.80 -1.10 -0.50 . . . -0.50 + -0.70 -0.60 -1.90 -0.50 . . -0.50 . -0.70 -0.60 -1.00 -0.50 . . -0.70 . + -1.10 -1.60 -1.20 -0.50 . -0.80 . -0.50 -0.50 -0.90 -0.80 0.80 . -1.20 . -0.50 + -0.40 -0.60 -0.80 -0.50 -0.70 . -0.70 . -0.10 -0.60 -0.00 -0.50 -0.80 . -0.80 . diff --git a/gtfold-mfe/data/Turner99/base_data/tstackh.dat b/gtfold-mfe/data/Turner99/base_data/tstackh.dat new file mode 100644 index 0000000..6959647 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tstackh.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . -0.30 -0.50 -0.30 -0.30 + . . . . . . . . . . . . -0.10 -0.20 -1.50 -0.20 + . . . . . . . . . . . . -1.10 -1.20 -0.20 0.20 + . . . . . . . . . . . . -0.30 -0.30 -0.60 -1.10 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . -1.50 -1.50 -1.40 -1.80 . . . . + . . . . . . . . -1.00 -0.90 -2.90 -0.80 . . . . + . . . . . . . . -2.20 -2.00 -1.60 -1.10 . . . . + . . . . . . . . -1.70 -1.40 -1.80 -2.00 . . . . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . -1.10 -1.50 -1.30 -2.10 . . . . 0.20 -0.50 -0.30 -0.30 + . . . . -1.10 -0.70 -2.40 -0.50 . . . . -0.10 -0.20 -1.50 -0.20 + . . . . -2.40 -2.90 -1.40 -1.20 . . . . -0.90 -1.10 -0.30 0.00 + . . . . -1.90 -1.00 -2.20 -1.50 . . . . -0.30 -0.30 -0.40 -1.10 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + -0.50 -0.30 -0.60 -0.50 . . . . -0.50 -0.30 -0.60 -0.50 . . . . + -0.20 -0.10 -1.20 -0.00 . . . . -0.20 -0.10 -1.70 0.00 . . . . + -1.40 -1.20 -0.70 -0.20 . . . . -0.80 -1.20 -0.30 -0.70 . . . . + -0.30 -0.10 -0.50 -0.80 . . . . -0.60 -0.10 -0.60 -0.80 . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/tstacki.dat b/gtfold-mfe/data/Turner99/base_data/tstacki.dat new file mode 100644 index 0000000..bf5d98c --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tstacki.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . . . . . 0.70 0.70 -0.40 0.70 + . . . . . . . . . . . . 0.70 0.70 0.70 0.70 + . . . . . . . . . . . . -0.40 0.70 0.70 0.70 + . . . . . . . . . . . . 0.70 0.70 0.70 0.00 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . . . . . -0.00 -0.00 -1.10 -0.00 . . . . + . . . . . . . . -0.00 -0.00 -0.00 -0.00 . . . . + . . . . . . . . -1.10 -0.00 -0.00 -0.00 . . . . + . . . . . . . . -0.00 -0.00 -0.00 -0.70 . . . . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . . -0.00 -0.00 -1.10 -0.00 . . . . 0.70 0.70 -0.40 0.70 + . . . . -0.00 -0.00 -0.00 -0.00 . . . . 0.70 0.70 0.70 0.70 + . . . . -1.10 -0.00 -0.00 -0.00 . . . . -0.40 0.70 0.70 0.70 + . . . . -0.00 -0.00 -0.00 -0.70 . . . . 0.70 0.70 0.70 0.00 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.70 0.70 -0.40 0.70 . . . . 0.70 0.70 -0.40 0.70 . . . . + 0.70 0.70 0.70 0.70 . . . . 0.70 0.70 0.70 0.70 . . . . + -0.40 0.70 0.70 0.70 . . . . -0.40 0.70 0.70 0.70 . . . . + 0.70 0.70 0.70 0.00 . . . . 0.70 0.70 0.70 0.00 . . . . diff --git a/gtfold-mfe/data/Turner99/base_data/tstackm.dat b/gtfold-mfe/data/Turner99/base_data/tstackm.dat new file mode 100644 index 0000000..f38c845 --- /dev/null +++ b/gtfold-mfe/data/Turner99/base_data/tstackm.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.70 -0.10 -0.70 -0.10 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.00 . . . -1.00 . . . -2.20 -0.80 -1.00 -0.80 -0.90 + . . -1.50 . . . -1.50 . . . -2.70 . -0.60 -0.70 -2.20 -0.70 + . -1.50 . -1.00 . -1.50 . -1.00 . -2.70 . -2.20 -0.80 -2.10 -0.80 -0.80 + -1.00 . -1.50 . -1.00 . -1.50 . -2.20 . -2.70 . -1.10 -0.80 -1.10 -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -1.00 . . . -1.00 -1.70 -1.70 -1.70 -1.70 . . . -1.00 + . . -1.50 . . . -1.50 . -1.00 -1.10 -3.30 -0.80 . . -1.50 . + . -1.50 . -1.00 . -1.50 . -1.00 -1.70 -2.40 -1.70 -1.70 . -1.50 . -1.00 + -1.00 . -1.50 . -1.00 . -1.50 . -1.60 -1.40 -1.60 -1.20 -1.00 . -1.50 . + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + . . . -2.20 -1.10 -1.50 -1.30 -1.90 . . . -1.00 -0.80 -1.00 -0.80 -1.30 + . . -2.70 . -1.10 -0.70 -3.40 -0.50 . . -1.50 . -0.60 -0.70 -2.50 -0.70 + . -2.70 . -2.20 -1.60 -3.30 -1.40 -1.30 . -1.50 . -1.00 -0.80 -2.10 -0.80 -0.80 + -2.20 . -2.70 . -1.70 -1.00 -2.00 -0.70 -1.00 . -1.50 . -1.40 -0.80 1.30 -0.80 + Y Y Y Y + ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + -1.00 -0.80 -1.10 -1.30 . . . -1.00 -1.00 -0.80 -1.10 -1.00 . . . -2.00 + -0.70 -0.60 -2.40 -0.50 . . -1.50 . -0.70 -0.60 -1.50 -0.50 . . -2.50 . + -1.10 -2.10 -1.20 -1.00 . -1.50 . -1.00 -0.70 -1.40 -0.80 0.30 . -2.50 . -2.00 + -0.90 -0.60 -1.40 -0.50 -1.00 . -1.50 . -0.50 -0.60 -0.50 -0.50 -2.00 . -2.50 . From 6fcd379ad7f3142572caf34b270c0a1c7e66e28f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:20:55 -0400 Subject: [PATCH 065/187] moved .dat files to base_data dir --- gtfold-mfe/data/Turner99/asint1x2.dat | 353 --------- gtfold-mfe/data/Turner99/coaxial.dat | 63 -- gtfold-mfe/data/Turner99/coaxstack.dat | 63 -- gtfold-mfe/data/Turner99/dangle.dat | 72 -- gtfold-mfe/data/Turner99/int11.dat | 101 --- gtfold-mfe/data/Turner99/int21.dat | 353 --------- gtfold-mfe/data/Turner99/int22.dat | 928 ------------------------ gtfold-mfe/data/Turner99/loop.dat | 34 - gtfold-mfe/data/Turner99/miscloop.dat | 42 -- gtfold-mfe/data/Turner99/sint2.dat | 101 --- gtfold-mfe/data/Turner99/sint4.dat | 928 ------------------------ gtfold-mfe/data/Turner99/stack.dat | 63 -- gtfold-mfe/data/Turner99/tloop.dat | 32 - gtfold-mfe/data/Turner99/triloop.dat | 2 - gtfold-mfe/data/Turner99/tstack.dat | 63 -- gtfold-mfe/data/Turner99/tstackcoax.dat | 63 -- gtfold-mfe/data/Turner99/tstackh.dat | 63 -- gtfold-mfe/data/Turner99/tstacki.dat | 63 -- gtfold-mfe/data/Turner99/tstackm.dat | 63 -- 19 files changed, 3450 deletions(-) delete mode 100644 gtfold-mfe/data/Turner99/asint1x2.dat delete mode 100644 gtfold-mfe/data/Turner99/coaxial.dat delete mode 100644 gtfold-mfe/data/Turner99/coaxstack.dat delete mode 100644 gtfold-mfe/data/Turner99/dangle.dat delete mode 100644 gtfold-mfe/data/Turner99/int11.dat delete mode 100644 gtfold-mfe/data/Turner99/int21.dat delete mode 100644 gtfold-mfe/data/Turner99/int22.dat delete mode 100644 gtfold-mfe/data/Turner99/loop.dat delete mode 100644 gtfold-mfe/data/Turner99/miscloop.dat delete mode 100644 gtfold-mfe/data/Turner99/sint2.dat delete mode 100644 gtfold-mfe/data/Turner99/sint4.dat delete mode 100644 gtfold-mfe/data/Turner99/stack.dat delete mode 100644 gtfold-mfe/data/Turner99/tloop.dat delete mode 100644 gtfold-mfe/data/Turner99/triloop.dat delete mode 100644 gtfold-mfe/data/Turner99/tstack.dat delete mode 100644 gtfold-mfe/data/Turner99/tstackcoax.dat delete mode 100644 gtfold-mfe/data/Turner99/tstackh.dat delete mode 100644 gtfold-mfe/data/Turner99/tstacki.dat delete mode 100644 gtfold-mfe/data/Turner99/tstackm.dat diff --git a/gtfold-mfe/data/Turner99/asint1x2.dat b/gtfold-mfe/data/Turner99/asint1x2.dat deleted file mode 100644 index d17afd2..0000000 --- a/gtfold-mfe/data/Turner99/asint1x2.dat +++ /dev/null @@ -1,353 +0,0 @@ -Data tables for asymmetric interior loops of size 3 -Free energies at 37 degrees for RNA -Data arrangement: - Y - ------------------ -(X) A C G U - ------------------ - 5' --> 3' - X - A A - U U - YA - 3' <-- 5' -(A) . . . . -(C) . . . . -(G) . . . . -(U) . . . . - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.20 3.00 2.40 4.80 2.30 2.20 1.10 4.00 2.40 2.20 1.60 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 - 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 - 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 - 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.50 4.00 2.20 4.00 1.30 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.80 1.40 1.20 4.80 0.80 0.60 0.40 4.00 1.00 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.20 3.00 2.40 4.80 2.40 2.20 1.60 4.00 2.50 2.20 2.10 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 - 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 - 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 - 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.30 4.00 2.20 4.00 1.20 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.80 1.40 1.20 4.80 1.00 0.60 0.40 4.00 1.20 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 diff --git a/gtfold-mfe/data/Turner99/coaxial.dat b/gtfold-mfe/data/Turner99/coaxial.dat deleted file mode 100644 index 9987fef..0000000 --- a/gtfold-mfe/data/Turner99/coaxial.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . . . . -0.90 - . . . . . . . . . . . . . . -2.20 . - . . . . . . . . . . . . . -2.10 . -0.60 - . . . . . . . . . . . . -1.10 . -1.40 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . -2.10 . . . . - . . . . . . . . . . -3.30 . . . . . - . . . . . . . . . -2.40 . -1.40 . . . . - . . . . . . . . -2.10 . -2.10 . . . . . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . -2.40 . . . . . . . -1.30 - . . . . . . -3.40 . . . . . . . -2.50 . - . . . . . -3.30 . -1.50 . . . . . -2.10 . -0.50 - . . . . -2.20 . -2.50 . . . . . -1.40 . 1.30 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.30 . . . . . . . -1.00 . . . . - . . -2.40 . . . . . . . -1.50 . . . . . - . -2.10 . -1.00 . . . . . -1.40 . 0.30 . . . . - -0.90 . -1.30 . . . . . -0.60 . -0.50 . . . . . diff --git a/gtfold-mfe/data/Turner99/coaxstack.dat b/gtfold-mfe/data/Turner99/coaxstack.dat deleted file mode 100644 index 7125756..0000000 --- a/gtfold-mfe/data/Turner99/coaxstack.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : COAXIAL STACKING ENERGIES - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . -2.10 -2.10 -2.10 -2.50 - . . . . . . . . . . . . -2.10 -2.10 -2.50 -2.10 - . . . . . . . . . . . . -2.10 -2.50 -2.10 -2.30 - . . . . . . . . . . . . -2.50 -2.10 -2.30 -2.10 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . -2.10 -2.10 -2.10 -2.50 . . . . - . . . . . . . . -2.10 -2.10 -2.50 -2.10 . . . . - . . . . . . . . -2.10 -2.50 -2.10 -2.30 . . . . - . . . . . . . . -2.50 -2.10 -2.30 -2.10 . . . . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . -2.10 -2.10 -2.10 -2.50 . . . . -2.10 -2.10 -2.10 -2.50 - . . . . -2.10 -2.10 -2.50 -2.10 . . . . -2.10 -2.10 -2.50 -2.10 - . . . . -2.10 -2.50 -2.10 -2.30 . . . . -2.10 -2.50 -2.10 -2.30 - . . . . -2.50 -2.10 -2.30 -2.10 . . . . -2.50 -2.10 -2.30 -2.10 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - -2.10 -2.10 -2.10 -2.50 . . . . -2.10 -2.10 -2.10 -2.50 . . . . - -2.10 -2.10 -2.50 -2.10 . . . . -2.10 -2.10 -2.50 -2.10 . . . . - -2.10 -2.50 -2.10 -2.30 . . . . -2.10 -2.50 -2.10 -2.30 . . . . - -2.50 -2.10 -2.30 -2.10 . . . . -2.50 -2.10 -2.30 -2.10 . . . . diff --git a/gtfold-mfe/data/Turner99/dangle.dat b/gtfold-mfe/data/Turner99/dangle.dat deleted file mode 100644 index 2f2d2da..0000000 --- a/gtfold-mfe/data/Turner99/dangle.dat +++ /dev/null @@ -1,72 +0,0 @@ - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - A C G U - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . -0.80 -0.50 -0.80 -0.60 - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - A C G U - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . -1.70 -0.80 -1.70 -1.20 . . . . - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - A C G U - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . -1.10 -0.40 -1.30 -0.60 . . . . -0.80 -0.50 -0.80 -0.60 - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - A C G U - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' --0.70 -0.10 -0.70 -0.10 . . . . -0.70 -0.10 -0.70 -0.10 . . . . - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - A A A A - AX CX GX UX - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . -0.30 -0.10 -0.20 -0.20 - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - C C C C - AX CX GX UX - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . -0.20 -0.30 -0.0 -0.0 . . . . - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - G G G G - AX CX GX UX - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . -0.50 -0.30 -0.20 -0.10 . . . . -0.30 -0.10 -0.20 -0.20 - X X X X - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - U U U U - AX CX GX UX - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' --0.30 -0.30 -0.40 -0.20 . . . . -0.30 -0.30 -0.40 -0.20 . . . . diff --git a/gtfold-mfe/data/Turner99/int11.dat b/gtfold-mfe/data/Turner99/int11.dat deleted file mode 100644 index 3e0f630..0000000 --- a/gtfold-mfe/data/Turner99/int11.dat +++ /dev/null @@ -1,101 +0,0 @@ -Data table for symetric interior loops of size 2 -Free energies at 37 degrees for RNA -Data Arrangement: - Y - ------------------ -(X) A C G U - ------------------ - 5' --> 3' - X - A A - U U - Y - 3' <-- 5' -(A) . . . . -(C) . . . . -(G) . . . . -(U) . . . . - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 - 1.10 1.10 1.10 1.10 0.40 0.00 0.40 -0.30 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.10 1.10 1.10 1.10 0.80 0.40 0.40 0.40 0.40 0.30 -0.10 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 1.10 1.10 0.40 0.40 0.40 0.40 -0.40 0.50 0.40 0.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 -1.00 1.10 0.40 0.40 -2.10 0.40 0.40 0.40 -1.70 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 - 1.10 1.10 1.10 1.10 0.40 0.40 0.40 -0.70 0.40 0.50 0.40 -0.30 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/Turner99/int21.dat b/gtfold-mfe/data/Turner99/int21.dat deleted file mode 100644 index d17afd2..0000000 --- a/gtfold-mfe/data/Turner99/int21.dat +++ /dev/null @@ -1,353 +0,0 @@ -Data tables for asymmetric interior loops of size 3 -Free energies at 37 degrees for RNA -Data arrangement: - Y - ------------------ -(X) A C G U - ------------------ - 5' --> 3' - X - A A - U U - YA - 3' <-- 5' -(A) . . . . -(C) . . . . -(G) . . . . -(U) . . . . - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.20 3.00 2.40 4.80 2.30 2.20 1.10 4.00 2.40 2.20 1.60 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 - 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 - 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 - 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.50 4.00 2.20 4.00 1.30 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.80 1.40 1.20 4.80 0.80 0.60 0.40 4.00 1.00 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.20 3.00 2.40 4.80 2.40 2.20 1.60 4.00 2.50 2.20 2.10 4.00 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 - 3.10 3.00 4.80 3.00 2.30 2.20 4.00 2.20 2.30 2.20 4.00 2.20 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 - 2.50 4.80 1.60 4.80 1.70 4.00 0.80 4.00 1.70 4.00 0.80 4.00 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.90 2.50 2.40 4.80 2.10 1.70 1.60 4.00 2.10 1.70 1.60 4.00 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 - 3.00 3.30 4.80 3.00 2.20 2.50 4.00 2.20 2.20 2.50 4.00 2.20 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 3.00 4.80 2.10 4.00 2.20 4.00 1.30 4.00 2.20 4.00 1.20 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.80 1.40 1.20 4.80 1.00 0.60 0.40 4.00 1.20 0.60 0.40 4.00 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 1.60 4.80 3.00 4.80 0.80 4.00 2.20 4.00 0.80 4.00 2.20 4.00 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 3.30 2.70 4.80 3.00 2.50 1.90 4.00 2.20 2.50 1.90 4.00 2.20 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 - 4.80 4.80 4.80 4.80 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 - 4.80 2.50 4.80 2.00 4.00 1.70 4.00 1.20 4.00 1.70 4.00 1.20 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YA YA YA YA YA YA - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 - 3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 - 3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YC YC YC YC YC YC - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 - 3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 5.50 3.70 5.50 2.80 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YG YG YG YG YG YG - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 2.50 2.10 1.90 5.50 1.80 1.40 1.20 4.80 1.80 1.40 1.20 4.80 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 2.50 2.10 1.90 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 2.30 5.50 3.70 5.50 1.60 4.80 3.00 4.80 1.60 4.80 3.00 4.80 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 2.30 5.50 3.70 5.50 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - YU YU YU YU YU YU - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 4.00 3.40 5.50 3.70 3.30 2.70 4.80 3.00 3.30 2.70 4.80 3.00 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 4.00 3.40 5.50 3.70 - 5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 - 5.50 3.20 5.50 2.70 4.80 2.50 4.80 2.00 4.80 2.50 4.80 2.00 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 5.50 3.20 5.50 2.70 diff --git a/gtfold-mfe/data/Turner99/int22.dat b/gtfold-mfe/data/Turner99/int22.dat deleted file mode 100644 index 2357f6f..0000000 --- a/gtfold-mfe/data/Turner99/int22.dat +++ /dev/null @@ -1,928 +0,0 @@ -Data tables for symetric interior loops of size 4 -Free energies at 37 degrees for RNA -Data arrangement: - Y - ---------------------------------------------------------------- -(X) A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - ---------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ A - U /\ | U - 3' <------ 5' -(AA) . . . . . . . . . . . . . . . . -(AC) . . . . . . . . . . . . . . . . -(AG) . . . . . . . . . . . . . . . . -(AU) . . . . . . . . . . . . . . . . -(CA) . . . . . . . . . . . . . . . . -(CC) . . . . . . . . . . . . . . . . -(CG) . . . . . . . . . . . . . . . . -(CU) . . . . . . . . . . . . . . . . -(GA) . . . . . . . . . . . . . . . . -(GC) . . . . . . . . . . . . . . . . -(GG) . . . . . . . . . . . . . . . . -(GU) . . . . . . . . . . . . . . . . -(UA) . . . . . . . . . . . . . . . . -(UC) . . . . . . . . . . . . . . . . -(UG) . . . . . . . . . . . . . . . . -(UU) . . . . . . . . . . . . . . . . - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ A - U /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.60 1.00 2.00 2.10 2.70 2.00 2.70 1.00 2.00 1.40 0.30 2.00 2.40 1.50 2.20 - 2.30 0.90 2.10 2.00 1.30 2.30 2.00 2.30 2.10 2.00 1.70 -1.50 2.00 2.00 -0.20 2.30 - 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2.70 1.90 1.10 2.00 1.80 1.90 2.00 0.90 1.70 2.00 2.40 0.00 2.00 1.90 0.40 1.10 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 - 1.10 0.80 -0.90 2.00 0.80 1.80 2.00 0.90 -0.30 2.00 0.70 -0.30 2.00 1.90 0.10 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.50 1.20 -0.50 2.00 1.20 1.80 2.00 0.80 0.10 2.00 1.10 -0.70 2.00 1.90 -0.30 1.50 - 1.60 0.30 0.40 2.00 0.30 1.30 2.00 0.40 1.00 2.00 1.20 -2.60 2.00 1.40 -2.20 1.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.70 1.90 1.10 2.00 1.80 1.90 2.00 0.90 1.70 2.00 2.40 0.00 2.00 1.90 0.40 1.10 - 0.30 -0.90 -0.90 2.00 -1.00 0.10 2.00 -0.90 -0.30 2.00 0.00 -3.90 2.00 0.10 -3.50 0.10 - 2.30 1.00 1.10 2.00 1.00 1.00 2.00 0.00 1.70 2.00 1.90 -0.10 2.00 1.10 0.30 0.30 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ G - G /\ | C - 3' <------ 5' - 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 - 2.00 1.90 1.00 2.00 2.40 2.20 2.00 2.10 1.00 2.00 1.80 -0.70 2.00 2.10 0.80 1.20 - 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.60 1.50 0.60 2.00 1.90 1.80 2.00 1.60 0.60 2.00 1.30 -1.10 2.00 1.60 0.40 0.70 - 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 - 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.40 1.30 0.40 2.00 1.70 2.20 2.00 2.00 0.40 2.00 1.10 -0.30 2.00 2.00 1.20 1.50 - 1.50 0.40 1.30 2.00 0.80 1.70 2.00 1.50 1.30 2.00 1.20 -2.20 2.00 1.50 -0.70 1.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 - 0.20 -0.90 0.00 2.00 -0.40 0.40 2.00 0.30 0.00 2.00 0.00 -3.50 2.00 0.30 -2.00 0.20 - 2.20 1.10 2.00 2.00 1.50 1.40 2.00 1.20 2.00 2.00 1.90 0.30 2.00 1.20 1.80 0.30 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ U - G /\ | A - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 - 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 - 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ G - G /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.90 1.30 2.00 2.30 2.30 2.00 2.30 1.30 2.00 1.70 -0.50 2.00 2.00 0.80 1.50 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 - 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 - 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ U - G /\ | G - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 - 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 - 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/Turner99/loop.dat b/gtfold-mfe/data/Turner99/loop.dat deleted file mode 100644 index 927fbbd..0000000 --- a/gtfold-mfe/data/Turner99/loop.dat +++ /dev/null @@ -1,34 +0,0 @@ -DESTABILIZING ENERGIES BY SIZE OF LOOP (INTERPOLATE WHERE NEEDED) -hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges -SIZE INTERNAL BULGE HAIRPIN -------------------------------------------------------- -1 . 3.80 . -2 . 2.80 . -3 . 3.20 5.70 -4 1.70 3.60 5.60 -5 1.80 4.00 5.60 -6 2.00 4.40 5.40 -7 2.20 4.60 5.90 -8 2.30 4.70 5.60 -9 2.40 4.80 6.40 -10 2.50 4.90 6.50 -11 2.60 5.00 6.60 -12 2.70 5.10 6.70 -13 2.80 5.20 6.80 -14 2.90 5.30 6.90 -15 3.00 5.40 6.90 -16 3.00 5.40 7.00 -17 3.10 5.50 7.10 -18 3.10 5.50 7.10 -19 3.20 5.60 7.20 -20 3.30 5.70 7.20 -21 3.30 5.70 7.30 -22 3.40 5.80 7.30 -23 3.40 5.80 7.40 -24 3.40 5.80 7.40 -25 3.50 5.90 7.50 -26 3.50 5.90 7.50 -27 3.60 6.00 7.50 -28 3.60 6.00 7.60 -29 3.60 6.00 7.60 -30 3.70 6.10 7.70 diff --git a/gtfold-mfe/data/Turner99/miscloop.dat b/gtfold-mfe/data/Turner99/miscloop.dat deleted file mode 100644 index cd585c1..0000000 --- a/gtfold-mfe/data/Turner99/miscloop.dat +++ /dev/null @@ -1,42 +0,0 @@ -Miscellaneous free energy rules -------------------------------- -Extrapolation for large loops based on polymer theory -internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) ---> -1.079 -asymmetric internal loops: the ninio equation -the maximum correction ---> -3.00 -the f(m) array (see Ninio for details) ---> - .50 .50 .50 .50 -multibranched loops - offset, free base penalty, helix penalty ---> - 3.40 .00 .40 -efn2 multibranched loops - offset, free base penalty, helix penalty ---> - 10.10 -0.30 -0.30 -terminal AU penalty ---> - 0.50 -bonus for GGG hairpin ---> --2.20 -c hairpin slope ---> -0.30 -c hairpin intercept ---> -1.60 -c hairpin of 3 ---> -1.40 -Intermolecular initiation free energy ---> -4.10 -GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) ---> -1 diff --git a/gtfold-mfe/data/Turner99/sint2.dat b/gtfold-mfe/data/Turner99/sint2.dat deleted file mode 100644 index 3e0f630..0000000 --- a/gtfold-mfe/data/Turner99/sint2.dat +++ /dev/null @@ -1,101 +0,0 @@ -Data table for symetric interior loops of size 2 -Free energies at 37 degrees for RNA -Data Arrangement: - Y - ------------------ -(X) A C G U - ------------------ - 5' --> 3' - X - A A - U U - Y - 3' <-- 5' -(A) . . . . -(C) . . . . -(G) . . . . -(U) . . . . - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - A A A C A G A U A G A U - U U U G U C U A U U U G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - C A C C C G C U C G C U - G U G G G C G A G U G G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 - 1.10 1.10 1.10 1.10 0.40 0.00 0.40 -0.30 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - C U C G C C C A C U C G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.10 1.10 1.10 1.10 0.80 0.40 0.40 0.40 0.40 0.30 -0.10 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 1.10 1.10 0.40 0.40 0.40 0.40 -0.40 0.50 0.40 0.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - 1.10 1.10 -1.00 1.10 0.40 0.40 -2.10 0.40 0.40 0.40 -1.70 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 - 1.10 1.10 1.10 1.10 0.40 0.40 0.40 -0.70 0.40 0.50 0.40 -0.30 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - A U A G A C A A A U A G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - G A G C G G G U G G G U - U U U G U C U A U U U G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - Y Y Y Y Y Y - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - X X X X X X - U A U C U G U U U G U U - G U G G G C G A G U G G - Y Y Y Y Y Y - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 - 1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 - 1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/Turner99/sint4.dat b/gtfold-mfe/data/Turner99/sint4.dat deleted file mode 100644 index 1939411..0000000 --- a/gtfold-mfe/data/Turner99/sint4.dat +++ /dev/null @@ -1,928 +0,0 @@ -Data tables for symetric interior loops of size 4 -Free energies at 37 degrees for RNA -Data arrangement: - Y - ---------------------------------------------------------------- -(X) A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - ---------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ A - U /\ | U - 3' <------ 5' -(AA) . . . . . . . . . . . . . . . . -(AC) . . . . . . . . . . . . . . . . -(AG) . . . . . . . . . . . . . . . . -(AU) . . . . . . . . . . . . . . . . -(CA) . . . . . . . . . . . . . . . . -(CC) . . . . . . . . . . . . . . . . -(CG) . . . . . . . . . . . . . . . . -(CU) . . . . . . . . . . . . . . . . -(GA) . . . . . . . . . . . . . . . . -(GC) . . . . . . . . . . . . . . . . -(GG) . . . . . . . . . . . . . . . . -(GU) . . . . . . . . . . . . . . . . -(UA) . . . . . . . . . . . . . . . . -(UC) . . . . . . . . . . . . . . . . -(UG) . . . . . . . . . . . . . . . . -(UU) . . . . . . . . . . . . . . . . - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ A - U /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.60 1.00 2.00 2.10 2.70 2.00 2.70 1.00 2.00 1.40 0.30 2.00 2.40 1.50 2.20 - 2.30 0.90 2.10 2.00 1.30 2.30 2.00 2.30 2.10 2.00 1.70 -1.50 2.00 2.00 -0.20 2.30 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 - 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ C - U /\ | G - 3' <------ 5' - 2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 - 2.00 1.70 0.00 2.00 1.70 1.70 2.00 0.70 0.60 2.00 1.60 -1.20 2.00 1.80 -0.80 1.00 - 0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.90 1.60 -0.10 2.00 1.60 1.60 2.00 0.60 0.50 2.00 1.50 -1.30 2.00 1.70 -0.90 0.90 - 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 - 0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.40 1.20 -0.60 2.00 1.10 1.80 2.00 0.80 0.00 2.00 1.10 -0.70 2.00 1.80 -0.30 1.40 - 1.70 0.40 0.50 2.00 0.40 1.40 2.00 0.50 1.10 2.00 1.30 -2.50 2.00 1.50 -2.10 1.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 - 0.70 -0.50 -0.50 2.00 -0.60 0.50 2.00 -0.50 0.10 2.00 0.40 -3.50 2.00 0.50 -3.10 0.50 - 2.00 0.80 0.80 2.00 0.70 0.80 2.00 -0.20 1.50 2.00 1.70 -0.30 2.00 0.80 0.10 0.00 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ G - U /\ | C - 3' <------ 5' - 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 - 1.90 1.80 0.90 2.00 2.20 2.10 2.00 1.90 0.90 2.00 1.60 -0.80 2.00 1.90 0.70 1.00 - 0.80 0.70 -0.20 2.00 1.10 2.00 2.00 1.80 -0.20 2.00 0.50 -0.10 2.00 1.80 1.40 1.80 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.80 1.70 0.80 2.00 2.10 2.00 2.00 1.80 0.80 2.00 1.50 -0.90 2.00 1.80 0.60 0.90 - 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 - 0.80 0.70 -0.20 2.00 1.10 2.00 2.00 1.80 -0.20 2.00 0.50 -0.10 2.00 1.80 1.40 1.80 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.30 1.20 0.30 2.00 1.70 2.10 2.00 2.00 0.30 2.00 1.10 -0.40 2.00 2.00 1.10 1.50 - 1.60 0.50 1.40 2.00 0.90 1.80 2.00 1.60 1.40 2.00 1.30 -2.10 2.00 1.60 -0.60 1.60 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 - 0.60 -0.50 0.40 2.00 0.00 0.80 2.00 0.70 0.40 2.00 0.40 -3.10 2.00 0.70 -1.60 0.60 - 1.90 0.80 1.80 2.00 1.30 1.10 2.00 1.00 1.80 2.00 1.70 0.00 2.00 1.00 1.60 0.10 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ U - U /\ | A - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 - 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.50 2.30 1.30 2.00 2.40 2.20 2.00 2.20 1.30 2.00 1.80 0.10 2.00 2.20 1.10 1.40 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.80 0.80 2.00 1.90 2.40 2.00 2.40 0.80 2.00 1.40 0.70 2.00 2.40 1.60 2.00 - 2.30 1.10 1.90 2.00 1.20 2.00 2.00 2.00 1.90 2.00 1.60 -1.10 2.00 2.00 -0.10 2.00 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 - 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ G - U /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.60 1.00 2.00 2.10 2.70 2.00 2.70 1.00 2.00 1.40 0.30 2.00 2.40 1.50 2.20 - 2.30 0.90 2.10 2.00 1.30 2.30 2.00 2.30 2.10 2.00 1.70 -1.50 2.00 2.00 -0.20 2.30 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 - 2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - A \/ \_/ U - U /\ | G - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.60 2.40 1.40 2.00 2.50 2.30 2.00 2.30 1.40 2.00 1.90 0.20 2.00 2.30 1.20 1.50 - 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2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - C \/ \_/ A - G /\ | U - 3' <------ 5' - 2.00 1.60 1.00 2.00 2.00 2.60 2.00 2.60 1.00 2.00 1.40 0.20 2.00 2.30 1.50 2.20 - 2.40 1.90 1.30 2.00 2.40 2.40 2.00 2.40 1.30 2.00 1.70 -0.40 2.00 2.10 0.80 1.50 - 1.00 0.60 0.00 2.00 1.00 2.00 2.00 2.00 0.00 2.00 0.40 0.00 2.00 1.70 1.30 2.00 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.90 1.50 0.90 2.00 1.90 1.90 2.00 1.90 0.90 2.00 1.30 -0.90 2.00 1.60 0.40 1.10 - 2.80 1.80 2.20 2.00 2.20 2.20 2.00 2.20 2.20 2.00 2.20 0.40 2.00 1.90 1.70 1.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.70 1.60 2.00 2.00 2.10 2.10 2.00 2.10 2.00 2.00 2.00 0.30 2.00 1.80 1.50 1.20 - 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3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.50 1.30 0.30 2.00 1.40 2.20 2.00 2.20 0.30 2.00 0.80 0.90 2.00 2.20 1.90 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.80 0.80 2.00 1.90 2.40 2.00 2.40 0.80 2.00 1.40 0.70 2.00 2.40 1.60 2.00 - 2.30 1.10 1.90 2.00 1.20 2.00 2.00 2.00 1.90 2.00 1.60 -1.10 2.00 2.00 -0.10 2.00 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.30 0.10 0.90 2.00 0.20 1.00 2.00 1.00 0.90 2.00 0.70 -2.10 2.00 1.00 -1.10 1.10 - 2.70 1.40 2.20 2.00 1.50 1.40 2.00 1.40 2.20 2.00 2.00 1.10 2.00 1.40 2.00 0.60 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ A - G /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.90 1.30 2.00 2.30 2.30 2.00 2.30 1.30 2.00 1.70 -0.50 2.00 2.00 0.80 1.50 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 - 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 - 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ C - G /\ | G - 3' <------ 5' - 2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 - 2.10 1.90 0.10 2.00 1.80 1.90 2.00 0.90 0.70 2.00 1.80 -1.00 2.00 1.90 -0.60 1.10 - 1.10 0.80 -0.90 2.00 0.80 1.80 2.00 0.90 -0.30 2.00 0.70 -0.30 2.00 1.90 0.10 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.70 1.40 -0.30 2.00 1.40 1.40 2.00 0.40 0.30 2.00 1.30 -1.50 2.00 1.50 -1.10 0.70 - 2.70 1.90 1.10 2.00 1.80 1.90 2.00 0.90 1.70 2.00 2.40 0.00 2.00 1.90 0.40 1.10 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.40 1.60 0.80 2.00 1.50 1.60 2.00 0.60 1.40 2.00 2.10 -0.30 2.00 1.60 0.10 0.80 - 1.10 0.80 -0.90 2.00 0.80 1.80 2.00 0.90 -0.30 2.00 0.70 -0.30 2.00 1.90 0.10 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.50 1.20 -0.50 2.00 1.20 1.80 2.00 0.80 0.10 2.00 1.10 -0.70 2.00 1.90 -0.30 1.50 - 1.60 0.30 0.40 2.00 0.30 1.30 2.00 0.40 1.00 2.00 1.20 -2.60 2.00 1.40 -2.20 1.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.70 1.90 1.10 2.00 1.80 1.90 2.00 0.90 1.70 2.00 2.40 0.00 2.00 1.90 0.40 1.10 - 0.30 -0.90 -0.90 2.00 -1.00 0.10 2.00 -0.90 -0.30 2.00 0.00 -3.90 2.00 0.10 -3.50 0.10 - 2.30 1.00 1.10 2.00 1.00 1.00 2.00 0.00 1.70 2.00 1.90 -0.10 2.00 1.10 0.30 0.30 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ G - G /\ | C - 3' <------ 5' - 2.00 1.90 1.00 2.00 2.40 2.80 2.00 2.70 1.00 2.00 1.80 0.30 2.00 2.70 1.80 2.20 - 2.00 1.90 1.00 2.00 2.40 2.20 2.00 2.10 1.00 2.00 1.80 -0.70 2.00 2.10 0.80 1.20 - 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.60 1.50 0.60 2.00 1.90 1.80 2.00 1.60 0.60 2.00 1.30 -1.10 2.00 1.60 0.40 0.70 - 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.60 1.70 2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 - 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 1.40 1.30 0.40 2.00 1.70 2.20 2.00 2.00 0.40 2.00 1.10 -0.30 2.00 2.00 1.20 1.50 - 1.50 0.40 1.30 2.00 0.80 1.70 2.00 1.50 1.30 2.00 1.20 -2.20 2.00 1.50 -0.70 1.50 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 - 0.20 -0.90 0.00 2.00 -0.40 0.40 2.00 0.30 0.00 2.00 0.00 -3.50 2.00 0.30 -2.00 0.20 - 2.20 1.10 2.00 2.00 1.50 1.40 2.00 1.20 2.00 2.00 1.90 0.30 2.00 1.20 1.80 0.30 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ U - G /\ | A - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 - 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 - 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ G - G /\ | U - 3' <------ 5' - 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 - 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 1.90 1.30 2.00 2.30 2.30 2.00 2.30 1.30 2.00 1.70 -0.50 2.00 2.00 0.80 1.50 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 - 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 - 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 - 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 - 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 - Y - --------------------------------------------------------------------------------------------- - A A A A C C C C G G G G U U U U - A C G U A C G U A C G U A C G U - --------------------------------------------------------------------------------------------- - 5' ------> 3' - U \/ \_/ U - G /\ | G - 3' <------ 5' - 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 - 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 - 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 - 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 - 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 - 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 - 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 - 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/Turner99/stack.dat b/gtfold-mfe/data/Turner99/stack.dat deleted file mode 100644 index ba2d3f5..0000000 --- a/gtfold-mfe/data/Turner99/stack.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . . . . -0.90 - . . . . . . . . . . . . . . -2.20 . - . . . . . . . . . . . . . -2.10 . -0.60 - . . . . . . . . . . . . -1.10 . -1.40 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . -2.10 . . . . - . . . . . . . . . . -3.30 . . . . . - . . . . . . . . . -2.40 . -1.40 . . . . - . . . . . . . . -2.10 . -2.10 . . . . . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . -2.40 . . . . . . . -1.30 - . . . . . . -3.40 . . . . . . . -2.50 . - . . . . . -3.30 . -1.50 . . . . . -2.10 . -0.50 - . . . . -2.20 . -2.50 . . . . . -1.40 . 1.30 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.30 . . . . . . . -1.00 . . . . - . . -2.40 . . . . . . . -1.50 . . . . . - . -2.10 . -1.00 . . . . . -1.40 . 0.30 . . . . - -0.90 . -1.30 . . . . . -0.60 . -0.50 . . . . . diff --git a/gtfold-mfe/data/Turner99/tloop.dat b/gtfold-mfe/data/Turner99/tloop.dat deleted file mode 100644 index ad64bf4..0000000 --- a/gtfold-mfe/data/Turner99/tloop.dat +++ /dev/null @@ -1,32 +0,0 @@ - Seq Energy - ------------- - GGGGAC -3.00 - GGUGAC -3.00 - CGAAAG -3.00 - GGAGAC -3.00 - CGCAAG -3.00 - GGAAAC -3.00 - CGGAAG -3.00 - CUUCGG -3.00 - CGUGAG -3.00 - CGAAGG -2.50 - CUACGG -2.50 - GGCAAC -2.50 - CGCGAG -2.50 - UGAGAG -2.50 - CGAGAG -2.00 - AGAAAU -2.00 - CGUAAG -2.00 - CUAACG -2.00 - UGAAAG -2.00 - GGAAGC -1.50 - GGGAAC -1.50 - UGAAAA -1.50 - AGCAAU -1.50 - AGUAAU -1.50 - CGGGAG -1.50 - AGUGAU -1.50 - GGCGAC -1.50 - GGGAGC -1.50 - GUGAAC -1.50 - UGGAAA -1.50 diff --git a/gtfold-mfe/data/Turner99/triloop.dat b/gtfold-mfe/data/Turner99/triloop.dat deleted file mode 100644 index 75c3bfc..0000000 --- a/gtfold-mfe/data/Turner99/triloop.dat +++ /dev/null @@ -1,2 +0,0 @@ - Seq Energy - ------------- diff --git a/gtfold-mfe/data/Turner99/tstack.dat b/gtfold-mfe/data/Turner99/tstack.dat deleted file mode 100644 index 97a4115..0000000 --- a/gtfold-mfe/data/Turner99/tstack.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.00 . . . -1.00 . . . -2.20 -0.80 -1.00 -0.80 . - . . -1.50 . . . -1.50 . . . -2.70 . -0.60 -0.70 . -0.70 - . -1.50 . -1.00 . -1.50 . -1.00 . -2.70 . -2.20 -0.80 . -0.80 . - -1.00 . -1.50 . -1.00 . -1.50 . -2.20 . -2.70 . . -0.80 . -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.00 . . . -1.00 -1.50 -1.50 -1.40 . . . . -1.00 - . . -1.50 . . . -1.50 . -1.00 -1.10 . -0.80 . . -1.50 . - . -1.50 . -1.00 . -1.50 . -1.00 -1.40 . -1.60 . . -1.50 . -1.00 - -1.00 . -1.50 . -1.00 . -1.50 . . -1.40 . -1.20 -1.00 . -1.50 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -2.20 -1.10 -1.50 -1.30 . . . . -1.00 -0.30 -1.00 -0.80 . - . . -2.70 . -1.10 -0.70 . -0.50 . . -1.50 . -0.60 -0.70 . -0.70 - . -2.70 . -2.20 -1.60 . -1.40 . . -1.50 . -1.00 -0.60 . -0.80 . - -2.20 . -2.70 . . -1.00 . -0.70 -1.00 . -1.50 . . -0.80 . -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - -1.00 -0.80 -1.10 . . . . -1.00 -1.00 -0.80 -1.10 . . . . -2.00 - -0.70 -0.60 . -0.50 . . -1.50 . -0.70 -0.60 . -0.50 . . -2.50 . - -1.10 . -1.20 . . -1.50 . -1.00 -0.50 . -0.80 -0.80 . -2.50 . -2.00 - . -0.60 . -0.50 -1.00 . -1.50 . . -0.60 -1.10 -0.50 -2.00 . -2.50 . diff --git a/gtfold-mfe/data/Turner99/tstackcoax.dat b/gtfold-mfe/data/Turner99/tstackcoax.dat deleted file mode 100644 index b90d0bc..0000000 --- a/gtfold-mfe/data/Turner99/tstackcoax.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : COAXIAL STACKING - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.00 . . . -0.70 . . . -1.10 -0.80 -1.00 -0.80 -0.40 - . . -1.10 . . . -1.10 . . . -1.60 . -0.60 -0.70 -1.70 -0.70 - . -1.50 . -1.00 . -1.00 . -0.70 . -1.40 . -0.50 -0.80 -1.60 -0.80 -0.10 - -0.80 . -0.30 . -0.60 . -0.60 . -0.80 . -0.60 . -0.60 -0.80 -0.90 -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -0.80 . . . -0.60 -1.50 -1.50 -1.40 -1.60 . . . -0.60 - . . -1.50 . . . -0.70 . -1.00 -1.10 -2.80 -0.80 . . -1.00 . - . -1.50 . -0.80 . -1.10 . -0.60 -1.40 -1.90 -1.60 -0.90 . -1.40 . -0.60 - -1.00 . -1.00 . -0.70 . -0.70 . -1.60 -1.40 -1.60 -1.20 -0.80 . -0.80 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.10 -1.10 -1.50 -1.30 -1.90 . . . -1.20 -0.30 -1.00 -0.80 -0.80 - . . -1.30 . -1.10 -0.70 -2.90 -0.50 . . -1.40 . -0.60 -0.70 -2.00 -0.70 - . -1.40 . -1.10 -1.60 -2.80 -1.40 -1.00 . -1.60 . -0.80 -0.60 -1.60 -0.80 0.00 - -0.80 . -0.80 . -1.70 -1.00 -2.00 -0.70 -0.80 . -0.80 . -0.90 -0.80 1.80 -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - -1.00 -0.80 -1.10 -0.80 . . . -0.50 -1.00 -0.80 -1.10 -0.50 . . . -0.50 - -0.70 -0.60 -1.90 -0.50 . . -0.50 . -0.70 -0.60 -1.00 -0.50 . . -0.70 . - -1.10 -1.60 -1.20 -0.50 . -0.80 . -0.50 -0.50 -0.90 -0.80 0.80 . -1.20 . -0.50 - -0.40 -0.60 -0.80 -0.50 -0.70 . -0.70 . -0.10 -0.60 -0.00 -0.50 -0.80 . -0.80 . diff --git a/gtfold-mfe/data/Turner99/tstackh.dat b/gtfold-mfe/data/Turner99/tstackh.dat deleted file mode 100644 index 6959647..0000000 --- a/gtfold-mfe/data/Turner99/tstackh.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . -0.30 -0.50 -0.30 -0.30 - . . . . . . . . . . . . -0.10 -0.20 -1.50 -0.20 - . . . . . . . . . . . . -1.10 -1.20 -0.20 0.20 - . . . . . . . . . . . . -0.30 -0.30 -0.60 -1.10 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . -1.50 -1.50 -1.40 -1.80 . . . . - . . . . . . . . -1.00 -0.90 -2.90 -0.80 . . . . - . . . . . . . . -2.20 -2.00 -1.60 -1.10 . . . . - . . . . . . . . -1.70 -1.40 -1.80 -2.00 . . . . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . -1.10 -1.50 -1.30 -2.10 . . . . 0.20 -0.50 -0.30 -0.30 - . . . . -1.10 -0.70 -2.40 -0.50 . . . . -0.10 -0.20 -1.50 -0.20 - . . . . -2.40 -2.90 -1.40 -1.20 . . . . -0.90 -1.10 -0.30 0.00 - . . . . -1.90 -1.00 -2.20 -1.50 . . . . -0.30 -0.30 -0.40 -1.10 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - -0.50 -0.30 -0.60 -0.50 . . . . -0.50 -0.30 -0.60 -0.50 . . . . - -0.20 -0.10 -1.20 -0.00 . . . . -0.20 -0.10 -1.70 0.00 . . . . - -1.40 -1.20 -0.70 -0.20 . . . . -0.80 -1.20 -0.30 -0.70 . . . . - -0.30 -0.10 -0.50 -0.80 . . . . -0.60 -0.10 -0.60 -0.80 . . . . diff --git a/gtfold-mfe/data/Turner99/tstacki.dat b/gtfold-mfe/data/Turner99/tstacki.dat deleted file mode 100644 index bf5d98c..0000000 --- a/gtfold-mfe/data/Turner99/tstacki.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . . . . . 0.70 0.70 -0.40 0.70 - . . . . . . . . . . . . 0.70 0.70 0.70 0.70 - . . . . . . . . . . . . -0.40 0.70 0.70 0.70 - . . . . . . . . . . . . 0.70 0.70 0.70 0.00 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . . . . . -0.00 -0.00 -1.10 -0.00 . . . . - . . . . . . . . -0.00 -0.00 -0.00 -0.00 . . . . - . . . . . . . . -1.10 -0.00 -0.00 -0.00 . . . . - . . . . . . . . -0.00 -0.00 -0.00 -0.70 . . . . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . . -0.00 -0.00 -1.10 -0.00 . . . . 0.70 0.70 -0.40 0.70 - . . . . -0.00 -0.00 -0.00 -0.00 . . . . 0.70 0.70 0.70 0.70 - . . . . -1.10 -0.00 -0.00 -0.00 . . . . -0.40 0.70 0.70 0.70 - . . . . -0.00 -0.00 -0.00 -0.70 . . . . 0.70 0.70 0.70 0.00 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - 0.70 0.70 -0.40 0.70 . . . . 0.70 0.70 -0.40 0.70 . . . . - 0.70 0.70 0.70 0.70 . . . . 0.70 0.70 0.70 0.70 . . . . - -0.40 0.70 0.70 0.70 . . . . -0.40 0.70 0.70 0.70 . . . . - 0.70 0.70 0.70 0.00 . . . . 0.70 0.70 0.70 0.00 . . . . diff --git a/gtfold-mfe/data/Turner99/tstackm.dat b/gtfold-mfe/data/Turner99/tstackm.dat deleted file mode 100644 index f38c845..0000000 --- a/gtfold-mfe/data/Turner99/tstackm.dat +++ /dev/null @@ -1,63 +0,0 @@ -Data Arangement: - Y - ------------------ - (X) A C G U - ------------------ - 5' ==> 3' - AX - AY - 3' <== 5' - (A) . . . . - (C) . . . . - (G) . . . . - (U) -0.70 -0.10 -0.70 -0.10 --------------------------------- -STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - AX AX AX AX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.00 . . . -1.00 . . . -2.20 -0.80 -1.00 -0.80 -0.90 - . . -1.50 . . . -1.50 . . . -2.70 . -0.60 -0.70 -2.20 -0.70 - . -1.50 . -1.00 . -1.50 . -1.00 . -2.70 . -2.20 -0.80 -2.10 -0.80 -0.80 - -1.00 . -1.50 . -1.00 . -1.50 . -2.20 . -2.70 . -1.10 -0.80 -1.10 -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - CX CX CX CX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -1.00 . . . -1.00 -1.70 -1.70 -1.70 -1.70 . . . -1.00 - . . -1.50 . . . -1.50 . -1.00 -1.10 -3.30 -0.80 . . -1.50 . - . -1.50 . -1.00 . -1.50 . -1.00 -1.70 -2.40 -1.70 -1.70 . -1.50 . -1.00 - -1.00 . -1.50 . -1.00 . -1.50 . -1.60 -1.40 -1.60 -1.20 -1.00 . -1.50 . - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - GX GX GX GX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - . . . -2.20 -1.10 -1.50 -1.30 -1.90 . . . -1.00 -0.80 -1.00 -0.80 -1.30 - . . -2.70 . -1.10 -0.70 -3.40 -0.50 . . -1.50 . -0.60 -0.70 -2.50 -0.70 - . -2.70 . -2.20 -1.60 -3.30 -1.40 -1.30 . -1.50 . -1.00 -0.80 -2.10 -0.80 -0.80 - -2.20 . -2.70 . -1.70 -1.00 -2.00 -0.70 -1.00 . -1.50 . -1.40 -0.80 1.30 -0.80 - Y Y Y Y - ------------------ ------------------ ------------------ ------------------ - A C G U A C G U A C G U A C G U - ------------------ ------------------ ------------------ ------------------ - 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' - UX UX UX UX - AY CY GY UY - 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' - -1.00 -0.80 -1.10 -1.30 . . . -1.00 -1.00 -0.80 -1.10 -1.00 . . . -2.00 - -0.70 -0.60 -2.40 -0.50 . . -1.50 . -0.70 -0.60 -1.50 -0.50 . . -2.50 . - -1.10 -2.10 -1.20 -1.00 . -1.50 . -1.00 -0.70 -1.40 -0.80 0.30 . -2.50 . -2.00 - -0.90 -0.60 -1.40 -0.50 -1.00 . -1.50 . -0.50 -0.60 -0.50 -0.50 -2.00 . -2.50 . From cbaa6e8a13f09b8ff14fbbdd5fad235d8fe474e4 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:23:00 -0400 Subject: [PATCH 066/187] rmeoved .dat entries --- gtfold-mfe/data/Turner99/Makefile.am | 22 +--------------------- gtfold-mfe/data/Turner99/Makefile.in | 24 ++---------------------- 2 files changed, 3 insertions(+), 43 deletions(-) diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index cb09a05..c8cf6c6 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -15,27 +15,7 @@ gtfold_data_DATA = \ tloop.DAT\ tstackh.DAT\ tstacki.DAT\ - tstackm.DAT\ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat - + tstackm.DAT EXTRA_DIST = $(gtfold_data_DATA) diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index d042a79..084882b 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -112,7 +112,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -188,26 +187,7 @@ gtfold_data_DATA = \ tloop.DAT\ tstackh.DAT\ tstacki.DAT\ - tstackm.DAT\ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat + tstackm.DAT EXTRA_DIST = $(gtfold_data_DATA) CLEANFILES = *~ From d2f0de250f17a19dd2fae5887c20ea9b8d92af4f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 21 Jun 2011 13:51:17 -0400 Subject: [PATCH 067/187] fix for contact dist --- gtfold-mfe/src/constraints.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index c491068..08f67bc 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -494,7 +494,7 @@ int canStack(int i, int j) { int withinCD(int i, int j){ //ZS: This function returns 1 if i and j are within the required contact distance from each other. if (LIMIT_DISTANCE){ - return (j-i>=contactDistance); + return (j-i<=contactDistance); } else return 1; } From 4da0d65ff0c7adea819294bf54dc4e5b1b283064 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 21 Jun 2011 13:52:22 -0400 Subject: [PATCH 068/187] fixed subopt, change to take value kCal --- gtfold-mfe/include/options.h | 2 +- gtfold-mfe/include/subopt_traceback.h | 8 +- gtfold-mfe/src/main.cc | 2 +- gtfold-mfe/src/options.cc | 6 +- gtfold-mfe/src/subopt_traceback.cc | 128 ++++++++++++++------------ 5 files changed, 76 insertions(+), 70 deletions(-) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 0862b03..46b3a3a 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -27,7 +27,7 @@ extern string shapeFile; extern string outputFile; extern string paramDir; -extern int suboptDelta; +extern float suboptDelta; extern int nThreads; extern bool LIMIT_DISTANCE; diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h index a02839e..cccf44e 100644 --- a/gtfold-mfe/include/subopt_traceback.h +++ b/gtfold-mfe/include/subopt_traceback.h @@ -217,10 +217,10 @@ void push_to_gstack(ps_stack_t & gs, const ps_t& v); ss_map_t subopt_traceback(int len, int gap); -void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); +void traceV(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceW(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs); void traceWM(ps_t& ps, ps_map_t& filter); #endif diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 87a4c1c..49b3676 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -235,7 +235,7 @@ int main(int argc, char** argv) { if (SUBOPT_ENABLED) { t1 = get_seconds(); - ss_map_t subopt_data = subopt_traceback(seq.length(), suboptDelta); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); t1 = get_seconds() - t1; printf("Subopt traceback running time: %9.6f seconds\n\n", t1); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 1545f60..a37ee9a 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -23,7 +23,7 @@ string shapeFile = ""; string paramDir = "Turner99"; // default value -int suboptDelta = -1; +float suboptDelta = 0.0; int nThreads = -1; int contactDistance = -1; @@ -118,7 +118,7 @@ void parse_options(int argc, char** argv) { } else if(strcmp(argv[i], "--subopt") == 0) { SUBOPT_ENABLED = true; if(i < argc) - suboptDelta = atoi(argv[++i]); + suboptDelta = atof(argv[++i]); else help(); } @@ -196,7 +196,7 @@ void printRunConfiguration(string seq) { } if (SUBOPT_ENABLED) { - printf("+ calculating suboptimal structures within %d kcal/mol of MFE\n", suboptDelta); + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); standardRun = false; } diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 6375f2e..1cfe6d5 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -30,7 +30,9 @@ const char* lstr[] = {"W", "V", "VBI", "VM", "WM"}; -void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy); +void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs); +int delta = 0; +int mfe = INFINITY_; void print_stack(ps_stack_t temp) { @@ -45,15 +47,14 @@ void print_stack(ps_stack_t temp) std::cout << "}\n"; } -void process(ss_map_t& subopt_data, int energy, int len) +void process(ss_map_t& subopt_data, int len) { int count = 0 ; ps_stack_t gstack; - // initialize the partial structure - // segment stack = {[1,n]}, label = W, list_bp = {} + // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} ps_t first(0, len); - first.push(segment(5, len, lW, W[len])); + first.push(segment(1, len, lW, W[len])); gstack.push(first); // initialize the partial structure stacka while (1) @@ -65,11 +66,17 @@ void process(ss_map_t& subopt_data, int energy, int len) if (ps.empty()) { - //std::cout << ps.str << " dG =" << ps.ae_ << std::endl; - if (subopt_data.find(ps.str) == subopt_data.end()) + ss_map_t::iterator it = subopt_data.find(ps.str); + if ( it == subopt_data.end()) { subopt_data.insert(std::make_pair(ps.str,ps.ae_)); count++; + } else + { + int energy = it->second; + if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ >= mfe + delta)) { + subopt_data[it->first] = ps.ae_; + } } continue; } @@ -79,12 +86,13 @@ void process(ss_map_t& subopt_data, int energy, int len) ps.pop(); size_t s1 = gstack.size(); - if (smt.j_ - smt.i_ >=4) + if (smt.j_ - smt.i_ >= TURN) { - (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy); + (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); } - - if (gstack.size() == s1 && ps.total() == energy) + + // discard this segment, use remaining ones + if (gstack.size() == s1 && ps.total() <= mfe + delta) { ps_t ps1(ps); gstack.push(ps1); @@ -93,31 +101,27 @@ void process(ss_map_t& subopt_data, int energy, int len) } } -ss_map_t subopt_traceback(int len, int delta) +ss_map_t subopt_traceback(int len, int _delta) { trace_func[0] = traceW; trace_func[1] = traceV; - trace_func[2] = traceVBI; trace_func[3] = traceVM; - //trace_func[4] = traceWM; - int mfe = W[len]; - int level = 0; + mfe = W[len]; + delta = _delta; ss_map_t subopt_data; - - for (level = mfe; level <= mfe + delta; level += 10) - process(subopt_data, level, len); + process(subopt_data, len); return subopt_data; } -void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) +void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { // Hairpin Loop - if (eH(i,j) + ps.total() == energy ) + if (eH(i,j) + ps.total() <= mfe + delta ) { - // std::cout << "Hairpin " << i << ' ' << j << std::endl; + //std::cout << "Hairpin " << i << ' ' << j << std::endl; ps_t ps1(ps); ps1.accumulate(eH(i,j)); ps1.update(i, j, '(', ')'); @@ -125,7 +129,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() == energy) + if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { // std::cout << "Stack " << i << ' ' << j << std::endl; ps_t ps1(ps); @@ -136,19 +140,20 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } // Internal Loop - if (VBI(i,j) + ps.total() == energy ) + if (VBI(i,j) + ps.total() <= mfe + delta ) { //std::cout << "Internal " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVBI, VBI(i,j))); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); + //ps_t ps1(ps); + //ps1.push(segment(i, j, lVBI, VBI(i,j))); + //ps1.update(i, j, 'i', 'i'); + //push_to_gstack(gstack, ps1); + traceVBI(i,j,ps,gstack); } // Multiloop - if ( VM(i,j) + ps.total() == energy ) + if ( VM(i,j) + ps.total() <= mfe + delta ) { - // std::cout << "Multi " << i << ' ' << j << std::endl; + //std::cout << "Multi " << i << ' ' << j << std::endl; ps_t ps1(ps); ps1.push(segment(i, j, lVM, VM(i,j))); ps1.update(i, j, '(', ')'); @@ -157,19 +162,21 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } -void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) +void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { int p,q; for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p) { int minq = j-i+p-MAXLOOP-2; if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); - for (q = minq; q < j; q++) + for (q = minq; q <= maxq; q++) { - if (V(p, q) + eL(i, j, p, q) + ps.total() == energy ) + if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta && PP[p][q] == 1) { ps_t ps1(ps); + ps1.update(i, j, '(', ')'); ps1.push(segment(p, q, lV, V(p, q))); ps1.accumulate(eL(i, j, p, q)); push_to_gstack(gstack, ps1); @@ -178,16 +185,14 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) } } -void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) +void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack) { - if ( (h>=j) || j == 0 || j == 1) return; - - for (int i = h; i < j; ++i) + for (int i = 1; i < j-TURN; ++i) { int wim1 = MIN(0, W[i-1]); int wij = V(i,j) + auPenalty(i, j) + wim1; - if (wij + ps.total() == energy ) + if (wij + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(i, j, lV, V(i,j))); @@ -195,9 +200,10 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) ps1.accumulate(auPenalty(i, j)); push_to_gstack(gstack, ps1); } - + + int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - if (wijd + ps.total() == energy ) + if (wijd + ps.total() <= mfe + delta ) { ps_t ps3(ps); ps3.push(segment(i, j-1, lV, V(i, j-1))); @@ -207,7 +213,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - if (widj + ps.total() == energy ) + if (widj + ps.total() <= mfe + delta ) { ps_t ps4(ps); ps4.push(segment(i+1, j, lV, V(i+1,j))); @@ -217,7 +223,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1; - if (widjd + ps.total() == energy ) + if (widjd + ps.total() <= mfe + delta ) { ps_t ps2(ps); ps2.push(segment(i+1, j-1, lV, V(i+1,j-1))); @@ -225,9 +231,9 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); push_to_gstack(gstack, ps2); } - } + } - if (W[j-1] + ps.total() == energy ) + if (W[j-1] + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(1, j-1, lW, W[j-1])); @@ -235,7 +241,7 @@ void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) } } -void traceWM(ps_t& ps, ps_map_t& filter, int energy) +void traceWM(ps_t& ps, ps_map_t& filter) { ps_stack_t wm_stack; wm_stack.push(ps); @@ -276,7 +282,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) int h = i1; int k = j1; int wmij = V(h,k) + auPenalty(h,k) + Eb; - if (pss.total() + wmij == energy ) + if (pss.total() + wmij <= mfe + delta ) { ps_t ps1(pss); ps1.push_v(segment(h,k,lV, V(h,k))); @@ -285,7 +291,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ; - if (pss.total() + wmijd == energy ) + if (pss.total() + wmijd <= mfe + delta ) { ps_t ps1(pss); ps1.push_v(segment(h,k-1,lV, V(h,k-1))); @@ -294,7 +300,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ; - if (pss.total() + wmidj == energy ) + if (pss.total() + wmidj <= mfe + delta ) { ps_t ps1(pss); ps1.push_v(segment(h+1, k, lV, V(h+1,k))); @@ -303,7 +309,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec ; - if (pss.total() + wmidjd == energy ) + if (pss.total() + wmidjd <= mfe + delta ) { ps_t ps1(pss); ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1))); @@ -312,7 +318,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } - if (pss.total() + WM(i1,j1-1) + Ec == energy ) + if (pss.total() + WM(i1,j1-1) + Ec <= mfe + delta ) { ps_t ps1(pss); ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1))); @@ -320,7 +326,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) wm_stack.push(ps1); } - if (pss.total() + WM[i1+1][j1] + Ec == energy ) + if (pss.total() + WM[i1+1][j1] + Ec <= mfe + delta ) { ps_t ps1(pss); ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1))); @@ -330,7 +336,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) for (int h = i1+1; h <= j1-1; ++h) { - if (WM(i1,h) + WM(h+1,j1) + pss.total() == energy ) + if (WM(i1,h) + WM(h+1,j1) + pss.total() <= mfe + delta ) { ps_t ps1(pss); ps1.push(segment(i1, h, lWM, WM(i1,h))); @@ -341,7 +347,7 @@ void traceWM(ps_t& ps, ps_map_t& filter, int energy) } } -void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) +void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { std::map filter; int h; @@ -354,43 +360,43 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) int common = auPenalty(i,j) + Ea + Eb; dG = common + WM[i+1][h-1] + WM[h][j-1]; - if (dG + ps.total() == energy ) + if (dG + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); ps1.push(segment(h, j-1, lWM, WM[h][j-1])); ps1.accumulate(common) ; - traceWM(ps1, filter, energy); + traceWM(ps1, filter); } dG = common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec; - if (dG + ps.total() == energy ) + if (dG + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); ps1.push(segment(h, j-1, lWM, WM[h][j-1])); ps1.accumulate(common + d5 + Ec); - traceWM(ps1, filter, energy); + traceWM(ps1, filter); } dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec; - if (dG + ps.total() == energy ) + if (dG + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); ps1.push(segment(h, j-2, lWM, WM[h][j-2])); ps1.accumulate(common + d3 + Ec); - traceWM(ps1, filter, energy); + traceWM(ps1, filter); } dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec; - if (dG + ps.total() == energy ) + if (dG + ps.total() <= mfe + delta ) { ps_t ps1(ps); ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); ps1.push(segment(h, j-2, lWM, WM[h][j-2])); ps1.accumulate(common + d3 + d5 + 2*Ec) ; - traceWM(ps1, filter, energy); + traceWM(ps1, filter); } } From 0ed558f5b3b83838850113236e36be0269d01874 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 22 Jun 2011 13:41:55 -0400 Subject: [PATCH 069/187] fix for allowable basepair --- gtfold-mfe/src/algorithms.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 6f4a314..c428607 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -37,7 +37,7 @@ void initializeMatrix(int len) { for (i = 1; i <= len; ++i) for (j = len; j >= i; --j) - if (canPair(RNA[i],RNA[j]) && j-i >= TURN) + if (canPair(RNA[i],RNA[j]) && j-i > TURN) PP[i][j] = 1; } From a21bebc689ce891497a423bb885b8e5ac873ff12 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 22 Jun 2011 13:48:21 -0400 Subject: [PATCH 070/187] subopt changes --- gtfold-mfe/src/main.cc | 18 ++++++++++++------ gtfold-mfe/src/subopt_traceback.cc | 6 ++++-- 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 49b3676..7f11741 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -165,14 +165,20 @@ void print_header() { printf("Georgia Institute of Technology\n\n"); } -void save_subopt_file(string outputFile, ss_map_t& ss_data) +void save_subopt_file(string outputFile, ss_map_t& ss_data, + const string& seq, int energy) { ofstream outfile; outfile.open(outputFile.c_str()); - - for (ss_map_t::iterator it = ss_data.begin(); - it != ss_data.end(); ++it) { - outfile << it->first << '\t' << it->second/100.0 << std::endl; + char buff[1024]; + + sprintf(buff,"%s\t%0.2f", seq.c_str(), energy/100.0); + outfile << buff << std::endl; + for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) + { + sprintf(buff,"%s %0.2f", (it->first).c_str(), it->second/100.0); + //outfile << it->first << '\t' << it->second/100.0 << std::endl; + outfile << buff << std::endl; } outfile.close(); @@ -250,7 +256,7 @@ int main(int argc, char** argv) { suboptfile += ".ss"; printf("Suboptimal structures saved in %s\n", suboptfile.c_str()); - save_subopt_file(suboptfile, subopt_data); + save_subopt_file(suboptfile, subopt_data, seq, energy); free_fold(seq.length()); exit(0); } diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 1cfe6d5..d5e4729 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -66,15 +66,17 @@ void process(ss_map_t& subopt_data, int len) if (ps.empty()) { + //std::cout << ps.str << ' ' << ps.ae_/100.0 << std::endl; ss_map_t::iterator it = subopt_data.find(ps.str); if ( it == subopt_data.end()) { subopt_data.insert(std::make_pair(ps.str,ps.ae_)); count++; - } else + } + else { int energy = it->second; - if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ >= mfe + delta)) { + if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ <= mfe + delta)) { subopt_data[it->first] = ps.ae_; } } From e98313ff9119072e16d58fc65134732923d9e325 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 23 Jun 2011 14:05:03 -0400 Subject: [PATCH 071/187] adding UNAfold parameters --- gtfold-mfe/data/UNAParams/asint1x2.DAT | 96 ++++ gtfold-mfe/data/UNAParams/dangle.DAT | 8 + gtfold-mfe/data/UNAParams/extinction.DAT | 22 + gtfold-mfe/data/UNAParams/hexaloop.DAT | 0 gtfold-mfe/data/UNAParams/loop.DAT | 30 ++ gtfold-mfe/data/UNAParams/miscloop.DAT | 13 + gtfold-mfe/data/UNAParams/sint2.DAT | 24 + gtfold-mfe/data/UNAParams/sint4.DAT | 576 +++++++++++++++++++++++ gtfold-mfe/data/UNAParams/stack.DAT | 16 + gtfold-mfe/data/UNAParams/tloop.DAT | 30 ++ gtfold-mfe/data/UNAParams/triloop.DAT | 0 gtfold-mfe/data/UNAParams/tstacke.DAT | 16 + gtfold-mfe/data/UNAParams/tstackh.DAT | 16 + gtfold-mfe/data/UNAParams/tstacki.DAT | 16 + gtfold-mfe/data/UNAParams/tstacki23.DAT | 16 + gtfold-mfe/data/UNAParams/tstackm.DAT | 16 + 16 files changed, 895 insertions(+) create mode 100644 gtfold-mfe/data/UNAParams/asint1x2.DAT create mode 100644 gtfold-mfe/data/UNAParams/dangle.DAT create mode 100644 gtfold-mfe/data/UNAParams/extinction.DAT create mode 100644 gtfold-mfe/data/UNAParams/hexaloop.DAT create mode 100644 gtfold-mfe/data/UNAParams/loop.DAT create mode 100644 gtfold-mfe/data/UNAParams/miscloop.DAT create mode 100644 gtfold-mfe/data/UNAParams/sint2.DAT create mode 100644 gtfold-mfe/data/UNAParams/sint4.DAT create mode 100644 gtfold-mfe/data/UNAParams/stack.DAT create mode 100644 gtfold-mfe/data/UNAParams/tloop.DAT create mode 100644 gtfold-mfe/data/UNAParams/triloop.DAT create mode 100644 gtfold-mfe/data/UNAParams/tstacke.DAT create mode 100644 gtfold-mfe/data/UNAParams/tstackh.DAT create mode 100644 gtfold-mfe/data/UNAParams/tstacki.DAT create mode 100644 gtfold-mfe/data/UNAParams/tstacki23.DAT create mode 100644 gtfold-mfe/data/UNAParams/tstackm.DAT diff --git a/gtfold-mfe/data/UNAParams/asint1x2.DAT b/gtfold-mfe/data/UNAParams/asint1x2.DAT new file mode 100644 index 0000000..0dfe3c4 --- /dev/null +++ b/gtfold-mfe/data/UNAParams/asint1x2.DAT @@ -0,0 +1,96 @@ +3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 +3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 +3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 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-0.80 -0.80 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -0.80 -1.10 -0.80 +inf inf inf inf inf inf inf inf -1.70 -1.70 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -1.10 -3.30 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -2.40 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.60 -1.40 -1.60 -1.20 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -1.90 inf inf inf inf -0.80 -1.00 -0.80 -1.30 +inf inf inf inf -1.10 -0.70 -3.40 -0.50 inf inf inf inf -0.60 -0.70 -2.50 -0.70 +inf inf inf inf -1.60 -3.30 -1.40 -1.30 inf inf inf inf -0.80 -2.10 -0.80 -0.80 +inf inf inf inf -1.70 -1.00 -2.00 -0.70 inf inf inf inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf inf -1.00 -0.80 -1.10 -1.00 inf inf inf inf +-0.70 -0.60 -2.40 -0.50 inf inf inf inf -0.70 -0.60 -1.50 -0.50 inf inf inf inf +-1.10 -2.10 -1.20 -1.00 inf inf inf inf -0.70 -1.40 -0.80 0.30 inf inf inf inf +-0.90 -0.60 -1.40 -0.50 inf inf inf inf -0.50 -0.60 -0.50 -0.50 inf inf inf inf From b41b45940c9cb1d5eb67af47bf1865ff97eefdad Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 23 Jun 2011 14:25:35 -0400 Subject: [PATCH 072/187] changes to seperate unamode(--unamode), terminal mismatch(-m) --- gtfold-mfe/include/algorithms.h | 2 +- gtfold-mfe/include/options.h | 1 + gtfold-mfe/include/traceback.h | 2 +- gtfold-mfe/src/algorithms.c | 12 ++++++------ gtfold-mfe/src/loader.cc | 14 +++++++++++--- gtfold-mfe/src/main.cc | 6 +++--- gtfold-mfe/src/options.cc | 16 +++++++++++++++- gtfold-mfe/src/traceback.c | 21 +++++++++++---------- 8 files changed, 49 insertions(+), 25 deletions(-) diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h index 9b3dee0..d37a205 100644 --- a/gtfold-mfe/include/algorithms.h +++ b/gtfold-mfe/include/algorithms.h @@ -23,7 +23,7 @@ #ifdef __cplusplus extern "C" { #endif - int calculate(int len, int nThreads, int t_mismatch); + int calculate(int len, int nThreads, int unamode ,int t_mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 46b3a3a..24217bf 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -20,6 +20,7 @@ extern bool VERBOSE; extern bool SHAPE_ENABLED; extern bool PARAM_DIR; extern bool T_MISMATCH; +extern bool UNAMODE; extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h index 47a4f19..f250058 100644 --- a/gtfold-mfe/include/traceback.h +++ b/gtfold-mfe/include/traceback.h @@ -26,7 +26,7 @@ #ifdef __cplusplus extern "C" { #endif - void trace(int len, int vbose, int t_mismatch); + void trace(int len, int vv, int mode, int mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index c428607..b61aa1e 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -120,7 +120,7 @@ int calcVBI2(int i, int j, int len) { return energy; } -int calculate(int len, int nThreads, int t_mismatch) { +int calculate(int len, int nThreads, int unamode, int mismatch) { int b, i, j; #ifdef _OPENMP if (nThreads>0) omp_set_num_threads(nThreads); @@ -132,7 +132,7 @@ int calculate(int len, int nThreads, int t_mismatch) { #endif initializeMatrix(len); - if (t_mismatch) { + if (unamode) { prefilter(len,2,2); } @@ -149,7 +149,7 @@ int calculate(int len, int nThreads, int t_mismatch) { int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack // Internal Loop BEGIN - if (t_mismatch) + if (unamode) VBI(i,j) = calcVBI1(i,j); else VBI(i,j) = calcVBI(i,j); @@ -166,7 +166,7 @@ int calculate(int len, int nThreads, int t_mismatch) { VMij = MIN(VMij, (VMidj + d5 +Ec)) ; VMij = MIN(VMij, (VMijd + d3 +Ec)); - if (t_mismatch) { + if (unamode || mismatch) { VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec)); } else { VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); @@ -195,7 +195,7 @@ int calculate(int len, int nThreads, int t_mismatch) { newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle - if (t_mismatch) { + if (unamode || mismatch) { if (i Date: Thu, 23 Jun 2011 14:26:37 -0400 Subject: [PATCH 073/187] changes to seperate unamode(--unamode), terminal mismatch(-m) --- gtfold-mfe/include/loader.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index c7eff12..41d7c6b 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -25,7 +25,7 @@ #include "constants.h" #include "data.h" -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int t_mismatch); +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode,int t_mismatch); int initStackValues(const std::string& fileName, const std::string& dirPath); int initMiscloopValues(const std::string& fileName, const std::string& dirPath); From 69a7bc85632899a3b466add2000541e7cedaa407 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 23 Jun 2011 14:38:40 -0400 Subject: [PATCH 074/187] adding file --- gtfold-mfe/data/Turner99/tstacke.DAT | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 gtfold-mfe/data/Turner99/tstacke.DAT diff --git a/gtfold-mfe/data/Turner99/tstacke.DAT b/gtfold-mfe/data/Turner99/tstacke.DAT new file mode 100644 index 0000000..342f641 --- /dev/null +++ b/gtfold-mfe/data/Turner99/tstacke.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -1.00 -0.80 inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.60 -0.70 inf -0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 inf -0.80 inf +inf inf inf inf inf inf inf inf inf inf inf inf inf -0.80 inf -0.80 +inf inf inf inf inf inf inf inf -1.50 -1.50 -1.40 inf inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -1.10 inf -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.40 inf -1.60 inf inf inf inf inf +inf inf inf inf inf inf inf inf inf -1.40 inf -1.20 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 inf inf inf inf inf -0.30 -1.00 -0.80 inf +inf inf inf inf -1.10 -0.70 inf -0.50 inf inf inf inf -0.60 -0.70 inf -0.70 +inf inf inf inf -1.60 inf -1.40 inf inf inf inf inf -0.60 inf -0.80 inf +inf inf inf inf inf -1.00 inf -0.70 inf inf inf inf inf -0.80 inf -0.80 +-1.00 -0.80 -1.10 inf inf inf inf inf -1.00 -0.80 -1.10 inf inf inf inf inf +-0.70 -0.60 inf -0.50 inf inf inf inf -0.70 -0.60 inf -0.50 inf inf inf inf +-1.10 inf -1.20 inf inf inf inf inf -0.50 inf -0.80 -0.80 inf inf inf inf +inf -0.60 inf -0.50 inf inf inf inf inf -0.60 -1.10 -0.50 inf inf inf inf From 4117ca866687fd68f6e7971e6e0b47189f4768bd Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 23 Jun 2011 14:39:44 -0400 Subject: [PATCH 075/187] added print statement --- gtfold-mfe/src/options.cc | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 2155a83..a9a3cb0 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -182,7 +182,11 @@ void printRunConfiguration(string seq) { printf("Run Configuration:\n"); if (UNAMODE == true) { - printf("- running in unamode\n"); + printf("+ running in unamode\n"); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } From 4d4789689b70f7dbaadd2aaf2a0c0545db69091c Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 12:30:32 -0400 Subject: [PATCH 076/187] added entry tstacke; removed sint2, sint4 --- gtfold-mfe/data/Turner99/Makefile.am | 3 +-- gtfold-mfe/data/Turner99/Makefile.in | 3 +-- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index c8cf6c6..4390f87 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -10,11 +10,10 @@ gtfold_data_DATA = \ int11.DAT\ int21.DAT\ int22.DAT\ - sint2.DAT\ - sint4.DAT\ tloop.DAT\ tstackh.DAT\ tstacki.DAT\ + tstacke.DAT\ tstackm.DAT diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index 084882b..d21f2af 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -182,11 +182,10 @@ gtfold_data_DATA = \ int11.DAT\ int21.DAT\ int22.DAT\ - sint2.DAT\ - sint4.DAT\ tloop.DAT\ tstackh.DAT\ tstacki.DAT\ + tstacke.DAT\ tstackm.DAT EXTRA_DIST = $(gtfold_data_DATA) From bd2db4003e93b1f077ed059ec4d4ddafba37f237 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 12:31:57 -0400 Subject: [PATCH 077/187] added Makefiles under UNAParams --- gtfold-mfe/data/UNAParams/Makefile.am | 24 ++ gtfold-mfe/data/UNAParams/Makefile.in | 400 ++++++++++++++++++++++++++ 2 files changed, 424 insertions(+) create mode 100644 gtfold-mfe/data/UNAParams/Makefile.am create mode 100644 gtfold-mfe/data/UNAParams/Makefile.in diff --git a/gtfold-mfe/data/UNAParams/Makefile.am b/gtfold-mfe/data/UNAParams/Makefile.am new file mode 100644 index 0000000..640c6c6 --- /dev/null +++ b/gtfold-mfe/data/UNAParams/Makefile.am @@ -0,0 +1,24 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/UNAParams + +gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + asint1x2.DAT\ + sint2.DAT\ + sint4.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstackm.DAT\ + tstacke.DAT\ + tstacki23.DAT + + +EXTRA_DIST = $(gtfold_data_DATA) + +CLEANFILES = *~ + diff --git a/gtfold-mfe/data/UNAParams/Makefile.in b/gtfold-mfe/data/UNAParams/Makefile.in new file mode 100644 index 0000000..fa1fe8e --- /dev/null +++ b/gtfold-mfe/data/UNAParams/Makefile.in @@ -0,0 +1,400 @@ +# Makefile.in generated by automake 1.11 from Makefile.am. +# @configure_input@ + +# 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require special tools to rebuild." +clean: clean-am + +clean-am: clean-generic mostlyclean-am + +distclean: distclean-am + -rm -f Makefile +distclean-am: clean-am distclean-generic + +dvi: dvi-am + +dvi-am: + +html: html-am + +html-am: + +info: info-am + +info-am: + +install-data-am: install-gtfold_dataDATA + +install-dvi: install-dvi-am + +install-dvi-am: + +install-exec-am: + +install-html: install-html-am + +install-html-am: + +install-info: install-info-am + +install-info-am: + +install-man: + +install-pdf: install-pdf-am + +install-pdf-am: + +install-ps: install-ps-am + +install-ps-am: + +installcheck-am: + +maintainer-clean: maintainer-clean-am + -rm -f Makefile +maintainer-clean-am: distclean-am maintainer-clean-generic + +mostlyclean: mostlyclean-am + +mostlyclean-am: mostlyclean-generic + +pdf: pdf-am + +pdf-am: + +ps: ps-am + +ps-am: + +uninstall-am: uninstall-gtfold_dataDATA + +.MAKE: install-am install-strip + +.PHONY: all all-am check check-am clean clean-generic distclean \ + distclean-generic distdir dvi dvi-am html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am \ + install-gtfold_dataDATA install-html install-html-am \ + install-info install-info-am install-man install-pdf \ + install-pdf-am install-ps install-ps-am install-strip \ + installcheck installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am uninstall uninstall-am \ + uninstall-gtfold_dataDATA + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: From 89d7ef3d08996a6ffd96bee227d11f0970c11b04 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 12:33:36 -0400 Subject: [PATCH 078/187] added entry UNAParams --- gtfold-mfe/data/Makefile.am | 2 +- gtfold-mfe/data/Makefile.in | 9 ++++----- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am index d9d1d43..b6af86e 100644 --- a/gtfold-mfe/data/Makefile.am +++ b/gtfold-mfe/data/Makefile.am @@ -1,2 +1,2 @@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams Turner04 Turner99 Andronescu diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in index 20b49f3..f591147 100644 --- a/gtfold-mfe/data/Makefile.in +++ b/gtfold-mfe/data/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -128,7 +128,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -190,7 +189,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams Turner04 Turner99 Andronescu all: all-recursive .SUFFIXES: @@ -232,7 +231,7 @@ $(am__aclocal_m4_deps): # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -257,7 +256,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ From f06c44fd26142141f0e8784f742dd97730922ee0 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 12:39:29 -0400 Subject: [PATCH 079/187] added entry UNAParams --- gtfold-mfe/configure | 4340 ++++++++++++++++++++++++--------------- gtfold-mfe/configure.in | 6 +- 2 files changed, 2653 insertions(+), 1693 deletions(-) diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index 679f8a1..37e6205 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -1,22 +1,18 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.67 for gtfold 1.18. -# +# Generated by GNU Autoconf 2.63 for gtfold 2.0. # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software -# Foundation, Inc. -# -# +# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -24,15 +20,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -40,13 +44,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -57,7 +55,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -80,6 +78,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -89,15 +94,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -109,16 +114,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -130,299 +131,330 @@ export LC_ALL LANGUAGE=C export LANGUAGE +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + # CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH +$as_unset CDPATH + if test "x$CONFIG_SHELL" = x; then - as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : - emulate sh - NULLCMD=: - # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which - # is contrary to our usage. Disable this feature. - alias -g '\${1+\"\$@\"}'='\"\$@\"' - setopt NO_GLOB_SUBST + if (eval ":") 2>/dev/null; then + as_have_required=yes else - case \`(set -o) 2>/dev/null\` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; -esac + as_have_required=no fi -" - as_required="as_fn_return () { (exit \$1); } -as_fn_success () { as_fn_return 0; } -as_fn_failure () { as_fn_return 1; } -as_fn_ret_success () { return 0; } -as_fn_ret_failure () { return 1; } + + if test $as_have_required = yes && (eval ": +(as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} exitcode=0 -as_fn_success || { exitcode=1; echo as_fn_success failed.; } -as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } -as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } -as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } -if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : - -else - exitcode=1; echo positional parameters were not saved. -fi -test x\$exitcode = x0 || exit 1" - as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO - as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO - eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && - test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 -test \$(( 1 + 1 )) = 2 || exit 1" - if (eval "$as_required") 2>/dev/null; then : - as_have_required=yes +if as_func_success; then + : else - as_have_required=no + exitcode=1 + echo as_func_success failed. fi - if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -as_found=false + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : +else + exitcode=1 + echo positional parameters were not saved. +fi + +test \$exitcode = 0) || { (exit 1); exit 1; } + +( + as_lineno_1=\$LINENO + as_lineno_2=\$LINENO + test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" && + test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; } +") 2> /dev/null; then + : +else + as_candidate_shells= + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - as_found=: - case $as_dir in #( + case $as_dir in /*) for as_base in sh bash ksh sh5; do - # Try only shells that exist, to save several forks. - as_shell=$as_dir/$as_base - if { test -f "$as_shell" || test -f "$as_shell.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : - CONFIG_SHELL=$as_shell as_have_required=yes - if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : - break 2 -fi -fi + as_candidate_shells="$as_candidate_shells $as_dir/$as_base" done;; esac - as_found=false done -$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : - CONFIG_SHELL=$SHELL as_have_required=yes -fi; } IFS=$as_save_IFS - if test "x$CONFIG_SHELL" != x; then : - # We cannot yet assume a decent shell, so we have to provide a - # neutralization value for shells without unset; and this also - # works around shells that cannot unset nonexistent variables. - BASH_ENV=/dev/null - ENV=/dev/null - (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} -fi + for as_shell in $as_candidate_shells $SHELL; do + # Try only shells that exist, to save several forks. + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { ("$as_shell") 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac - if test x$as_have_required = xno; then : - $as_echo "$0: This script requires a shell more modern than all" - $as_echo "$0: the shells that I found on your system." - if test x${ZSH_VERSION+set} = xset ; then - $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" - $as_echo "$0: be upgraded to zsh 4.3.4 or later." - else - $as_echo "$0: Please tell bug-autoconf@gnu.org about your system, -$0: including any error possibly output before this -$0: message. Then install a modern shell, or manually run -$0: the script under such a shell if you do have one." - fi - exit 1 -fi fi + + +: +_ASEOF +}; then + CONFIG_SHELL=$as_shell + as_have_required=yes + if { "$as_shell" 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac + fi -SHELL=${CONFIG_SHELL-/bin/sh} -export SHELL -# Unset more variables known to interfere with behavior of common tools. -CLICOLOR_FORCE= GREP_OPTIONS= -unset CLICOLOR_FORCE GREP_OPTIONS -## --------------------- ## -## M4sh Shell Functions. ## -## --------------------- ## -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} + +: +(as_func_return () { + (exit $1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 } -as_unset=as_fn_unset -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status +exitcode=0 +if as_func_success; then + : +else + exitcode=1 + echo as_func_success failed. +fi -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' +if as_func_ret_success; then + : else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = "$1" ); then + : else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith + exitcode=1 + echo positional parameters were not saved. +fi +test $exitcode = 0) || { (exit 1); exit 1; } -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error +( + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; } -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr +_ASEOF +}; then + break +fi + +fi + + done + + if test "x$CONFIG_SHELL" != x; then + for as_var in BASH_ENV ENV + do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var + done + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} +fi + + + if test $as_have_required = no; then + echo This script requires a shell more modern than all the + echo shells that I found on your system. Please install a + echo modern shell, or manually run the script under such a + echo shell if you do have one. + { (exit 1); exit 1; } +fi + + +fi + +fi + + + +(eval "as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} + +exitcode=0 +if as_func_success; then + : else - as_expr=false + exitcode=1 + echo as_func_success failed. fi -if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then - as_basename=basename +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_basename=false + exitcode=1 + echo as_func_ret_success failed. fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : else - as_dirname=false + exitcode=1 + echo positional parameters were not saved. fi -as_me=`$as_basename -- "$0" || -$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ - s//\1/ - q - } - /^X\/\(\/\/\)$/{ - s//\1/ - q - } - /^X\/\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` +test \$exitcode = 0") || { + echo No shell found that supports shell functions. + echo Please tell bug-autoconf@gnu.org about your system, + echo including any error possibly output before this message. + echo This can help us improve future autoconf versions. + echo Configuration will now proceed without shell functions. +} -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits - as_lineno_1=$LINENO as_lineno_1a=$LINENO - as_lineno_2=$LINENO as_lineno_2a=$LINENO - eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && - test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { - # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) sed -n ' p /[$]LINENO/= @@ -439,7 +471,8 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the @@ -449,18 +482,29 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits exit } + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -490,7 +534,7 @@ rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -509,10 +553,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -526,11 +570,11 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -test -n "$DJDIR" || exec 7<&0 &1 + +exec 7<&0 &1 # Name of the host. -# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` @@ -545,14 +589,14 @@ cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= +SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='gtfold' PACKAGE_TARNAME='gtfold' -PACKAGE_VERSION='1.18' -PACKAGE_STRING='gtfold 1.18' +PACKAGE_VERSION='2.0' +PACKAGE_STRING='gtfold 2.0' PACKAGE_BUGREPORT='' -PACKAGE_URL='' ac_unique_file="README" # Factoring default headers for most tests. @@ -688,7 +732,6 @@ bindir program_transform_name prefix exec_prefix -PACKAGE_URL PACKAGE_BUGREPORT PACKAGE_STRING PACKAGE_VERSION @@ -778,9 +821,8 @@ do fi case $ac_option in - *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; - *=) ac_optarg= ;; - *) ac_optarg=yes ;; + *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *) ac_optarg=yes ;; esac # Accept the important Cygnus configure options, so we can diagnose typos. @@ -825,7 +867,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -851,7 +894,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1055,7 +1099,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1071,7 +1116,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1101,17 +1147,17 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) as_fn_error $? "unrecognized option: \`$ac_option' -Try \`$0 --help' for more information" + -*) { $as_echo "$as_me: error: unrecognized option: $ac_option +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - case $ac_envvar in #( - '' | [0-9]* | *[!_$as_cr_alnum]* ) - as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; - esac + expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && + { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2 + { (exit 1); exit 1; }; } eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1128,13 +1174,15 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - as_fn_error $? "missing argument to $ac_option" + { $as_echo "$as_me: error: missing argument to $ac_option" >&2 + { (exit 1); exit 1; }; } fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; - fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; + fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2 + { (exit 1); exit 1; }; } ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1157,7 +1205,8 @@ do [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac - as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" + { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 + { (exit 1); exit 1; }; } done # There might be people who depend on the old broken behavior: `$host' @@ -1171,8 +1220,8 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host. - If a cross compiler is detected then cross compile mode will be used" >&2 + $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. + If a cross compiler is detected then cross compile mode will be used." >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi @@ -1187,9 +1236,11 @@ test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || - as_fn_error $? "working directory cannot be determined" + { $as_echo "$as_me: error: working directory cannot be determined" >&2 + { (exit 1); exit 1; }; } test "X$ac_ls_di" = "X$ac_pwd_ls_di" || - as_fn_error $? "pwd does not report name of working directory" + { $as_echo "$as_me: error: pwd does not report name of working directory" >&2 + { (exit 1); exit 1; }; } # Find the source files, if location was not specified. @@ -1228,11 +1279,13 @@ else fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." - as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" + { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 + { (exit 1); exit 1; }; } fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( - cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" + cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2 + { (exit 1); exit 1; }; } pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then @@ -1258,7 +1311,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures gtfold 1.18 to adapt to many kinds of systems. +\`configure' configures gtfold 2.0 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1272,7 +1325,7 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print \`checking ...' messages + -q, --quiet, --silent do not print \`checking...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files @@ -1329,7 +1382,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of gtfold 1.18:";; + short | recursive ) echo "Configuration of gtfold 2.0:";; esac cat <<\_ACEOF @@ -1349,537 +1402,93 @@ Some influential environment variables: LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory LIBS libraries to pass to the linker, e.g. -l - CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if + CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I if you have headers in a nonstandard directory - CXX C++ compiler command - CXXFLAGS C++ compiler flags - CPP C preprocessor - -Use these variables to override the choices made by `configure' or to help -it to find libraries and programs with nonstandard names/locations. - -Report bugs to the package provider. -_ACEOF -ac_status=$? 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Invocation command line was +It was created by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was $ $0 $@ @@ -1915,8 +1524,8 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - $as_echo "PATH: $as_dir" - done + $as_echo "PATH: $as_dir" +done IFS=$as_save_IFS } >&5 @@ -1953,9 +1562,9 @@ do ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; + 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; 2) - as_fn_append ac_configure_args1 " '$ac_arg'" + ac_configure_args1="$ac_configure_args1 '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1971,13 +1580,13 @@ do -* ) ac_must_keep_next=true ;; esac fi - as_fn_append ac_configure_args " '$ac_arg'" + ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac done done -{ ac_configure_args0=; unset ac_configure_args0;} -{ ac_configure_args1=; unset ac_configure_args1;} +$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } +$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there @@ -1989,9 +1598,11 @@ trap 'exit_status=$? { echo - $as_echo "## ---------------- ## + cat <<\_ASBOX +## ---------------- ## ## Cache variables. ## -## ---------------- ##" +## ---------------- ## +_ASBOX echo # The following way of writing the cache mishandles newlines in values, ( @@ -2000,13 +1611,13 @@ trap 'exit_status=$? case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -2025,9 +1636,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; ) echo - $as_echo "## ----------------- ## + cat <<\_ASBOX +## ----------------- ## ## Output variables. ## -## ----------------- ##" +## ----------------- ## +_ASBOX echo for ac_var in $ac_subst_vars do @@ -2040,9 +1653,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; echo if test -n "$ac_subst_files"; then - $as_echo "## ------------------- ## + cat <<\_ASBOX +## ------------------- ## ## File substitutions. ## -## ------------------- ##" +## ------------------- ## +_ASBOX echo for ac_var in $ac_subst_files do @@ -2056,9 +1671,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; fi if test -s confdefs.h; then - $as_echo "## ----------- ## + cat <<\_ASBOX +## ----------- ## ## confdefs.h. ## -## ----------- ##" +## ----------- ## +_ASBOX echo cat confdefs.h echo @@ -2072,39 +1689,37 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; exit $exit_status ' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal + trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h -$as_echo "/* confdefs.h */" > confdefs.h - # Predefined preprocessor variables. cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF -cat >>confdefs.h <<_ACEOF -#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" -_ACEOF cat >>confdefs.h <<_ACEOF -#define PACKAGE_URL "$PACKAGE_URL" +#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF @@ -2113,12 +1728,7 @@ _ACEOF ac_site_file1=NONE ac_site_file2=NONE if test -n "$CONFIG_SITE"; then - # We do not want a PATH search for config.site. - case $CONFIG_SITE in #(( - -*) ac_site_file1=./$CONFIG_SITE;; - */*) ac_site_file1=$CONFIG_SITE;; - *) ac_site_file1=./$CONFIG_SITE;; - esac + ac_site_file1=$CONFIG_SITE elif test "x$prefix" != xNONE; then ac_site_file1=$prefix/share/config.site ac_site_file2=$prefix/etc/config.site @@ -2129,23 +1739,19 @@ fi for ac_site_file in "$ac_site_file1" "$ac_site_file2" do test "x$ac_site_file" = xNONE && continue - if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 + if test -r "$ac_site_file"; then + { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 - . "$ac_site_file" \ - || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "failed to load site script $ac_site_file -See \`config.log' for more details" "$LINENO" 5 ; } + . "$ac_site_file" fi done if test -r "$cache_file"; then - # Some versions of bash will fail to source /dev/null (special files - # actually), so we avoid doing that. DJGPP emulates it as a regular file. - if test /dev/null != "$cache_file" && test -f "$cache_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 + # Some versions of bash will fail to source /dev/null (special + # files actually), so we avoid doing that. + if test -f "$cache_file"; then + { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5 $as_echo "$as_me: loading cache $cache_file" >&6;} case $cache_file in [\\/]* | ?:[\\/]* ) . "$cache_file";; @@ -2153,7 +1759,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;} esac fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5 $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi @@ -2168,11 +1774,11 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; @@ -2182,17 +1788,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else - { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi - { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 + { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5 $as_echo "$as_me: former value: \`$ac_old_val'" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 + { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5 $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac @@ -2204,20 +1810,43 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) as_fn_append ac_configure_args " '$ac_arg'" ;; + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 + { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } fi -## -------------------- ## -## Main body of script. ## -## -------------------- ## + + + + + + + + + + + + + + + + + + + + + + + + ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -2249,7 +1878,9 @@ for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do fi done if test -z "$ac_aux_dir"; then - as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5 +$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;} + { (exit 1); exit 1; }; } fi # These three variables are undocumented and unsupported, @@ -2263,27 +1894,35 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. # Make sure we can run config.sub. $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || - as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5 +$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;} + { (exit 1); exit 1; }; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +{ $as_echo "$as_me:$LINENO: checking build system type" >&5 $as_echo_n "checking build system type... " >&6; } -if test "${ac_cv_build+set}" = set; then : +if test "${ac_cv_build+set}" = set; then $as_echo_n "(cached) " >&6 else ac_build_alias=$build_alias test "x$ac_build_alias" = x && ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` test "x$ac_build_alias" = x && - as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5 $as_echo "$ac_cv_build" >&6; } case $ac_cv_build in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5 +$as_echo "$as_me: error: invalid value of canonical build" >&2;} + { (exit 1); exit 1; }; };; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' @@ -2299,24 +1938,28 @@ IFS=$ac_save_IFS case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +{ $as_echo "$as_me:$LINENO: checking host system type" >&5 $as_echo_n "checking host system type... " >&6; } -if test "${ac_cv_host+set}" = set; then : +if test "${ac_cv_host+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$host_alias" = x; then ac_cv_host=$ac_cv_build else ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5 $as_echo "$ac_cv_host" >&6; } case $ac_cv_host in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5 +$as_echo "$as_me: error: invalid value of canonical host" >&2;} + { (exit 1); exit 1; }; };; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' @@ -2332,24 +1975,28 @@ IFS=$ac_save_IFS case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 +{ $as_echo "$as_me:$LINENO: checking target system type" >&5 $as_echo_n "checking target system type... " >&6; } -if test "${ac_cv_target+set}" = set; then : +if test "${ac_cv_target+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$target_alias" = x; then ac_cv_target=$ac_cv_host else ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5 $as_echo "$ac_cv_target" >&6; } case $ac_cv_target in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5 +$as_echo "$as_me: error: invalid value of canonical target" >&2;} + { (exit 1); exit 1; }; };; esac target=$ac_cv_target ac_save_IFS=$IFS; IFS='-' @@ -2388,10 +2035,10 @@ am__api_version='1.11' # OS/2's system install, which has a completely different semantic # ./install, which can be erroneously created by make from ./install.sh. # Reject install programs that cannot install multiple files. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 $as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if test "${ac_cv_path_install+set}" = set; then : +if test "${ac_cv_path_install+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2399,11 +2046,11 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - # Account for people who put trailing slashes in PATH elements. -case $as_dir/ in #(( - ./ | .// | /[cC]/* | \ + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ - ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -2440,7 +2087,7 @@ case $as_dir/ in #(( ;; esac - done +done IFS=$as_save_IFS rm -rf conftest.one conftest.two conftest.dir @@ -2456,7 +2103,7 @@ fi INSTALL=$ac_install_sh fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 $as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. @@ -2467,7 +2114,7 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5 +{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5 $as_echo_n "checking whether build environment is sane... " >&6; } # Just in case sleep 1 @@ -2478,11 +2125,15 @@ am_lf=' ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) - as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5 +$as_echo "$as_me: error: unsafe absolute working directory name" >&2;} + { (exit 1); exit 1; }; };; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) - as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5 +$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;} + { (exit 1); exit 1; }; };; esac # Do `set' in a subshell so we don't clobber the current shell's @@ -2504,8 +2155,11 @@ if ( # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". - as_fn_error $? "ls -t appears to fail. Make sure there is not a broken -alias in your environment" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&5 +$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&2;} + { (exit 1); exit 1; }; } fi test "$2" = conftest.file @@ -2514,10 +2168,13 @@ then # Ok. : else - as_fn_error $? "newly created file is older than distributed files! -Check your system clock" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files! +Check your system clock" >&5 +$as_echo "$as_me: error: newly created file is older than distributed files! +Check your system clock" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +{ $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } test "$program_prefix" != NONE && program_transform_name="s&^&$program_prefix&;$program_transform_name" @@ -2545,7 +2202,7 @@ if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " else am_missing_run= - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5 + { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 $as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} fi @@ -2566,9 +2223,9 @@ if test "$cross_compiling" != no; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_STRIP+set}" = set; then : +if test "${ac_cv_prog_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then @@ -2579,24 +2236,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2606,9 +2263,9 @@ if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then @@ -2619,24 +2276,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2645,7 +2302,7 @@ fi else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2658,10 +2315,10 @@ fi fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5 +{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; } if test -z "$MKDIR_P"; then - if test "${ac_cv_path_mkdir+set}" = set; then : + if test "${ac_cv_path_mkdir+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2669,7 +2326,7 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in mkdir gmkdir; do + for ac_prog in mkdir gmkdir; do for ac_exec_ext in '' $ac_executable_extensions; do { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #( @@ -2681,12 +2338,11 @@ do esac done done - done +done IFS=$as_save_IFS fi - test -d ./--version && rmdir ./--version if test "${ac_cv_path_mkdir+set}" = set; then MKDIR_P="$ac_cv_path_mkdir -p" else @@ -2694,10 +2350,11 @@ fi # value for MKDIR_P within a source directory, because that will # break other packages using the cache if that directory is # removed, or if the value is a relative name. + test -d ./--version && rmdir ./--version MKDIR_P="$ac_install_sh -d" fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5 +{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5 $as_echo "$MKDIR_P" >&6; } mkdir_p="$MKDIR_P" @@ -2710,9 +2367,9 @@ for ac_prog in gawk mawk nawk awk do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_AWK+set}" = set; then : +if test "${ac_cv_prog_AWK+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$AWK"; then @@ -2723,24 +2380,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AWK="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi AWK=$ac_cv_prog_AWK if test -n "$AWK"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5 + { $as_echo "$as_me:$LINENO: result: $AWK" >&5 $as_echo "$AWK" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2748,11 +2405,11 @@ fi test -n "$AWK" && break done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } set x ${MAKE-make} ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` -if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then : +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2760,7 +2417,7 @@ SHELL = /bin/sh all: @echo '@@@%%%=$(MAKE)=@@@%%%' _ACEOF -# GNU make sometimes prints "make[1]: Entering ...", which would confuse us. +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. case `${MAKE-make} -f conftest.make 2>/dev/null` in *@@@%%%=?*=@@@%%%*) eval ac_cv_prog_make_${ac_make}_set=yes;; @@ -2770,11 +2427,11 @@ esac rm -f conftest.make fi if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } SET_MAKE= else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } SET_MAKE="MAKE=${MAKE-make}" fi @@ -2794,7 +2451,9 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then am__isrc=' -I$(srcdir)' # test to see if srcdir already configured if test -f $srcdir/config.status; then - as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } fi fi @@ -2810,7 +2469,7 @@ fi # Define the identity of the package. PACKAGE='gtfold' - VERSION='1.18' + VERSION='2.0' cat >>confdefs.h <<_ACEOF @@ -2852,11 +2511,13 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' # Check whether --enable-64bit was given. -if test "${enable_64bit+set}" = set; then : +if test "${enable_64bit+set}" = set; then enableval=$enable_64bit; case "${enableval}" in "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;; n | no) gtfold_cv_enable_64bit=no ;; - *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-64bit" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-64bit" >&2;} + { (exit 1); exit 1; }; } ;; esac else gtfold_cv_enable_64bit=no @@ -2887,9 +2548,9 @@ if test -n "$ac_tool_prefix"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then : +if test "${ac_cv_prog_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2900,24 +2561,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 + { $as_echo "$as_me:$LINENO: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2931,9 +2592,9 @@ if test -z "$CC"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then @@ -2944,24 +2605,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2974,7 +2635,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2983,37 +2644,57 @@ esac fi -test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "no acceptable C compiler found in \$PATH -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3029,8 +2710,8 @@ ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5 -$as_echo_n "checking whether the C compiler works... " >&6; } +{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... " >&6; } ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` # The possible output files: @@ -3046,17 +2727,17 @@ do done rm -f $ac_rmfiles -if { { ac_try="$ac_link_default" +if { (ac_try="$ac_link_default" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_link_default") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. # So ignore a value of `no', otherwise this would lead to `EXEEXT = no' # in a Makefile. We should not override ac_cv_exeext if it was cached, @@ -3073,7 +2754,7 @@ do # certainly right. break;; *.* ) - if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; then :; else ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` fi @@ -3092,132 +2773,124 @@ test "$ac_cv_exeext" = no && ac_cv_exeext= else ac_file='' fi -if test -z "$ac_file"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } -$as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error 77 "C compiler cannot create executables -See \`config.log' for more details" "$LINENO" 5 ; } -else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5 -$as_echo_n "checking for C compiler default output file name... " >&6; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5 $as_echo "$ac_file" >&6; } -ac_exeext=$ac_cv_exeext +if test -z "$ac_file"; then + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 -rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out -ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 -$as_echo_n "checking for suffix of executables... " >&6; } -if { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : - # If both `conftest.exe' and `conftest' are `present' (well, observable) -# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will -# work properly (i.e., refer to `conftest.exe'), while it won't with -# `rm'. -for ac_file in conftest.exe conftest conftest.*; do - test -f "$ac_file" || continue - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; - *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - break;; - * ) break;; - esac -done -else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } fi -rm -f conftest conftest$ac_cv_exeext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 -$as_echo "$ac_cv_exeext" >&6; } -rm -f conftest.$ac_ext -EXEEXT=$ac_cv_exeext -ac_exeext=$EXEEXT -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#include -int -main () -{ -FILE *f = fopen ("conftest.out", "w"); - return ferror (f) || fclose (f) != 0; +ac_exeext=$ac_cv_exeext - ; - return 0; -} -_ACEOF -ac_clean_files="$ac_clean_files conftest.out" # Check that the compiler produces executables we can run. If not, either # the compiler is broken, or we cross compile. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 -$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +$as_echo_n "checking whether the C compiler works... " >&6; } +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. if test "$cross_compiling" != yes; then - { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } - if { ac_try='./conftest$ac_cv_exeext' - { { case "(($ac_try" in + if { ac_try='./$ac_file' + { (case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_try") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; }; then + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then cross_compiling=no else if test "$cross_compiling" = maybe; then cross_compiling=yes else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot run C compiled programs. +{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs. If you meant to cross compile, use \`--host'. -See \`config.log' for more details" "$LINENO" 5 ; } +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 -$as_echo "$cross_compiling" >&6; } +{ $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } -rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + break;; + * ) break;; + esac +done +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +rm -f conftest$ac_cv_exeext +{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5 $as_echo_n "checking for suffix of object files... " >&6; } -if test "${ac_cv_objext+set}" = set; then : +if test "${ac_cv_objext+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3229,17 +2902,17 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { { ac_try="$ac_compile" +if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then for ac_file in conftest.o conftest.obj conftest.*; do test -f "$ac_file" || continue; case $ac_file in @@ -3252,23 +2925,31 @@ else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of object files: cannot compile -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi + rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 $as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; } -if test "${ac_cv_c_compiler_gnu+set}" = set; then : +if test "${ac_cv_c_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3282,16 +2963,37 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 $as_echo "$ac_cv_c_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GCC=yes @@ -3300,16 +3002,20 @@ else fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 $as_echo_n "checking whether $CC accepts -g... " >&6; } -if test "${ac_cv_prog_cc_g+set}" = set; then : +if test "${ac_cv_prog_cc_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_c_werror_flag=$ac_c_werror_flag ac_c_werror_flag=yes ac_cv_prog_cc_g=no CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3320,11 +3026,35 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes else - CFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3335,12 +3065,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_c_werror_flag=$ac_save_c_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_c_werror_flag=$ac_save_c_werror_flag CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3351,17 +3105,42 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_c_werror_flag=$ac_save_c_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 $as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS @@ -3378,14 +3157,18 @@ else CFLAGS= fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; } -if test "${ac_cv_prog_cc_c89+set}" = set; then : +if test "${ac_cv_prog_cc_c89+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -3442,9 +3225,32 @@ for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - if ac_fn_c_try_compile "$LINENO"; then : + rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_c89=$ac_arg +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done @@ -3455,19 +3261,17 @@ fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 + { $as_echo "$as_me:$LINENO: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 + { $as_echo "$as_me:$LINENO: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac -if test "x$ac_cv_prog_cc_c89" != xno; then : -fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -3486,7 +3290,7 @@ am__doit: .PHONY: am__doit END # If we don't find an include directive, just comment out the code. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 +{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 $as_echo_n "checking for style of include used by $am_make... " >&6; } am__include="#" am__quote= @@ -3514,12 +3318,12 @@ if test "$am__include" = "#"; then fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 +{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5 $as_echo "$_am_result" >&6; } rm -f confinc confmf # Check whether --enable-dependency-tracking was given. -if test "${enable_dependency_tracking+set}" = set; then : +if test "${enable_dependency_tracking+set}" = set; then enableval=$enable_dependency_tracking; fi @@ -3539,9 +3343,9 @@ fi depcc="$CC" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -3649,7 +3453,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 $as_echo "$am_cv_CC_dependencies_compiler_type" >&6; } CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type @@ -3678,9 +3482,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CXX+set}" = set; then : +if test "${ac_cv_prog_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then @@ -3691,24 +3495,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $CXX" >&5 $as_echo "$CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3722,9 +3526,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then @@ -3735,24 +3539,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 $as_echo "$ac_ct_CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3765,7 +3569,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -3776,36 +3580,53 @@ fi fi fi # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3819,16 +3640,37 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GXX=yes @@ -3837,16 +3679,20 @@ else fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 $as_echo_n "checking whether $CXX accepts -g... " >&6; } -if test "${ac_cv_prog_cxx_g+set}" = set; then : +if test "${ac_cv_prog_cxx_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_cxx_werror_flag=$ac_cxx_werror_flag ac_cxx_werror_flag=yes ac_cv_prog_cxx_g=no CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3857,11 +3703,35 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes else - CXXFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CXXFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3872,12 +3742,36 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_cxx_werror_flag=$ac_save_cxx_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cxx_werror_flag=$ac_save_cxx_werror_flag CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3888,17 +3782,42 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cxx_werror_flag=$ac_save_cxx_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 $as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS @@ -3923,9 +3842,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu depcc="$CXX" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -4033,7 +3952,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5 $as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; } CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type @@ -4048,25 +3967,116 @@ else fi -#AC_PROG_LIBTOOL +#AC_PROG_LIBTOOL +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + $as_echo_n "(cached) " >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + fi + done + done + ;; +esac + +done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + INSTALL=$ac_install_sh + fi +fi +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' OPENMP_CFLAGS= # Check whether --enable-openmp was given. -if test "${enable_openmp+set}" = set; then : +if test "${enable_openmp+set}" = set; then enableval=$enable_openmp; fi if test "$enable_openmp" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5 + { $as_echo "$as_me:$LINENO: checking for $CC option to support OpenMP" >&5 $as_echo_n "checking for $CC option to support OpenMP... " >&6; } -if test "${ac_cv_prog_c_openmp+set}" = set; then : +if test "${ac_cv_prog_c_openmp+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4075,15 +4085,37 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp='none needed' else - ac_cv_prog_c_openmp='unsupported' + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_prog_c_openmp='unsupported' for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do ac_save_CFLAGS=$CFLAGS CFLAGS="$CFLAGS $ac_option" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4092,27 +4124,56 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp=$ac_option +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext CFLAGS=$ac_save_CFLAGS if test "$ac_cv_prog_c_openmp" != unsupported; then break fi done fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_c_openmp" >&5 $as_echo "$ac_cv_prog_c_openmp" >&6; } case $ac_cv_prog_c_openmp in #( "none needed" | unsupported) - ;; #( + ;; #( *) - OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; + OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; esac fi @@ -4120,14 +4181,18 @@ $as_echo "$ac_cv_prog_c_openmp" >&6; } #AC_DEFINE([_RAND],[],[RNG library to use]) -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for log2 in -lm" >&5 +{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5 $as_echo_n "checking for log2 in -lm... " >&6; } -if test "${ac_cv_lib_m_log2+set}" = set; then : +if test "${ac_cv_lib_m_log2+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4145,20 +4210,47 @@ return log2 (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_m_log2=yes else - ac_cv_lib_m_log2=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_m_log2=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_log2" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5 $as_echo "$ac_cv_lib_m_log2" >&6; } -if test "x$ac_cv_lib_m_log2" = x""yes; then : +if test "x$ac_cv_lib_m_log2" = x""yes; then -$as_echo "#define HAVE_LOG2 /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define HAVE_LOG2 /**/ +_ACEOF fi @@ -4168,14 +4260,14 @@ ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 +{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 $as_echo_n "checking how to run the C preprocessor... " >&6; } # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then - if test "${ac_cv_prog_CPP+set}" = set; then : + if test "${ac_cv_prog_CPP+set}" = set; then $as_echo_n "(cached) " >&6 else # Double quotes because CPP needs to be expanded @@ -4190,7 +4282,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4199,34 +4295,78 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then break fi @@ -4238,7 +4378,7 @@ fi else ac_cv_prog_CPP=$CPP fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 +{ $as_echo "$as_me:$LINENO: result: $CPP" >&5 $as_echo "$CPP" >&6; } ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes @@ -4249,7 +4389,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4258,40 +4402,87 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : - +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "C preprocessor \"$CPP\" fails sanity check -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi ac_ext=c @@ -4301,9 +4492,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5 $as_echo_n "checking for grep that handles long lines and -e... " >&6; } -if test "${ac_cv_path_GREP+set}" = set; then : +if test "${ac_cv_path_GREP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$GREP"; then @@ -4314,7 +4505,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in grep ggrep; do + for ac_prog in grep ggrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue @@ -4334,7 +4525,7 @@ case `"$ac_path_GREP" --version 2>&1` in $as_echo 'GREP' >> "conftest.nl" "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_GREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_GREP="$ac_path_GREP" @@ -4349,24 +4540,26 @@ esac $ac_path_GREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then - as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_GREP=$GREP fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 $as_echo "$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +{ $as_echo "$as_me:$LINENO: checking for egrep" >&5 $as_echo_n "checking for egrep... " >&6; } -if test "${ac_cv_path_EGREP+set}" = set; then : +if test "${ac_cv_path_EGREP+set}" = set; then $as_echo_n "(cached) " >&6 else if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 @@ -4380,7 +4573,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in egrep; do + for ac_prog in egrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue @@ -4400,7 +4593,7 @@ case `"$ac_path_EGREP" --version 2>&1` in $as_echo 'EGREP' >> "conftest.nl" "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_EGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_EGREP="$ac_path_EGREP" @@ -4415,10 +4608,12 @@ esac $ac_path_EGREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_EGREP"; then - as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_EGREP=$EGREP @@ -4426,17 +4621,21 @@ fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 $as_echo "$ac_cv_path_EGREP" >&6; } EGREP="$ac_cv_path_EGREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... " >&6; } -if test "${ac_cv_header_stdc+set}" = set; then : +if test "${ac_cv_header_stdc+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4451,23 +4650,48 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_stdc=yes else - ac_cv_header_stdc=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_stdc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then : - + $EGREP "memchr" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4477,14 +4701,18 @@ fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then : - + $EGREP "free" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4494,10 +4722,14 @@ fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. - if test "$cross_compiling" = yes; then : + if test "$cross_compiling" = yes; then : else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4524,49 +4756,269 @@ main () return 0; } _ACEOF -if ac_fn_c_try_run "$LINENO"; then : - +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : else - ac_cv_header_stdc=no + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no fi -rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ - conftest.$ac_objext conftest.beam conftest.$ac_ext +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext fi + fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -$as_echo "#define STDC_HEADERS 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF fi #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) # On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default -" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + eval "$as_ac_Header=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_Header=no" +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi - -done - - -for ac_header in stdlib.h string.h sys/time.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + +done + + + + + +for ac_header in stdlib.h string.h sys/time.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5 +$as_echo_n "checking $ac_header usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5 +$as_echo_n "checking $ac_header presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + +fi +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -4576,12 +5028,16 @@ fi done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5 +{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 $as_echo_n "checking for an ANSI C-conforming const... " >&6; } -if test "${ac_cv_c_const+set}" = set; then : +if test "${ac_cv_c_const+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4641,29 +5097,56 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_const=yes else - ac_cv_c_const=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_const=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 $as_echo "$ac_cv_c_const" >&6; } if test $ac_cv_c_const = no; then -$as_echo "#define const /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define const /**/ +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5 +{ $as_echo "$as_me:$LINENO: checking for inline" >&5 $as_echo_n "checking for inline... " >&6; } -if test "${ac_cv_c_inline+set}" = set; then : +if test "${ac_cv_c_inline+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_c_inline=no for ac_kw in inline __inline__ __inline; do - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifndef __cplusplus typedef int foo_t; @@ -4672,17 +5155,41 @@ $ac_kw foo_t foo () {return 0; } #endif _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_inline=$ac_kw +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext test "$ac_cv_c_inline" != no && break done fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 $as_echo "$ac_cv_c_inline" >&6; } + case $ac_cv_c_inline in inline | yes) ;; *) @@ -4698,9 +5205,102 @@ _ACEOF ;; esac -ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" -if test "x$ac_cv_type_size_t" = x""yes; then : +{ $as_echo "$as_me:$LINENO: checking for size_t" >&5 +$as_echo_n "checking for size_t... " >&6; } +if test "${ac_cv_type_size_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_type_size_t=no +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof (size_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof ((size_t))) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_type_size_t=yes +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5 +$as_echo "$ac_cv_type_size_t" >&6; } +if test "x$ac_cv_type_size_t" = x""yes; then + : else cat >>confdefs.h <<_ACEOF @@ -4709,12 +5309,16 @@ _ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether time.h and sys/time.h may both be included" >&5 +{ $as_echo "$as_me:$LINENO: checking whether time.h and sys/time.h may both be included" >&5 $as_echo_n "checking whether time.h and sys/time.h may both be included... " >&6; } -if test "${ac_cv_header_time+set}" = set; then : +if test "${ac_cv_header_time+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4729,27 +5333,54 @@ return 0; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_time=yes else - ac_cv_header_time=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_time=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_time" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_time" >&5 $as_echo "$ac_cv_header_time" >&6; } if test $ac_cv_header_time = yes; then -$as_echo "#define TIME_WITH_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TIME_WITH_SYS_TIME 1 +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5 +{ $as_echo "$as_me:$LINENO: checking whether struct tm is in sys/time.h or time.h" >&5 $as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; } -if test "${ac_cv_struct_tm+set}" = set; then : +if test "${ac_cv_struct_tm+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4764,18 +5395,41 @@ struct tm tm; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_struct_tm=time.h else - ac_cv_struct_tm=sys/time.h + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_struct_tm=sys/time.h fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_struct_tm" >&5 $as_echo "$ac_cv_struct_tm" >&6; } if test $ac_cv_struct_tm = sys/time.h; then -$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TM_IN_SYS_TIME 1 +_ACEOF fi @@ -4799,9 +5453,13 @@ fi If Sun cc is present, define appropriate compiler flags -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5 $as_echo_n "checking for Sun C compiler... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4815,22 +5473,47 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sunpro_cc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sunpro_cc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test "$gtfold_cv_check_sunpro_cc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler architecture target" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun C compiler architecture target" >&5 $as_echo_n "checking for Sun C compiler architecture target... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4844,15 +5527,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi @@ -4860,9 +5564,13 @@ if test "$gtfold_cv_check_sunpro_cc" == "yes"; then if test "$gtfold_cv_check_sun_sparc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun sparc v9 architecture" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun sparc v9 architecture" >&5 $as_echo_n "checking for Sun sparc v9 architecture... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4876,15 +5584,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparcv9=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparcv9=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi fi @@ -4907,14 +5636,18 @@ fi if test "$enable_openmp" != 'no'; then if test "x${GCC}" = "xyes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lomp... " >&6; } -if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4932,29 +5665,58 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_omp_GOMP_parallel_start=yes else - ac_cv_lib_omp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_omp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_omp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then LIB_OMP="-lgomp" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lgomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lgomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lgomp... " >&6; } -if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lgomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4972,30 +5734,59 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_gomp_GOMP_parallel_start=yes else - ac_cv_lib_gomp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_gomp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_gomp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then GOMP_LIBS="-lgomp" fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5013,29 +5804,58 @@ return sunw_mp_register_warn (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_mtsk_sunw_mp_register_warn=yes else - ac_cv_lib_mtsk_sunw_mp_register_warn=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 $as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then LIB_OMP="-lmtsk" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5044,40 +5864,156 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext #ifdef __cplusplus extern "C" #endif -char sunw_mp_register_warn (); +char sunw_mp_register_warn (); +int +main () +{ +return sunw_mp_register_warn (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_mtsk_sunw_mp_register_warn=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then + GOMP_LIBS="-lmtsk" +fi + + fi + LIBS="$GOMP_LIBS $LIBS" +fi + + + + + +for ac_func in floor gettimeofday pow +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + int main () { -return sunw_mp_register_warn (); +return $ac_func (); ; return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : - ac_cv_lib_mtsk_sunw_mp_register_warn=yes +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" else - ac_cv_lib_mtsk_sunw_mp_register_warn=no -fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext -LIBS=$ac_check_lib_save_LIBS -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 -$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : - GOMP_LIBS="-lmtsk" -fi + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 - fi - LIBS="$GOMP_LIBS $LIBS" + eval "$as_ac_var=no" fi - -for ac_func in floor gettimeofday pow -do : - as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` -ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" -if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 _ACEOF @@ -5087,12 +6023,14 @@ done # Check whether --enable-debug was given. -if test "${enable_debug+set}" = set; then : +if test "${enable_debug+set}" = set; then enableval=$enable_debug; case "${enableval}" in "" | y | ye | yes) debug=true; CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;; n | no) debug=false ;; - *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-debug" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-debug" >&2;} + { (exit 1); exit 1; }; } ;; esac else debug=false @@ -5109,7 +6047,7 @@ fi ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile" -ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile" +ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile" cat >confcache <<\_ACEOF @@ -5139,13 +6077,13 @@ _ACEOF case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -5153,8 +6091,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) - # `set' does not quote correctly, so add quotes: double-quote - # substitution turns \\\\ into \\, and sed turns \\ into \. + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" @@ -5177,11 +6115,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then test "x$cache_file" != "x/dev/null" && - { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} cat confcache >$cache_file else - { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi @@ -5195,15 +6133,14 @@ DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= -U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. - as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" - as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' + ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext" + ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs @@ -5219,30 +6156,41 @@ else fi if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then - as_fn_error $? "conditional \"AMDEP\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCC\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCXX\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then - as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi : ${CONFIG_STATUS=./config.status} ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} -as_write_fail=0 -cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 +cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -5252,18 +6200,17 @@ cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 debug=false ac_cs_recheck=false ac_cs_silent=false - SHELL=\${CONFIG_SHELL-$SHELL} -export SHELL -_ASEOF -cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -5271,15 +6218,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -5287,13 +6242,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -5304,7 +6253,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -5327,6 +6276,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -5336,15 +6292,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -5356,16 +6312,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -5377,89 +6329,7 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH - - -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error - - -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status - -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} -} -as_unset=as_fn_unset -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' -else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' -else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith - - +# Required to use basename. if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr @@ -5473,12 +6343,8 @@ else as_basename=false fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi +# Name of the executable. as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ @@ -5498,25 +6364,76 @@ $as_echo X/"$0" | } s/.*/./; q'` -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits +# CDPATH. +$as_unset CDPATH + + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | + sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno + N + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ + t loop + s/-\n.*// + ' >$as_me.lineno && + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" + # Exit status is that of the last command. + exit +} + + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -5545,56 +6462,8 @@ fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ - - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -5613,10 +6482,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -5631,19 +6500,13 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 -## ----------------------------------- ## -## Main body of $CONFIG_STATUS script. ## -## ----------------------------------- ## -_ASEOF -test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 -cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 -# Save the log message, to keep $0 and so on meaningful, and to +# Save the log message, to keep $[0] and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by gtfold $as_me 1.18, which was -generated by GNU Autoconf 2.67. Invocation command line was +This file was extended by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -5675,15 +6538,13 @@ _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files and other configuration actions -from templates according to the current configuration. Unless the files -and actions are specified as TAGs, all are instantiated by default. +\`$as_me' instantiates files from templates according to the +current configuration. -Usage: $0 [OPTION]... [TAG]... +Usage: $0 [OPTION]... [FILE]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit - --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files @@ -5702,17 +6563,16 @@ $config_headers Configuration commands: $config_commands -Report bugs to the package provider." +Report bugs to ." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 -ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -gtfold config.status 1.18 -configured by $0, generated by GNU Autoconf 2.67, - with options \\"\$ac_cs_config\\" +gtfold config.status 2.0 +configured by $0, generated by GNU Autoconf 2.63, + with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" -Copyright (C) 2010 Free Software Foundation, Inc. +Copyright (C) 2008 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -5730,16 +6590,11 @@ ac_need_defaults=: while test $# != 0 do case $1 in - --*=?*) + --*=*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; - --*=) - ac_option=`expr "X$1" : 'X\([^=]*\)='` - ac_optarg= - ac_shift=: - ;; *) ac_option=$1 ac_optarg=$2 @@ -5753,29 +6608,27 @@ do ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; - --config | --confi | --conf | --con | --co | --c ) - $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; - '') as_fn_error $? "missing file argument" ;; esac - as_fn_append CONFIG_FILES " '$ac_optarg'" + CONFIG_FILES="$CONFIG_FILES '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - as_fn_append CONFIG_HEADERS " '$ac_optarg'" + CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'" ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - as_fn_error $? "ambiguous option: \`$1' -Try \`$0 --help' for more information.";; + { $as_echo "$as_me: error: ambiguous option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; };; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ @@ -5783,10 +6636,11 @@ Try \`$0 --help' for more information.";; ac_cs_silent=: ;; # This is an error. - -*) as_fn_error $? "unrecognized option: \`$1' -Try \`$0 --help' for more information." ;; + -*) { $as_echo "$as_me: error: unrecognized option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; - *) as_fn_append ac_config_targets " $1" + *) ac_config_targets="$ac_config_targets $1" ac_need_defaults=false ;; esac @@ -5846,8 +6700,11 @@ do "data/Turner99/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner99/Makefile" ;; "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;; "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;; + "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;; - *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 +$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} + { (exit 1); exit 1; }; };; esac done @@ -5874,7 +6731,7 @@ $debug || trap 'exit_status=$? { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 - trap 'as_fn_exit 1' 1 2 13 15 + trap '{ (exit 1); exit 1; }' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. @@ -5885,7 +6742,11 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 +} || +{ + $as_echo "$as_me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -5893,13 +6754,7 @@ $debug || if test -n "$CONFIG_FILES"; then -ac_cr=`echo X | tr X '\015'` -# On cygwin, bash can eat \r inside `` if the user requested igncr. -# But we know of no other shell where ac_cr would be empty at this -# point, so we can use a bashism as a fallback. -if test "x$ac_cr" = x; then - eval ac_cr=\$\'\\r\' -fi +ac_cr=' ' ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then ac_cs_awk_cr='\\r' @@ -5916,18 +6771,24 @@ _ACEOF echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 -ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } +ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -5949,7 +6810,7 @@ s/'"$ac_delim"'$// t delim :nl h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p @@ -5963,7 +6824,7 @@ s/.\{148\}// t nl :delim h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p @@ -6016,28 +6877,22 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 +$as_echo "$as_me: error: could not setup config files machinery" >&2;} + { (exit 1); exit 1; }; } _ACEOF -# VPATH may cause trouble with some makes, so we remove sole $(srcdir), -# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ -h -s/// -s/^/:/ -s/[ ]*$/:/ -s/:\$(srcdir):/:/g -s/:\${srcdir}:/:/g -s/:@srcdir@:/:/g -s/^:*// + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/ +s/:*\${srcdir}:*/:/ +s/:*@srcdir@:*/:/ +s/^\([^=]*=[ ]*\):*/\1/ s/:*$// -x -s/\(=[ ]*\).*/\1/ -G -s/\n// s/^[^=]*=[ ]*$// }' fi @@ -6065,7 +6920,9 @@ for ac_last_try in false false :; do if test -z "$ac_t"; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6150,7 +7007,9 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - as_fn_error $? "could not setup config headers machinery" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5 +$as_echo "$as_me: error: could not setup config headers machinery" >&2;} + { (exit 1); exit 1; }; } fi # test -n "$CONFIG_HEADERS" @@ -6163,7 +7022,9 @@ do esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;; + :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5 +$as_echo "$as_me: error: invalid tag $ac_tag" >&2;} + { (exit 1); exit 1; }; };; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -6191,10 +7052,12 @@ do [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5 +$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} + { (exit 1); exit 1; }; };; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac - as_fn_append ac_file_inputs " '$ac_f'" + ac_file_inputs="$ac_file_inputs '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't @@ -6205,7 +7068,7 @@ do `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 + { $as_echo "$as_me:$LINENO: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. @@ -6218,7 +7081,9 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; esac ;; esac @@ -6246,7 +7111,47 @@ $as_echo X"$ac_file" | q } s/.*/./; q'` - as_dir="$ac_dir"; as_fn_mkdir_p + { as_dir="$ac_dir" + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } ac_builddir=. case "$ac_dir" in @@ -6303,6 +7208,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= + ac_sed_dataroot=' /datarootdir/ { p @@ -6312,11 +7218,12 @@ ac_sed_dataroot=' /@docdir@/p /@infodir@/p /@localedir@/p -/@mandir@/p' +/@mandir@/p +' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 @@ -6326,7 +7233,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g - s&\\\${datarootdir}&$datarootdir&g' ;; + s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF @@ -6355,22 +7262,26 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir' +which seems to be undefined. Please make sure it is defined." >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&2;} +which seems to be undefined. Please make sure it is defined." >&2;} rm -f "$tmp/stdin" case $ac_file in -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; :H) # @@ -6381,19 +7292,25 @@ which seems to be undefined. Please make sure it is defined" >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then - { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 + { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || as_fn_error $? "could not create -" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5 +$as_echo "$as_me: error: could not create -" >&2;} + { (exit 1); exit 1; }; } fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -6431,7 +7348,7 @@ $as_echo X"$_am_arg" | s/.*/./; q'`/stamp-h$_am_stamp_count ;; - :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 + :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5 $as_echo "$as_me: executing $ac_file commands" >&6;} ;; esac @@ -6526,7 +7443,47 @@ $as_echo X"$file" | q } s/.*/./; q'` - as_dir=$dirpart/$fdir; as_fn_mkdir_p + { as_dir=$dirpart/$fdir + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } # echo "creating $dirpart/$file" echo '# dummy' > "$dirpart/$file" done @@ -6538,12 +7495,15 @@ $as_echo X"$file" | done # for ac_tag -as_fn_exit 0 +{ (exit 0); exit 0; } _ACEOF +chmod +x $CONFIG_STATUS ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || - as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } # configure is writing to config.log, and then calls config.status. @@ -6564,10 +7524,10 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit 1 + $ac_cs_success || { (exit 1); exit 1; } fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 + { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index ef1ddde..e4e1755 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -2,10 +2,10 @@ dnl Process this file with autoconf to produce a configure script. dnl AC_PREREQ([2.67]) dnl AC 2.62 needed for OpenMP -AC_PREREQ([2.67]) +AC_PREREQ([2.63]) dnl AC_INIT (package, version, [bug-report-email], [tarname]) -AC_INIT([gtfold],[1.18]) +AC_INIT([gtfold],[2.0]) dnl check for this file's existence to make sure that the directory dnl specified by --srcdir is the right one @@ -178,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue) dnl Create makefiles and other configuration files AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile]) -AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile]) +AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile]) dnl Generate `config.status' and launch it AC_OUTPUT From d9170d0601fcfdc1fee27aac89fafb450354c48e Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 12:50:16 -0400 Subject: [PATCH 080/187] delete these auto generated file --- gtfold-mfe/data/Andronescu/Makefile | 399 -------------------------- gtfold-mfe/data/Turner04/Makefile | 405 --------------------------- gtfold-mfe/data/Turner99/Makefile | 420 ---------------------------- gtfold-mfe/include/Makefile | 388 ------------------------- 4 files changed, 1612 deletions(-) delete mode 100644 gtfold-mfe/data/Andronescu/Makefile delete mode 100644 gtfold-mfe/data/Turner04/Makefile delete mode 100644 gtfold-mfe/data/Turner99/Makefile delete mode 100644 gtfold-mfe/include/Makefile diff --git a/gtfold-mfe/data/Andronescu/Makefile b/gtfold-mfe/data/Andronescu/Makefile deleted file mode 100644 index 8dc0b5c..0000000 --- a/gtfold-mfe/data/Andronescu/Makefile +++ /dev/null @@ -1,399 +0,0 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. -# data/Andronescu/Makefile. 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/usr/include/c++/4.5/bits/stl_uninitialized.h \ - /usr/include/c++/4.5/bits/stl_vector.h \ - /usr/include/c++/4.5/bits/stl_bvector.h \ - /usr/include/c++/4.5/bits/vector.tcc /usr/include/c++/4.5/algorithm \ - /usr/include/c++/4.5/utility /usr/include/c++/4.5/bits/stl_relops.h \ - /usr/include/c++/4.5/bits/stl_algo.h /usr/include/c++/4.5/cstdlib \ - /usr/include/c++/4.5/bits/algorithmfwd.h \ - /usr/include/c++/4.5/bits/stl_heap.h \ - /usr/include/c++/4.5/bits/stl_tempbuf.h ../include/global.h \ - ../include/constants.h ../include/options.h /usr/include/c++/4.5/cstring \ - ../include/constraints.h - -/usr/include/stdlib.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - 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-/usr/include/c++/4.5/ostream: - -/usr/include/c++/4.5/ios: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/c++/4.5/cstddef: - -/usr/include/bits/wchar.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/c++/4.5/bits/ios_base.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/bits/locale_classes.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -/usr/include/c++/4.5/bits/locale_classes.tcc: - -/usr/include/c++/4.5/streambuf: - -/usr/include/c++/4.5/bits/streambuf.tcc: - -/usr/include/c++/4.5/bits/basic_ios.h: - -/usr/include/c++/4.5/bits/locale_facets.h: - -/usr/include/c++/4.5/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.5/bits/streambuf_iterator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.5/bits/locale_facets.tcc: - -/usr/include/c++/4.5/bits/basic_ios.tcc: - -/usr/include/c++/4.5/bits/ostream.tcc: - -/usr/include/c++/4.5/istream: - -/usr/include/c++/4.5/bits/istream.tcc: - -/usr/include/c++/4.5/fstream: - -/usr/include/c++/4.5/bits/codecvt.h: - -/usr/include/c++/4.5/cstdio: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: - -/usr/include/c++/4.5/bits/fstream.tcc: - -/usr/include/c++/4.5/vector: - -/usr/include/c++/4.5/bits/stl_construct.h: - -/usr/include/c++/4.5/bits/stl_uninitialized.h: - -/usr/include/c++/4.5/bits/stl_vector.h: - -/usr/include/c++/4.5/bits/stl_bvector.h: - -/usr/include/c++/4.5/bits/vector.tcc: - -/usr/include/c++/4.5/algorithm: - -/usr/include/c++/4.5/utility: - -/usr/include/c++/4.5/bits/stl_relops.h: - -/usr/include/c++/4.5/bits/stl_algo.h: - -/usr/include/c++/4.5/cstdlib: - -/usr/include/c++/4.5/bits/algorithmfwd.h: - -/usr/include/c++/4.5/bits/stl_heap.h: - -/usr/include/c++/4.5/bits/stl_tempbuf.h: - -../include/global.h: - -../include/constants.h: - -../include/options.h: - -/usr/include/c++/4.5/cstring: - -../include/constraints.h: diff --git a/gtfold-mfe/src/.deps/energy.Po b/gtfold-mfe/src/.deps/energy.Po deleted file mode 100644 index 1ddcb82..0000000 --- a/gtfold-mfe/src/.deps/energy.Po +++ /dev/null @@ -1,124 +0,0 @@ -energy.o: energy.c /usr/include/stdlib.h /usr/include/features.h \ - /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/sys/types.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \ - /usr/include/bits/sigset.h /usr/include/bits/time.h \ - /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \ - /usr/include/alloca.h /usr/include/bits/stdlib.h /usr/include/stdio.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - ../include/energy.h ../include/data.h ../include/constants.h \ - ../include/utils.h ../include/global.h ../include/constants.h \ - ../include/shapereader.h - -/usr/include/stdlib.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/sys/types.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/bits/time.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -/usr/include/stdio.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -../include/energy.h: - -../include/data.h: - -../include/constants.h: - -../include/utils.h: - -../include/global.h: - -../include/constants.h: - -../include/shapereader.h: diff --git a/gtfold-mfe/src/.deps/global.Po b/gtfold-mfe/src/.deps/global.Po deleted file mode 100644 index 58728cf..0000000 --- a/gtfold-mfe/src/.deps/global.Po +++ /dev/null @@ -1,93 +0,0 @@ -global.o: global.c /usr/include/stdio.h /usr/include/features.h \ - /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h ../include/global.h ../include/constants.h \ - ../include/constraints.h - -/usr/include/stdio.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/sys/types.h: - -/usr/include/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/bits/time.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -../include/global.h: - -../include/constants.h: - -../include/constraints.h: diff --git a/gtfold-mfe/src/.deps/loader.Po b/gtfold-mfe/src/.deps/loader.Po deleted file mode 100644 index 926b316..0000000 --- a/gtfold-mfe/src/.deps/loader.Po +++ /dev/null @@ -1,370 +0,0 @@ -loader.o: loader.cc /usr/include/c++/4.5/iostream \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/bits/predefs.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ - /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ - /usr/include/c++/4.5/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ - /usr/include/ctype.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.5/bits/ios_base.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc \ - /usr/include/c++/4.5/bits/locale_classes.tcc \ - /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ - /usr/include/c++/4.5/bits/basic_ios.h \ - /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ - /usr/include/wctype.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.5/bits/streambuf_iterator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.5/bits/locale_facets.tcc \ - /usr/include/c++/4.5/bits/basic_ios.tcc \ - /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ - /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \ - /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \ - /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.5/bits/fstream.tcc /usr/include/c++/4.5/sstream \ - /usr/include/c++/4.5/bits/sstream.tcc /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - /usr/include/c++/4.5/cstring /usr/include/string.h \ - /usr/include/bits/string3.h /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h ../include/data.h ../include/constants.h \ - ../include/utils.h ../include/constants.h ../include/global.h \ - ../include/loader.h ../include/data.h - -/usr/include/c++/4.5/iostream: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/ostream: - -/usr/include/c++/4.5/ios: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/c++/4.5/cstddef: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/wchar.h: - -/usr/include/stdio.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/wchar.h: - -/usr/include/xlocale.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ios_base.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/bits/locale_classes.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -/usr/include/c++/4.5/bits/locale_classes.tcc: - -/usr/include/c++/4.5/streambuf: - -/usr/include/c++/4.5/bits/streambuf.tcc: - -/usr/include/c++/4.5/bits/basic_ios.h: - -/usr/include/c++/4.5/bits/locale_facets.h: - -/usr/include/c++/4.5/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.5/bits/streambuf_iterator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.5/bits/locale_facets.tcc: - -/usr/include/c++/4.5/bits/basic_ios.tcc: - -/usr/include/c++/4.5/bits/ostream.tcc: - -/usr/include/c++/4.5/istream: - -/usr/include/c++/4.5/bits/istream.tcc: - -/usr/include/c++/4.5/fstream: - -/usr/include/c++/4.5/bits/codecvt.h: - -/usr/include/c++/4.5/cstdio: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: - -/usr/include/c++/4.5/bits/fstream.tcc: - -/usr/include/c++/4.5/sstream: - -/usr/include/c++/4.5/bits/sstream.tcc: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -/usr/include/c++/4.5/cstring: - -/usr/include/string.h: - -/usr/include/bits/string3.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -../include/data.h: - -../include/constants.h: - -../include/utils.h: - -../include/constants.h: - -../include/global.h: - -../include/loader.h: - -../include/data.h: diff --git a/gtfold-mfe/src/.deps/main.Po b/gtfold-mfe/src/.deps/main.Po deleted file mode 100644 index 64c9b68..0000000 --- a/gtfold-mfe/src/.deps/main.Po +++ /dev/null @@ -1,440 +0,0 @@ -main.o: main.cc /usr/include/c++/4.5/iostream \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/bits/predefs.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ - /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ - /usr/include/c++/4.5/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ - /usr/include/ctype.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.5/bits/ios_base.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc \ - /usr/include/c++/4.5/bits/locale_classes.tcc \ - /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ - /usr/include/c++/4.5/bits/basic_ios.h \ - /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ - /usr/include/wctype.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.5/bits/streambuf_iterator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.5/bits/locale_facets.tcc \ - /usr/include/c++/4.5/bits/basic_ios.tcc \ - /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ - /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/iomanip \ - /usr/include/c++/4.5/fstream /usr/include/c++/4.5/bits/codecvt.h \ - /usr/include/c++/4.5/cstdio /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/include/bits/stdio2.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.5/bits/fstream.tcc /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - /usr/include/sys/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/c++/4.5/sstream /usr/include/c++/4.5/bits/sstream.tcc \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/sys/types.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h /usr/include/string.h \ - /usr/include/bits/string3.h ../include/main.h \ - /usr/include/c++/4.5/vector /usr/include/c++/4.5/bits/stl_construct.h \ - /usr/include/c++/4.5/bits/stl_uninitialized.h \ - /usr/include/c++/4.5/bits/stl_vector.h \ - /usr/include/c++/4.5/bits/stl_bvector.h \ - /usr/include/c++/4.5/bits/vector.tcc ../include/constants.h \ - ../include/utils.h ../include/loader.h ../include/data.h \ - ../include/options.h /usr/include/c++/4.5/cstring ../include/global.h \ - ../include/energy.h ../include/algorithms.h \ - ../include/algorithms-partition.h ../include/partition-dangle.h \ - ../include/constraints.h ../include/traceback.h \ - ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \ - /usr/include/assert.h /usr/include/c++/4.5/stack \ - /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_deque.h \ - /usr/include/c++/4.5/bits/deque.tcc \ - /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \ - /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \ - /usr/include/c++/4.5/bits/stl_multimap.h ../include/shapereader.h - -/usr/include/c++/4.5/iostream: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/ostream: - -/usr/include/c++/4.5/ios: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/c++/4.5/cstddef: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/wchar.h: - -/usr/include/stdio.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/wchar.h: - -/usr/include/xlocale.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ios_base.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/bits/locale_classes.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -/usr/include/c++/4.5/bits/locale_classes.tcc: - -/usr/include/c++/4.5/streambuf: - -/usr/include/c++/4.5/bits/streambuf.tcc: - -/usr/include/c++/4.5/bits/basic_ios.h: - -/usr/include/c++/4.5/bits/locale_facets.h: - -/usr/include/c++/4.5/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.5/bits/streambuf_iterator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.5/bits/locale_facets.tcc: - -/usr/include/c++/4.5/bits/basic_ios.tcc: - -/usr/include/c++/4.5/bits/ostream.tcc: - -/usr/include/c++/4.5/istream: - -/usr/include/c++/4.5/bits/istream.tcc: - -/usr/include/c++/4.5/iomanip: - -/usr/include/c++/4.5/fstream: - -/usr/include/c++/4.5/bits/codecvt.h: - -/usr/include/c++/4.5/cstdio: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: - -/usr/include/c++/4.5/bits/fstream.tcc: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -/usr/include/sys/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/c++/4.5/sstream: - -/usr/include/c++/4.5/bits/sstream.tcc: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -/usr/include/string.h: - -/usr/include/bits/string3.h: - -../include/main.h: - -/usr/include/c++/4.5/vector: - -/usr/include/c++/4.5/bits/stl_construct.h: - -/usr/include/c++/4.5/bits/stl_uninitialized.h: - -/usr/include/c++/4.5/bits/stl_vector.h: - -/usr/include/c++/4.5/bits/stl_bvector.h: - -/usr/include/c++/4.5/bits/vector.tcc: - -../include/constants.h: - -../include/utils.h: - -../include/loader.h: - -../include/data.h: - -../include/options.h: - -/usr/include/c++/4.5/cstring: - -../include/global.h: - -../include/energy.h: - -../include/algorithms.h: - -../include/algorithms-partition.h: - -../include/partition-dangle.h: - -../include/constraints.h: - -../include/traceback.h: - -../include/subopt_traceback.h: - -/usr/include/c++/4.5/cassert: - -/usr/include/assert.h: - -/usr/include/c++/4.5/stack: - -/usr/include/c++/4.5/deque: - -/usr/include/c++/4.5/bits/stl_deque.h: - -/usr/include/c++/4.5/bits/deque.tcc: - -/usr/include/c++/4.5/bits/stl_stack.h: - -/usr/include/c++/4.5/map: - -/usr/include/c++/4.5/bits/stl_tree.h: - -/usr/include/c++/4.5/bits/stl_map.h: - -/usr/include/c++/4.5/bits/stl_multimap.h: - -../include/shapereader.h: diff --git a/gtfold-mfe/src/.deps/options.Po b/gtfold-mfe/src/.deps/options.Po deleted file mode 100644 index 7d4de3a..0000000 --- a/gtfold-mfe/src/.deps/options.Po +++ /dev/null @@ -1,262 +0,0 @@ -options.o: options.cc ../include/loader.h /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/bits/predefs.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \ - /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \ - /usr/include/c++/4.5/cctype /usr/include/ctype.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc ../include/constants.h \ - ../include/data.h ../include/options.h /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h /usr/include/c++/4.5/cstring \ - /usr/include/string.h /usr/include/bits/string3.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/bits/stdio_lim.h \ - /usr/include/bits/sys_errlist.h /usr/include/bits/stdio.h \ - /usr/include/bits/stdio2.h - -../include/loader.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/cstddef: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/wchar.h: - -/usr/include/stdio.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/wchar.h: - -/usr/include/xlocale.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -../include/constants.h: - -../include/data.h: - -../include/options.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -/usr/include/c++/4.5/cstring: - -/usr/include/string.h: - -/usr/include/bits/string3.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: diff --git a/gtfold-mfe/src/.deps/shapereader.Po b/gtfold-mfe/src/.deps/shapereader.Po deleted file mode 100644 index aa9b3a0..0000000 --- a/gtfold-mfe/src/.deps/shapereader.Po +++ /dev/null @@ -1,358 +0,0 @@ -shapereader.o: shapereader.cc /usr/include/c++/4.5/iostream \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/bits/predefs.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ - /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ - /usr/include/c++/4.5/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ - /usr/include/ctype.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/c++/4.5/bits/ios_base.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc \ - /usr/include/c++/4.5/bits/locale_classes.tcc \ - /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ - /usr/include/c++/4.5/bits/basic_ios.h \ - /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ - /usr/include/wctype.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.5/bits/streambuf_iterator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.5/bits/locale_facets.tcc \ - /usr/include/c++/4.5/bits/basic_ios.tcc \ - /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ - /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/fstream \ - /usr/include/c++/4.5/bits/codecvt.h /usr/include/c++/4.5/cstdio \ - /usr/include/libio.h /usr/include/_G_config.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h \ - /usr/include/c++/4.5/bits/fstream.tcc /usr/include/string.h \ - /usr/include/bits/string3.h /usr/include/stdlib.h \ - /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \ - /usr/include/sys/types.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/sys/sysmacros.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - ../include/shapereader.h ../include/global.h ../include/constants.h \ - ../include/options.h /usr/include/c++/4.5/cstring - -/usr/include/c++/4.5/iostream: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/ostream: - -/usr/include/c++/4.5/ios: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/c++/4.5/cstddef: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/wchar.h: - -/usr/include/stdio.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/wchar.h: - -/usr/include/xlocale.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ios_base.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/bits/locale_classes.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -/usr/include/c++/4.5/bits/locale_classes.tcc: - -/usr/include/c++/4.5/streambuf: - -/usr/include/c++/4.5/bits/streambuf.tcc: - -/usr/include/c++/4.5/bits/basic_ios.h: - -/usr/include/c++/4.5/bits/locale_facets.h: - -/usr/include/c++/4.5/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.5/bits/streambuf_iterator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.5/bits/locale_facets.tcc: - -/usr/include/c++/4.5/bits/basic_ios.tcc: - -/usr/include/c++/4.5/bits/ostream.tcc: - -/usr/include/c++/4.5/istream: - -/usr/include/c++/4.5/bits/istream.tcc: - -/usr/include/c++/4.5/fstream: - -/usr/include/c++/4.5/bits/codecvt.h: - -/usr/include/c++/4.5/cstdio: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/basic_file.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++io.h: - -/usr/include/c++/4.5/bits/fstream.tcc: - -/usr/include/string.h: - -/usr/include/bits/string3.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/sys/types.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -../include/shapereader.h: - -../include/global.h: - -../include/constants.h: - -../include/options.h: - -/usr/include/c++/4.5/cstring: diff --git a/gtfold-mfe/src/.deps/subopt_traceback.Po b/gtfold-mfe/src/.deps/subopt_traceback.Po deleted file mode 100644 index 6dac6fe..0000000 --- a/gtfold-mfe/src/.deps/subopt_traceback.Po +++ /dev/null @@ -1,346 +0,0 @@ -subopt_traceback.o: subopt_traceback.cc /usr/include/c++/4.5/cstdio \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/features.h /usr/include/bits/predefs.h \ - /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \ - /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/cstddef \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/stdio.h /usr/include/bits/types.h \ - /usr/include/bits/typesizes.h /usr/include/libio.h \ - /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - ../include/constants.h ../include/energy.h ../include/data.h \ - ../include/constants.h ../include/utils.h ../include/global.h \ - ../include/subopt_traceback.h /usr/include/c++/4.5/cassert \ - /usr/include/assert.h /usr/include/c++/4.5/iostream \ - /usr/include/c++/4.5/ostream /usr/include/c++/4.5/ios \ - /usr/include/c++/4.5/iosfwd /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/postypes.h /usr/include/c++/4.5/cwchar \ - /usr/include/bits/wchar.h /usr/include/xlocale.h \ - /usr/include/bits/wchar2.h /usr/include/c++/4.5/exception \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/cctype \ - /usr/include/ctype.h /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ios_base.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/bits/locale_classes.h /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc \ - /usr/include/c++/4.5/bits/locale_classes.tcc \ - /usr/include/c++/4.5/streambuf /usr/include/c++/4.5/bits/streambuf.tcc \ - /usr/include/c++/4.5/bits/basic_ios.h \ - /usr/include/c++/4.5/bits/locale_facets.h /usr/include/c++/4.5/cwctype \ - /usr/include/wctype.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h \ - /usr/include/c++/4.5/bits/streambuf_iterator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h \ - /usr/include/c++/4.5/bits/locale_facets.tcc \ - /usr/include/c++/4.5/bits/basic_ios.tcc \ - /usr/include/c++/4.5/bits/ostream.tcc /usr/include/c++/4.5/istream \ - /usr/include/c++/4.5/bits/istream.tcc /usr/include/c++/4.5/sstream \ - /usr/include/c++/4.5/bits/sstream.tcc /usr/include/c++/4.5/stack \ - /usr/include/c++/4.5/deque /usr/include/c++/4.5/bits/stl_construct.h \ - /usr/include/c++/4.5/bits/stl_uninitialized.h \ - /usr/include/c++/4.5/bits/stl_deque.h \ - /usr/include/c++/4.5/bits/deque.tcc \ - /usr/include/c++/4.5/bits/stl_stack.h /usr/include/c++/4.5/map \ - /usr/include/c++/4.5/bits/stl_tree.h /usr/include/c++/4.5/bits/stl_map.h \ - /usr/include/c++/4.5/bits/stl_multimap.h /usr/include/c++/4.5/vector \ - /usr/include/c++/4.5/bits/stl_vector.h \ - /usr/include/c++/4.5/bits/stl_bvector.h \ - /usr/include/c++/4.5/bits/vector.tcc - -/usr/include/c++/4.5/cstdio: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/cstddef: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/stdio.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -../include/constants.h: - -../include/energy.h: - -../include/data.h: - -../include/constants.h: - -../include/utils.h: - -../include/global.h: - -../include/subopt_traceback.h: - -/usr/include/c++/4.5/cassert: - -/usr/include/assert.h: - -/usr/include/c++/4.5/iostream: - -/usr/include/c++/4.5/ostream: - -/usr/include/c++/4.5/ios: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/bits/wchar.h: - -/usr/include/xlocale.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ios_base.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/bits/locale_classes.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: - -/usr/include/c++/4.5/bits/locale_classes.tcc: - -/usr/include/c++/4.5/streambuf: - -/usr/include/c++/4.5/bits/streambuf.tcc: - -/usr/include/c++/4.5/bits/basic_ios.h: - -/usr/include/c++/4.5/bits/locale_facets.h: - -/usr/include/c++/4.5/cwctype: - -/usr/include/wctype.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_base.h: - -/usr/include/c++/4.5/bits/streambuf_iterator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/ctype_inline.h: - -/usr/include/c++/4.5/bits/locale_facets.tcc: - -/usr/include/c++/4.5/bits/basic_ios.tcc: - -/usr/include/c++/4.5/bits/ostream.tcc: - -/usr/include/c++/4.5/istream: - -/usr/include/c++/4.5/bits/istream.tcc: - -/usr/include/c++/4.5/sstream: - -/usr/include/c++/4.5/bits/sstream.tcc: - -/usr/include/c++/4.5/stack: - -/usr/include/c++/4.5/deque: - -/usr/include/c++/4.5/bits/stl_construct.h: - -/usr/include/c++/4.5/bits/stl_uninitialized.h: - -/usr/include/c++/4.5/bits/stl_deque.h: - -/usr/include/c++/4.5/bits/deque.tcc: - -/usr/include/c++/4.5/bits/stl_stack.h: - -/usr/include/c++/4.5/map: - -/usr/include/c++/4.5/bits/stl_tree.h: - -/usr/include/c++/4.5/bits/stl_map.h: - -/usr/include/c++/4.5/bits/stl_multimap.h: - -/usr/include/c++/4.5/vector: - -/usr/include/c++/4.5/bits/stl_vector.h: - -/usr/include/c++/4.5/bits/stl_bvector.h: - -/usr/include/c++/4.5/bits/vector.tcc: diff --git a/gtfold-mfe/src/.deps/traceback.Po b/gtfold-mfe/src/.deps/traceback.Po deleted file mode 100644 index 28cf049..0000000 --- a/gtfold-mfe/src/.deps/traceback.Po +++ /dev/null @@ -1,134 +0,0 @@ -traceback.o: traceback.c /usr/include/stdio.h /usr/include/features.h \ - /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \ - /usr/include/bits/stdio.h /usr/include/bits/stdio2.h \ - /usr/include/stdlib.h /usr/include/bits/waitflags.h \ - /usr/include/bits/waitstatus.h /usr/include/endian.h \ - /usr/include/bits/endian.h /usr/include/bits/byteswap.h \ - /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \ - /usr/include/bits/select.h /usr/include/bits/sigset.h \ - /usr/include/bits/time.h /usr/include/sys/sysmacros.h \ - /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \ - /usr/include/bits/stdlib.h /usr/include/math.h \ - /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \ - /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \ - /usr/include/bits/nan.h /usr/include/bits/mathdef.h \ - /usr/include/bits/mathcalls.h /usr/include/bits/mathinline.h \ - /usr/include/assert.h ../include/data.h ../include/constants.h \ - ../include/constants.h ../include/constraints.h ../include/energy.h \ - ../include/data.h ../include/global.h ../include/traceback.h \ - ../include/utils.h ../include/shapereader.h - -/usr/include/stdio.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/libio.h: - -/usr/include/_G_config.h: - -/usr/include/wchar.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/stdio_lim.h: - -/usr/include/bits/sys_errlist.h: - -/usr/include/bits/stdio.h: - -/usr/include/bits/stdio2.h: - -/usr/include/stdlib.h: - -/usr/include/bits/waitflags.h: - -/usr/include/bits/waitstatus.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/sys/types.h: - -/usr/include/time.h: - -/usr/include/sys/select.h: - -/usr/include/bits/select.h: - -/usr/include/bits/sigset.h: - -/usr/include/bits/time.h: - -/usr/include/sys/sysmacros.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/alloca.h: - -/usr/include/bits/stdlib.h: - -/usr/include/math.h: - -/usr/include/bits/huge_val.h: - -/usr/include/bits/huge_valf.h: - -/usr/include/bits/huge_vall.h: - -/usr/include/bits/inf.h: - -/usr/include/bits/nan.h: - -/usr/include/bits/mathdef.h: - -/usr/include/bits/mathcalls.h: - -/usr/include/bits/mathinline.h: - -/usr/include/assert.h: - -../include/data.h: - -../include/constants.h: - -../include/constants.h: - -../include/constraints.h: - -../include/energy.h: - -../include/data.h: - -../include/global.h: - -../include/traceback.h: - -../include/utils.h: - -../include/shapereader.h: diff --git a/gtfold-mfe/src/.deps/utils.Po b/gtfold-mfe/src/.deps/utils.Po deleted file mode 100644 index d92a43a..0000000 --- a/gtfold-mfe/src/.deps/utils.Po +++ /dev/null @@ -1,217 +0,0 @@ -utils.o: utils.cc ../include/utils.h ../include/constants.h \ - /usr/include/string.h /usr/include/features.h \ - /usr/include/bits/predefs.h /usr/include/sys/cdefs.h \ - /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \ - /usr/include/gnu/stubs-64.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h \ - /usr/include/xlocale.h /usr/include/bits/string3.h \ - /usr/include/c++/4.5/string \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h \ - /usr/include/c++/4.5/bits/stringfwd.h \ - /usr/include/c++/4.5/bits/char_traits.h \ - /usr/include/c++/4.5/bits/stl_algobase.h /usr/include/c++/4.5/cstddef \ - /usr/include/c++/4.5/bits/functexcept.h \ - /usr/include/c++/4.5/exception_defines.h \ - /usr/include/c++/4.5/bits/cpp_type_traits.h \ - /usr/include/c++/4.5/ext/type_traits.h \ - /usr/include/c++/4.5/ext/numeric_traits.h \ - /usr/include/c++/4.5/bits/stl_pair.h /usr/include/c++/4.5/bits/move.h \ - /usr/include/c++/4.5/bits/concept_check.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_types.h \ - /usr/include/c++/4.5/bits/stl_iterator_base_funcs.h \ - /usr/include/c++/4.5/bits/stl_iterator.h \ - /usr/include/c++/4.5/debug/debug.h /usr/include/c++/4.5/bits/postypes.h \ - /usr/include/c++/4.5/cwchar /usr/include/wchar.h /usr/include/stdio.h \ - /usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h \ - /usr/include/bits/wchar.h /usr/include/bits/wchar2.h \ - /usr/include/c++/4.5/bits/allocator.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h \ - /usr/include/c++/4.5/ext/new_allocator.h /usr/include/c++/4.5/new \ - /usr/include/c++/4.5/exception /usr/include/c++/4.5/bits/localefwd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h \ - /usr/include/c++/4.5/clocale /usr/include/locale.h \ - /usr/include/bits/locale.h /usr/include/c++/4.5/iosfwd \ - /usr/include/c++/4.5/cctype /usr/include/ctype.h \ - /usr/include/bits/types.h /usr/include/bits/typesizes.h \ - /usr/include/endian.h /usr/include/bits/endian.h \ - /usr/include/bits/byteswap.h /usr/include/c++/4.5/bits/ostream_insert.h \ - /usr/include/c++/4.5/cxxabi-forced.h \ - /usr/include/c++/4.5/bits/stl_function.h \ - /usr/include/c++/4.5/backward/binders.h \ - /usr/include/c++/4.5/bits/basic_string.h \ - /usr/include/c++/4.5/ext/atomicity.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h \ - /usr/include/pthread.h /usr/include/sched.h /usr/include/time.h \ - /usr/include/bits/sched.h /usr/include/bits/time.h \ - /usr/include/bits/pthreadtypes.h /usr/include/bits/setjmp.h \ - /usr/include/unistd.h /usr/include/bits/posix_opt.h \ - /usr/include/bits/environments.h /usr/include/bits/confname.h \ - /usr/include/getopt.h /usr/include/bits/unistd.h \ - /usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h \ - /usr/include/c++/4.5/initializer_list \ - /usr/include/c++/4.5/bits/basic_string.tcc - -../include/utils.h: - -../include/constants.h: - -/usr/include/string.h: - -/usr/include/features.h: - -/usr/include/bits/predefs.h: - -/usr/include/sys/cdefs.h: - -/usr/include/bits/wordsize.h: - -/usr/include/gnu/stubs.h: - -/usr/include/gnu/stubs-64.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stddef.h: - -/usr/include/xlocale.h: - -/usr/include/bits/string3.h: - -/usr/include/c++/4.5/string: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++config.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/cpu_defines.h: - -/usr/include/c++/4.5/bits/stringfwd.h: - -/usr/include/c++/4.5/bits/char_traits.h: - -/usr/include/c++/4.5/bits/stl_algobase.h: - -/usr/include/c++/4.5/cstddef: - -/usr/include/c++/4.5/bits/functexcept.h: - -/usr/include/c++/4.5/exception_defines.h: - -/usr/include/c++/4.5/bits/cpp_type_traits.h: - -/usr/include/c++/4.5/ext/type_traits.h: - -/usr/include/c++/4.5/ext/numeric_traits.h: - -/usr/include/c++/4.5/bits/stl_pair.h: - -/usr/include/c++/4.5/bits/move.h: - -/usr/include/c++/4.5/bits/concept_check.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_types.h: - -/usr/include/c++/4.5/bits/stl_iterator_base_funcs.h: - -/usr/include/c++/4.5/bits/stl_iterator.h: - -/usr/include/c++/4.5/debug/debug.h: - -/usr/include/c++/4.5/bits/postypes.h: - -/usr/include/c++/4.5/cwchar: - -/usr/include/wchar.h: - -/usr/include/stdio.h: - -/usr/lib/x86_64-linux-gnu/gcc/x86_64-linux-gnu/4.5.2/include/stdarg.h: - -/usr/include/bits/wchar.h: - -/usr/include/bits/wchar2.h: - -/usr/include/c++/4.5/bits/allocator.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++allocator.h: - -/usr/include/c++/4.5/ext/new_allocator.h: - -/usr/include/c++/4.5/new: - -/usr/include/c++/4.5/exception: - -/usr/include/c++/4.5/bits/localefwd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/c++locale.h: - -/usr/include/c++/4.5/clocale: - -/usr/include/locale.h: - -/usr/include/bits/locale.h: - -/usr/include/c++/4.5/iosfwd: - -/usr/include/c++/4.5/cctype: - -/usr/include/ctype.h: - -/usr/include/bits/types.h: - -/usr/include/bits/typesizes.h: - -/usr/include/endian.h: - -/usr/include/bits/endian.h: - -/usr/include/bits/byteswap.h: - -/usr/include/c++/4.5/bits/ostream_insert.h: - -/usr/include/c++/4.5/cxxabi-forced.h: - -/usr/include/c++/4.5/bits/stl_function.h: - -/usr/include/c++/4.5/backward/binders.h: - -/usr/include/c++/4.5/bits/basic_string.h: - -/usr/include/c++/4.5/ext/atomicity.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/gthr-default.h: - -/usr/include/pthread.h: - -/usr/include/sched.h: - -/usr/include/time.h: - -/usr/include/bits/sched.h: - -/usr/include/bits/time.h: - -/usr/include/bits/pthreadtypes.h: - -/usr/include/bits/setjmp.h: - -/usr/include/unistd.h: - -/usr/include/bits/posix_opt.h: - -/usr/include/bits/environments.h: - -/usr/include/bits/confname.h: - -/usr/include/getopt.h: - -/usr/include/bits/unistd.h: - -/usr/include/c++/4.5/x86_64-linux-gnu/bits/atomic_word.h: - -/usr/include/c++/4.5/initializer_list: - -/usr/include/c++/4.5/bits/basic_string.tcc: From ae599b41e34f9caf258a729b2444bb2505f17ed7 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 14:41:23 -0400 Subject: [PATCH 083/187] added prefilter option, rectified unamode option --- gtfold-mfe/include/algorithms.h | 2 +- gtfold-mfe/include/global.h | 8 ++++++++ gtfold-mfe/include/options.h | 3 +++ gtfold-mfe/src/algorithms.c | 16 +++++++-------- gtfold-mfe/src/global.c | 8 ++++++++ gtfold-mfe/src/loader.cc | 12 ++++++++--- gtfold-mfe/src/main.cc | 11 ++++++++-- gtfold-mfe/src/options.cc | 36 ++++++++++++++++++++++++--------- 8 files changed, 72 insertions(+), 24 deletions(-) diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h index d37a205..1f0f1df 100644 --- a/gtfold-mfe/include/algorithms.h +++ b/gtfold-mfe/include/algorithms.h @@ -23,7 +23,7 @@ #ifdef __cplusplus extern "C" { #endif - int calculate(int len, int nThreads, int unamode ,int t_mismatch); + int calculate(int len);//, int nThreads, int unamode ,int t_mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h index fe2d9df..1bdc31e 100644 --- a/gtfold-mfe/include/global.h +++ b/gtfold-mfe/include/global.h @@ -7,6 +7,14 @@ extern unsigned char *RNA; extern int *structure; extern int* constraints; +extern int g_nthreads; +extern int g_unamode; +extern int g_mismatch; +extern int g_verbose; +extern int g_prefilter_mode; +extern int g_prefilter1; +extern int g_prefilter2; + extern unsigned int chPairKey; // The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 24217bf..58db1a8 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -30,6 +30,9 @@ extern string paramDir; extern float suboptDelta; extern int nThreads; +extern bool b_prefilter; +extern int prefilter1; +extern int prefilter2; extern bool LIMIT_DISTANCE; extern int contactDistance; diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index b61aa1e..a0fe2ae 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -120,10 +120,10 @@ int calcVBI2(int i, int j, int len) { return energy; } -int calculate(int len, int nThreads, int unamode, int mismatch) { +int calculate(int len) { //, int nThreads, int unamode, int mismatch) { int b, i, j; #ifdef _OPENMP - if (nThreads>0) omp_set_num_threads(nThreads); + if (g_nthreads > 0) omp_set_num_threads(g_nthreads); #endif #ifdef _OPENMP #pragma omp parallel @@ -132,8 +132,8 @@ int calculate(int len, int nThreads, int unamode, int mismatch) { #endif initializeMatrix(len); - if (unamode) { - prefilter(len,2,2); + if (g_unamode || g_prefilter_mode) { + prefilter(len,g_prefilter1,g_prefilter2); } for (b = TURN+1; b <= len-1; b++) { @@ -149,7 +149,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) { int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack // Internal Loop BEGIN - if (unamode) + if (g_unamode) VBI(i,j) = calcVBI1(i,j); else VBI(i,j) = calcVBI(i,j); @@ -166,7 +166,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) { VMij = MIN(VMij, (VMidj + d5 +Ec)) ; VMij = MIN(VMij, (VMijd + d3 +Ec)); - if (unamode || mismatch) { + if (g_unamode || g_mismatch) { VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec)); } else { VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); @@ -195,7 +195,7 @@ int calculate(int len, int nThreads, int unamode, int mismatch) { newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle - if (unamode || mismatch) { + if (g_unamode || g_mismatch) { if (i + using namespace std; bool ILSA; bool NOISOLATE; -//bool USERDATA; -//bool PARAMS; bool PARAM_DIR = false; bool LIMIT_DISTANCE; bool BPP_ENABLED; @@ -16,13 +16,16 @@ bool VERBOSE = false; bool SHAPE_ENABLED = false; bool T_MISMATCH = false; bool UNAMODE = false; +bool b_prefilter = false; string seqfile = ""; string constraintsFile = ""; string outputFile = ""; string shapeFile = ""; -string paramDir = "Turner99"; // default value +string paramDir; // default value +int prefilter1=2; +int prefilter2=2; float suboptDelta = 0.0; int nThreads = -1; @@ -47,7 +50,8 @@ void help() { printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); printf(" -t, --threads num Limit number of threads used\n"); - printf(" --unamode DIR Enable UNAfold mode. Path to directory containing UNAfold parameters\n"); + printf(" --unamode Enable UNAfold mode. \n"); + printf(" --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); @@ -105,14 +109,22 @@ void parse_options(int argc, char** argv) { else help(); } else if (strcmp(argv[i], "-m") == 0) { - T_MISMATCH = true; + T_MISMATCH = true; } else if (strcmp(argv[i], "--unamode") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { if(i < argc) { - paramDir = argv[++i]; - UNAMODE = true; - PARAM_DIR = true; - } - else + int value1 = -1, value2 = -1; + std::stringstream ss; + ss << argv[++i]; + sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); + if (value1 < 0 || value2 < 0) { + help(); + } + b_prefilter =true; + prefilter1 = value1; + prefilter2 = value2; + } else help(); } else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { @@ -189,6 +201,10 @@ void printRunConfiguration(string seq) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } + if (b_prefilter == true) { + printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); + standardRun = false; + } if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); From f3c2db0339a3afd46150c6dd95e875952ae8c789 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 14:57:39 -0400 Subject: [PATCH 084/187] removed unwanted print statement --- gtfold-mfe/src/energy.c | 2 -- 1 file changed, 2 deletions(-) diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 616ad48..bc71d37 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -192,7 +192,6 @@ inline int eL1(int i, int j, int ip, int jp) { } else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; - if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy); } else if (size1 == 1 && size2 == 2) { energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ @@ -264,7 +263,6 @@ inline int eL(int i, int j, int ip, int jp) { } else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; - if (i==1 && j==22) printf("2x2 loop at %d %d %d\n", i,j, energy); } else if (size1 == 1 && size2 == 2) { energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ From d768553d1212f85e3dc776d2835cbb81f6b31a89 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 15:04:27 -0400 Subject: [PATCH 085/187] added check for prefilter inputs --- gtfold-mfe/src/options.cc | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 8c2c224..a7b9ca8 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -118,7 +118,8 @@ void parse_options(int argc, char** argv) { std::stringstream ss; ss << argv[++i]; sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); - if (value1 < 0 || value2 < 0) { + if (value1 <= 0 || value2 <= 0) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); help(); } b_prefilter =true; From 69869ccfb4e76b2ffef83bb5f11d6d13a88db663 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 15:39:18 -0400 Subject: [PATCH 086/187] fixed formatting problem in help message --- gtfold-mfe/src/options.cc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index a7b9ca8..212fe3b 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -50,8 +50,8 @@ void help() { printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); printf(" -t, --threads num Limit number of threads used\n"); - printf(" --unamode Enable UNAfold mode. \n"); - printf(" --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n"); + printf(" --unamode Enable UNAfold mode. \n"); + printf(" --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); From 54a21b8fc6a066da4017ac0e1d65fb8ab6c14fd7 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 24 Jun 2011 16:22:38 -0400 Subject: [PATCH 087/187] added newline after Total --- gtfold-mfe/src/algorithms-partition.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index 1492a8e..a914ddd 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -119,7 +119,7 @@ void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { } } } - printf("Total partition number: %f", Q[1][len]); + printf("Total partition number: %f\n", Q[1][len]); } /** From fcb3e207d5eaa2b8fce32bf65b6d07724da049a5 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 27 Jun 2011 16:25:33 -0400 Subject: [PATCH 088/187] added prefix and workdir option, fixed -d option --- gtfold-mfe/include/algorithms-partition.h | 2 +- gtfold-mfe/include/options.h | 3 ++ gtfold-mfe/src/algorithms-partition.c | 11 ++-- gtfold-mfe/src/main.cc | 21 +++----- gtfold-mfe/src/options.cc | 61 +++++++++++++++++------ 5 files changed, 64 insertions(+), 34 deletions(-) diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h index ef55266..3bfb26d 100644 --- a/gtfold-mfe/include/algorithms-partition.h +++ b/gtfold-mfe/include/algorithms-partition.h @@ -15,7 +15,7 @@ typedef struct _pFuncData { */ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM); void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P); -void printBasePairProbabilities(int n, int *structure, double **P); +void printBasePairProbabilities(int n, int *structure, double **P, const char* bppfile); double probabilityUnpaired(int length, int i, double **P); diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 58db1a8..4d4dbf1 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -25,7 +25,10 @@ extern bool UNAMODE; extern string seqfile; extern string constraintsFile; extern string shapeFile; +extern string outputDir; extern string outputFile; +extern string bppOutFile; +extern string suboptFile; extern string paramDir; extern float suboptDelta; diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index a914ddd..fa3b9b8 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -199,16 +199,21 @@ void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, * unpaired. * @param P Partition function array */ -void printBasePairProbabilities(int n, int *structure, double **P) { +void printBasePairProbabilities(int n, int *structure, double **P, const char* outfile) { + FILE* outp = fopen(outfile,"w"); + if (outp == NULL) { + fprintf(stderr, "printBasePairProbabilities() : Cannot open %s",outfile); + } int i; for(i=1; i<=n; ++i) { int j = structure[i]; if(j) - printf("%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); + fprintf(outp, "%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); else - printf("%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); + fprintf(outp, "%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); } + fclose(outp); } /** diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 893e468..52172cd 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -250,20 +250,11 @@ int main(int argc, char** argv) { t1 = get_seconds(); ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); t1 = get_seconds() - t1; - printf("Subopt traceback running time: %9.6f seconds\n\n", t1); + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); - string suboptfile; - suboptfile += seqfile; - if(suboptfile.find("/") != string::npos) { - size_t pos = suboptfile.find_last_of("/"); - suboptfile.erase(0,pos+1); - } - if(suboptfile.find(".") != string::npos) - suboptfile.erase(suboptfile.rfind(".")); - suboptfile += ".ss"; - - printf("Suboptimal structures saved in %s\n", suboptfile.c_str()); - save_subopt_file(suboptfile, subopt_data, seq, energy); + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); free_fold(seq.length()); exit(0); } @@ -301,6 +292,7 @@ int main(int argc, char** argv) { } if(BPP_ENABLED){ + printf("\n"); printf("Calculating partition function\n"); double ** Q, **QM, **QB, **P; Q = mallocTwoD(seq.length() + 1, seq.length() + 1); @@ -311,7 +303,8 @@ int main(int argc, char** argv) { fill_partition_fn_arrays(seq.length(), Q, QB, QM); fillBasePairProbabilities(seq.length(), Q, QB, QM, P); - printBasePairProbabilities(seq.length(), structure, P); + printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str()); + printf("Saved BPP output in %s\n",bppOutFile.c_str()); freeTwoD(Q, seq.length() + 1, seq.length() + 1); freeTwoD(QM, seq.length() + 1, seq.length() + 1); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 212fe3b..6dad154 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -20,7 +20,11 @@ bool b_prefilter = false; string seqfile = ""; string constraintsFile = ""; +string outputPrefix = ""; string outputFile = ""; +string suboptFile = ""; +string bppOutFile = ""; +string outputDir = ""; string shapeFile = ""; string paramDir; // default value @@ -48,10 +52,11 @@ void help() { printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); printf(" -m Enable terminal mismatch calculations\n"); printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); - printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); + printf(" -o, --output NAME Name output files with prefix\n"); + printf(" -w, --workDir DIR Path to directory for output files\n"); printf(" -t, --threads num Limit number of threads used\n"); printf(" --unamode Enable UNAfold mode. \n"); - printf(" --prefilter value1,value2 Sets the prefilter mode similar to UNAfold\n"); + printf(" --prefilter value1,value2 \n\t\t\tSets the prefilter mode similar to UNAfold\n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); @@ -89,20 +94,30 @@ void parse_options(int argc, char** argv) { help(); } else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) { if(i < argc){ - LIMIT_DISTANCE = true; contactDistance = atoi(argv[++i]); + stringstream ss; + ss << contactDistance; + if (contactDistance >= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); } else help(); } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { NOISOLATE = true; - } else if(strcmp(argv[i], "--output") == 0 || strcmp(argv[i], "-o") == 0) { + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { if(i < argc) - outputFile = argv[++i]; + outputDir = argv[++i]; else help(); } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { + if(i < argc) { paramDir = argv[++i]; PARAM_DIR = true; } @@ -122,7 +137,7 @@ void parse_options(int argc, char** argv) { printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); help(); } - b_prefilter =true; + b_prefilter = true; prefilter1 = value1; prefilter2 = value2; } else @@ -165,24 +180,36 @@ void parse_options(int argc, char** argv) { } // If no output file specified, create one - if(outputFile.empty()) { - + if(outputPrefix.empty()) { // base it off the input file - outputFile += seqfile; + outputPrefix += seqfile; size_t pos; // extract file name from the path - if ((pos=outputFile.find_last_of('/')) > 0) { - outputFile = outputFile.substr(pos+1); + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); } // and if an extension exists, remove it ... - if(outputFile.find(".") != string::npos) - outputFile.erase(outputFile.rfind(".")); + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } - // ... and append the .ct - outputFile += ".ct"; + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + suboptFile += outputDir; + bppOutFile += outputDir; } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -227,11 +254,13 @@ void printRunConfiguration(string seq) { if (BPP_ENABLED == true) { printf("+ calculating base pair probabilities\n"); + printf("+ BPP output file: %s\n", bppOutFile.c_str()); standardRun = false; } if (SUBOPT_ENABLED) { printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); standardRun = false; } From 43b8ec5913c7ca17c829a2ac42c91d324ea9a784 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 27 Jun 2011 17:26:32 -0400 Subject: [PATCH 089/187] added Vienna energy params --- gtfold-mfe/configure | 3 +- gtfold-mfe/configure.in | 2 +- gtfold-mfe/data/Makefile.am | 2 +- gtfold-mfe/data/Makefile.in | 2 +- gtfold-mfe/data/RNAParams/Makefile.am | 23 + gtfold-mfe/data/RNAParams/Makefile.in | 399 +++++++++++++++++ gtfold-mfe/data/RNAParams/dangle.DAT | 8 + gtfold-mfe/data/RNAParams/int11.DAT | 24 ++ gtfold-mfe/data/RNAParams/int21.DAT | 96 +++++ gtfold-mfe/data/RNAParams/int22.DAT | 576 +++++++++++++++++++++++++ gtfold-mfe/data/RNAParams/loop.DAT | 30 ++ gtfold-mfe/data/RNAParams/miscloop.DAT | 12 + gtfold-mfe/data/RNAParams/sint2.DAT | 24 ++ gtfold-mfe/data/RNAParams/sint4.DAT | 576 +++++++++++++++++++++++++ gtfold-mfe/data/RNAParams/stack.DAT | 16 + gtfold-mfe/data/RNAParams/tloop.DAT | 30 ++ gtfold-mfe/data/RNAParams/tstacke.DAT | 16 + gtfold-mfe/data/RNAParams/tstackh.DAT | 16 + gtfold-mfe/data/RNAParams/tstacki.DAT | 16 + gtfold-mfe/data/RNAParams/tstackm.DAT | 16 + 20 files changed, 1883 insertions(+), 4 deletions(-) create mode 100644 gtfold-mfe/data/RNAParams/Makefile.am create mode 100644 gtfold-mfe/data/RNAParams/Makefile.in create mode 100644 gtfold-mfe/data/RNAParams/dangle.DAT create mode 100644 gtfold-mfe/data/RNAParams/int11.DAT create mode 100644 gtfold-mfe/data/RNAParams/int21.DAT create mode 100644 gtfold-mfe/data/RNAParams/int22.DAT create mode 100644 gtfold-mfe/data/RNAParams/loop.DAT create mode 100644 gtfold-mfe/data/RNAParams/miscloop.DAT create mode 100644 gtfold-mfe/data/RNAParams/sint2.DAT create mode 100644 gtfold-mfe/data/RNAParams/sint4.DAT create mode 100644 gtfold-mfe/data/RNAParams/stack.DAT create mode 100644 gtfold-mfe/data/RNAParams/tloop.DAT create mode 100644 gtfold-mfe/data/RNAParams/tstacke.DAT create mode 100644 gtfold-mfe/data/RNAParams/tstackh.DAT create mode 100644 gtfold-mfe/data/RNAParams/tstacki.DAT create mode 100644 gtfold-mfe/data/RNAParams/tstackm.DAT diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index 37e6205..c0dc675 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -6047,7 +6047,7 @@ fi ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile" -ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile" +ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile" cat >confcache <<\_ACEOF @@ -6701,6 +6701,7 @@ do "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;; "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;; "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;; + "data/RNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/RNAParams/Makefile" ;; *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 $as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index e4e1755..03441fc 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -178,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue) dnl Create makefiles and other configuration files AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile]) -AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile]) +AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile]) dnl Generate `config.status' and launch it AC_OUTPUT diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am index b6af86e..001e73e 100644 --- a/gtfold-mfe/data/Makefile.am +++ b/gtfold-mfe/data/Makefile.am @@ -1,2 +1,2 @@ -SUBDIRS = UNAParams Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in index f591147..a245c3c 100644 --- a/gtfold-mfe/data/Makefile.in +++ b/gtfold-mfe/data/Makefile.in @@ -189,7 +189,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -SUBDIRS = UNAParams Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu all: all-recursive .SUFFIXES: diff --git a/gtfold-mfe/data/RNAParams/Makefile.am b/gtfold-mfe/data/RNAParams/Makefile.am new file mode 100644 index 0000000..8655bda --- /dev/null +++ b/gtfold-mfe/data/RNAParams/Makefile.am @@ -0,0 +1,23 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/RNAParams + +gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT + + +EXTRA_DIST = $(gtfold_data_DATA) + +CLEANFILES = *~ + diff --git a/gtfold-mfe/data/RNAParams/Makefile.in b/gtfold-mfe/data/RNAParams/Makefile.in new file mode 100644 index 0000000..6f1691d --- /dev/null +++ b/gtfold-mfe/data/RNAParams/Makefile.in @@ 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2.00 2.10 1.90 2.00 1.80 1.70 2.00 2.10 0.00 2.00 1.80 1.50 0.90 + 1.00 0.90 0.00 2.00 1.30 2.20 2.00 2.00 0.00 2.00 0.70 0.10 2.00 2.00 1.60 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 1.40 1.30 0.40 2.00 1.70 2.20 2.00 2.00 0.40 2.00 1.10 -0.30 2.00 2.00 1.20 1.50 + 1.50 0.40 1.30 2.00 0.80 1.70 2.00 1.50 1.30 2.00 1.20 -2.20 2.00 1.50 -0.70 1.50 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.60 1.90 2.00 2.00 2.40 2.20 2.00 2.10 2.00 2.00 2.40 0.30 2.00 2.10 1.80 1.20 + 0.20 -0.90 0.00 2.00 -0.40 0.40 2.00 0.30 0.00 2.00 0.00 -3.50 2.00 0.30 -2.00 0.20 + 2.20 1.10 2.00 2.00 1.50 1.40 2.00 1.20 2.00 2.00 1.90 0.30 2.00 1.20 1.80 0.30 + 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 + 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 + 2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 + 2.80 2.30 1.70 2.00 2.80 2.80 2.00 2.80 1.70 2.00 2.10 0.00 2.00 2.50 1.20 1.90 + 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 1.90 1.30 2.00 2.30 2.30 2.00 2.30 1.30 2.00 1.70 -0.50 2.00 2.00 0.80 1.50 + 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 + 1.70 1.30 0.70 2.00 1.70 2.70 2.00 2.70 0.70 2.00 1.10 0.70 2.00 2.40 2.00 2.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.70 1.10 2.00 2.10 2.70 2.00 2.70 1.10 2.00 1.50 0.30 2.00 2.40 1.60 2.30 + 2.20 0.80 2.00 2.00 1.20 2.20 2.00 2.20 2.00 2.00 1.60 -1.60 2.00 1.90 -0.30 2.20 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.30 2.70 2.00 2.80 2.80 2.00 2.80 2.70 2.00 2.70 1.00 2.00 2.50 2.20 1.90 + 1.00 -0.50 0.70 2.00 0.00 1.00 2.00 1.00 0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 + 2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 + 2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 + 2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/RNAParams/loop.DAT b/gtfold-mfe/data/RNAParams/loop.DAT new file mode 100644 index 0000000..98c1285 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/loop.DAT @@ -0,0 +1,30 @@ +1 inf 3.80 inf +2 4.10 2.80 inf +3 5.10 3.20 5.70 +4 1.70 3.60 5.60 +5 1.80 4.00 5.60 +6 2.00 4.40 5.40 +7 2.20 4.59 5.90 +8 2.30 4.70 5.60 +9 2.40 4.80 6.40 +10 2.50 4.90 6.50 +11 2.60 5.00 6.60 +12 2.70 5.10 6.70 +13 2.78 5.19 6.78 +14 2.86 5.27 6.86 +15 2.94 5.34 6.94 +16 3.01 5.41 7.01 +17 3.07 5.48 7.07 +18 3.13 5.54 7.13 +19 3.19 5.60 7.19 +20 3.25 5.65 7.25 +21 3.30 5.71 7.30 +22 3.35 5.76 7.35 +23 3.40 5.80 7.40 +24 3.45 5.85 7.44 +25 3.49 5.89 7.49 +26 3.53 5.94 7.53 +27 3.57 5.98 7.57 +28 3.61 6.02 7.61 +29 3.65 6.05 7.65 +30 3.69 6.09 7.69 diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT new file mode 100644 index 0000000..3c000a5 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/miscloop.DAT @@ -0,0 +1,12 @@ +1.079 +3.00 +.50 .50 .50 .50 +3.40 .00 .40 +10.10 -0.30 -0.30 +0.50 +0.0 +0.30 +1.60 +1.40 +4.10 +0 diff --git a/gtfold-mfe/data/RNAParams/sint2.DAT b/gtfold-mfe/data/RNAParams/sint2.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/RNAParams/sint2.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 +1.10 1.10 1.10 1.10 0.40 0.00 0.40 -0.30 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.80 0.40 0.40 0.40 0.40 0.30 -0.10 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0.70 2.00 0.30 -2.90 2.00 0.70 -1.60 0.90 +2.90 1.50 2.70 2.00 1.90 1.90 2.00 1.90 2.70 2.00 2.30 0.90 2.00 1.60 2.20 1.10 +2.80 2.50 1.50 2.00 2.60 3.10 2.00 3.10 1.50 2.00 2.10 1.30 2.00 3.10 2.30 2.70 +2.80 2.50 1.50 2.00 2.60 2.50 2.00 2.50 1.50 2.00 2.10 0.30 2.00 2.50 1.30 1.70 +1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.30 2.10 1.10 2.00 2.20 2.00 2.00 2.00 1.10 2.00 1.60 -0.10 2.00 2.00 0.90 1.20 +3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 +1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 +2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 +1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 +2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/RNAParams/stack.DAT b/gtfold-mfe/data/RNAParams/stack.DAT new file mode 100644 index 0000000..04a6889 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/stack.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf inf inf inf -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf inf inf -2.20 inf +inf inf inf inf inf inf inf inf inf inf inf inf inf -2.10 inf -0.60 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 inf -1.40 inf +inf inf inf inf inf inf inf inf inf inf inf -2.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf -3.30 inf inf inf inf inf +inf inf inf inf inf inf inf inf inf -2.40 inf -1.40 inf inf inf inf +inf inf inf inf inf inf inf inf -2.10 inf -2.10 inf inf inf inf inf +inf inf inf inf inf inf inf -2.40 inf inf inf inf inf inf inf -1.30 +inf inf inf inf inf inf -3.40 inf inf inf inf inf inf inf -2.50 inf +inf inf inf inf inf -3.30 inf -1.50 inf inf inf inf inf -2.10 inf -0.50 +inf inf inf inf -2.20 inf -2.50 inf inf inf inf inf -1.40 inf 1.30 inf +inf inf inf -1.30 inf inf inf inf inf inf inf -1.00 inf inf inf inf +inf inf -2.40 inf inf inf inf inf inf inf -1.50 inf inf inf inf inf +inf -2.10 inf -1.00 inf inf inf inf inf -1.40 inf 0.30 inf inf inf inf +-0.90 inf -1.30 inf inf inf inf inf -0.60 inf -0.50 inf inf inf inf inf diff --git a/gtfold-mfe/data/RNAParams/tloop.DAT b/gtfold-mfe/data/RNAParams/tloop.DAT new file mode 100644 index 0000000..dda2750 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/tloop.DAT @@ -0,0 +1,30 @@ +GGGGAC -3.00 +GGUGAC -3.00 +CGAAAG -3.00 +GGAGAC -3.00 +CGCAAG -3.00 +GGAAAC -3.00 +CGGAAG -3.00 +CUUCGG -3.00 +CGUGAG -3.00 +CGAAGG -2.50 +CUACGG -2.50 +GGCAAC -2.50 +CGCGAG -2.50 +UGAGAG -2.50 +CGAGAG -2.00 +AGAAAU -2.00 +CGUAAG -2.00 +CUAACG -2.00 +UGAAAG -2.00 +GGAAGC -1.50 +GGGAAC -1.50 +UGAAAA -1.50 +AGCAAU -1.50 +AGUAAU -1.50 +CGGGAG -1.50 +AGUGAU -1.50 +GGCGAC -1.50 +GGGAGC -1.50 +GUGAAC -1.50 +UGGAAA -1.50 diff --git a/gtfold-mfe/data/RNAParams/tstacke.DAT b/gtfold-mfe/data/RNAParams/tstacke.DAT new file mode 100644 index 0000000..342f641 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/tstacke.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -1.00 -0.80 inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.60 -0.70 inf -0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 inf -0.80 inf +inf inf inf inf inf inf inf inf inf inf inf inf inf -0.80 inf -0.80 +inf inf inf inf inf inf inf inf -1.50 -1.50 -1.40 inf inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -1.10 inf -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.40 inf -1.60 inf inf inf inf inf +inf inf inf inf inf inf inf inf inf -1.40 inf -1.20 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 inf inf inf inf inf -0.30 -1.00 -0.80 inf +inf inf inf inf -1.10 -0.70 inf -0.50 inf inf inf inf -0.60 -0.70 inf -0.70 +inf inf inf inf -1.60 inf -1.40 inf inf inf inf inf -0.60 inf -0.80 inf +inf inf inf inf inf -1.00 inf -0.70 inf inf inf inf inf -0.80 inf -0.80 +-1.00 -0.80 -1.10 inf inf inf inf inf -1.00 -0.80 -1.10 inf inf inf inf inf +-0.70 -0.60 inf -0.50 inf inf inf inf -0.70 -0.60 inf -0.50 inf inf inf inf +-1.10 inf -1.20 inf inf inf inf inf -0.50 inf -0.80 -0.80 inf inf inf inf +inf -0.60 inf -0.50 inf inf inf inf inf -0.60 -1.10 -0.50 inf inf inf inf diff --git a/gtfold-mfe/data/RNAParams/tstackh.DAT b/gtfold-mfe/data/RNAParams/tstackh.DAT new file mode 100644 index 0000000..7648650 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/tstackh.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.50 -0.30 -0.30 +inf inf inf inf inf inf inf inf inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -1.20 -0.20 0.20 +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.30 -0.60 -1.10 +inf inf inf inf inf inf inf inf -1.50 -1.50 -1.40 -1.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -0.90 -2.90 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -2.20 -2.00 -1.60 -1.10 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -1.40 -1.80 -2.00 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -2.10 inf inf inf inf 0.20 -0.50 -0.30 -0.30 +inf inf inf inf -1.10 -0.70 -2.40 -0.50 inf inf inf inf -0.10 -0.20 -1.50 -0.20 +inf inf inf inf -2.40 -2.90 -1.40 -1.20 inf inf inf inf -0.90 -1.10 -0.30 0.00 +inf inf inf inf -1.90 -1.00 -2.20 -1.50 inf inf inf inf -0.30 -0.30 -0.40 -1.10 +-0.50 -0.30 -0.60 -0.50 inf inf inf inf -0.50 -0.30 -0.60 -0.50 inf inf inf inf +-0.20 -0.10 -1.20 -0.00 inf inf inf inf -0.20 -0.10 -1.70 0.00 inf inf inf inf +-1.40 -1.20 -0.70 -0.20 inf inf inf inf -0.80 -1.20 -0.30 -0.70 inf inf inf inf +-0.30 -0.10 -0.50 -0.80 inf inf inf inf -0.60 -0.10 -0.60 -0.80 inf inf inf inf diff --git a/gtfold-mfe/data/RNAParams/tstacki.DAT b/gtfold-mfe/data/RNAParams/tstacki.DAT new file mode 100644 index 0000000..dd7b5da --- /dev/null +++ b/gtfold-mfe/data/RNAParams/tstacki.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf inf inf inf inf inf inf inf inf 0.70 0.70 0.70 0.00 +inf inf inf inf inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf +inf inf inf inf inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf +inf inf inf inf -0.00 -0.00 -1.10 -0.00 inf inf inf inf 0.70 0.70 -0.40 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.00 inf inf inf inf 0.70 0.70 0.70 0.70 +inf inf inf inf -1.10 -0.00 -0.00 -0.00 inf inf inf inf -0.40 0.70 0.70 0.70 +inf inf inf inf -0.00 -0.00 -0.00 -0.70 inf inf inf inf 0.70 0.70 0.70 0.00 +0.70 0.70 -0.40 0.70 inf inf inf inf 0.70 0.70 -0.40 0.70 inf inf inf inf +0.70 0.70 0.70 0.70 inf inf inf inf 0.70 0.70 0.70 0.70 inf inf inf inf +-0.40 0.70 0.70 0.70 inf inf inf inf -0.40 0.70 0.70 0.70 inf inf inf inf +0.70 0.70 0.70 0.00 inf inf inf inf 0.70 0.70 0.70 0.00 inf inf inf inf diff --git a/gtfold-mfe/data/RNAParams/tstackm.DAT b/gtfold-mfe/data/RNAParams/tstackm.DAT new file mode 100644 index 0000000..b850f80 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf -1.00 inf inf inf -1.00 inf inf inf -2.20 -0.80 -1.00 -0.80 -0.90 +inf inf -1.50 inf inf inf -1.50 inf inf inf -2.70 inf -0.60 -0.70 -2.20 -0.70 +inf -1.50 inf -1.00 inf -1.50 inf -1.00 inf -2.70 inf -2.20 -0.80 -2.10 -0.80 -0.80 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -2.20 inf -2.70 inf -1.10 -0.80 -1.10 -0.80 +inf inf inf -1.00 inf inf inf -1.00 -1.70 -1.70 -1.70 -1.70 inf inf inf -1.00 +inf inf -1.50 inf inf inf -1.50 inf -1.00 -1.10 -3.30 -0.80 inf inf -1.50 inf +inf -1.50 inf -1.00 inf -1.50 inf -1.00 -1.70 -2.40 -1.70 -1.70 inf -1.50 inf -1.00 +-1.00 inf -1.50 inf -1.00 inf -1.50 inf -1.60 -1.40 -1.60 -1.20 -1.00 inf -1.50 inf +inf inf inf -2.20 -1.10 -1.50 -1.30 -1.90 inf inf inf -1.00 -0.80 -1.00 -0.80 -1.30 +inf inf -2.70 inf -1.10 -0.70 -3.40 -0.50 inf inf -1.50 inf -0.60 -0.70 -2.50 -0.70 +inf -2.70 inf -2.20 -1.60 -3.30 -1.40 -1.30 inf -1.50 inf -1.00 -0.80 -2.10 -0.80 -0.80 +-2.20 inf -2.70 inf -1.70 -1.00 -2.00 -0.70 -1.00 inf -1.50 inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf -1.00 -1.00 -0.80 -1.10 -1.00 inf inf inf -2.00 +-0.70 -0.60 -2.40 -0.50 inf inf -1.50 inf -0.70 -0.60 -1.50 -0.50 inf inf -2.50 inf +-1.10 -2.10 -1.20 -1.00 inf -1.50 inf -1.00 -0.70 -1.40 -0.80 0.30 inf -2.50 inf -2.00 +-0.90 -0.60 -1.40 -0.50 -1.00 inf -1.50 inf -0.50 -0.60 -0.50 -0.50 -2.00 inf -2.50 inf From 2e9862ac86e70b59b62ce1e0d8fcaab57b7238c1 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 27 Jun 2011 17:27:38 -0400 Subject: [PATCH 090/187] changes for --rnafold option --- gtfold-mfe/include/loader.h | 2 +- gtfold-mfe/include/options.h | 1 + gtfold-mfe/src/loader.cc | 10 ++++++++-- gtfold-mfe/src/main.cc | 5 +++-- gtfold-mfe/src/options.cc | 3 +++ 5 files changed, 16 insertions(+), 5 deletions(-) diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index 41d7c6b..1bac05c 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -25,7 +25,7 @@ #include "constants.h" #include "data.h" -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode,int t_mismatch); +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode, int rnamode, int t_mismatch); int initStackValues(const std::string& fileName, const std::string& dirPath); int initMiscloopValues(const std::string& fileName, const std::string& dirPath); diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 4d4dbf1..7c0cdbc 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -21,6 +21,7 @@ extern bool SHAPE_ENABLED; extern bool PARAM_DIR; extern bool T_MISMATCH; extern bool UNAMODE; +extern bool RNAMODE; extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 9144c07..0ab17e3 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -80,14 +80,20 @@ int init; int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ float prelog; -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int mismatch = 0) { +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, + int unamode = 0, int rnamode = 0, int mismatch = 0) { if (!userdatalogic && unamode) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; EN_DATADIR += "UNAParams"; + printf("readThermodynamicParameters() %d %s\n",unamode, EN_DATADIR.c_str()); + }else if (!userdatalogic && rnamode) { + EN_DATADIR.assign(xstr(DATADIR)); + EN_DATADIR += "/"; + EN_DATADIR += "RNAParams"; } - else if (!userdatalogic) { + else if (!userdatalogic) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; EN_DATADIR += "Turner99"; diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 52172cd..5a7f707 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -226,10 +226,11 @@ int main(int argc, char** argv) { exit(-1); } + printRunConfiguration(seq); + // Read in thermodynamic parameters. Always use Turner99 data (for now) - readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, T_MISMATCH); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); - printRunConfiguration(seq); init_fold(seq); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 6dad154..77dabb8 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -16,6 +16,7 @@ bool VERBOSE = false; bool SHAPE_ENABLED = false; bool T_MISMATCH = false; bool UNAMODE = false; +bool RNAMODE = false; bool b_prefilter = false; string seqfile = ""; @@ -127,6 +128,8 @@ void parse_options(int argc, char** argv) { T_MISMATCH = true; } else if (strcmp(argv[i], "--unamode") == 0) { UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; } else if (strcmp(argv[i], "--prefilter") == 0) { if(i < argc) { int value1 = -1, value2 = -1; From 8d711d36102ae88c429096c740b4d54f09a7c934 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 27 Jun 2011 18:03:36 -0400 Subject: [PATCH 091/187] fixed issue 17 --- gtfold-mfe/src/main.cc | 13 +++++++------ gtfold-mfe/src/traceback.c | 2 +- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 5a7f707..280ed9e 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -243,10 +243,13 @@ int main(int argc, char** argv) { printf("Done.\n\n"); printf("Results:\n"); - printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); + if (energy >= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); printf("- MFE runtime: %9.6f seconds\n", t1); - - + + if (SUBOPT_ENABLED) { t1 = get_seconds(); ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); @@ -263,17 +266,15 @@ int main(int argc, char** argv) { t1 = get_seconds(); trace(seq.length(), VERBOSE, UNAMODE, T_MISMATCH); t1 = get_seconds() - t1; - + printf("\n"); print_sequence(seq.length()); print_structure(seq.length()); if (CONS_ENABLED) print_constraints(seq.length()); - if (SHAPE_ENABLED && VERBOSE) print_shapeArray(seq.length()); - save_ct_file(outputFile, seq, energy); printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 1a9511f..6cea549 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -45,7 +45,7 @@ void trace(int len, int vv, int mode, int mismatch) { structure[i] = 0; if (W[len] >= MAXENG) { - printf("\n No Structure "); + printf("- No Structure \n"); return; } From f9305506acf16fe2fa86523b4aa228e27bacd7aa Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 29 Jun 2011 16:32:07 -0400 Subject: [PATCH 092/187] - changed --unamode to --unafold, - removed a debug statement --- gtfold-mfe/src/loader.cc | 1 - gtfold-mfe/src/options.cc | 7 ++++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 0ab17e3..8ec31df 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -87,7 +87,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; EN_DATADIR += "UNAParams"; - printf("readThermodynamicParameters() %d %s\n",unamode, EN_DATADIR.c_str()); }else if (!userdatalogic && rnamode) { EN_DATADIR.assign(xstr(DATADIR)); EN_DATADIR += "/"; diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 77dabb8..a690bc1 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -56,8 +56,9 @@ void help() { printf(" -o, --output NAME Name output files with prefix\n"); printf(" -w, --workDir DIR Path to directory for output files\n"); printf(" -t, --threads num Limit number of threads used\n"); - printf(" --unamode Enable UNAfold mode. \n"); - printf(" --prefilter value1,value2 \n\t\t\tSets the prefilter mode similar to UNAfold\n"); + printf(" --unafold Run as UNAFOLD default mode (version 3.8). \n"); + printf(" --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n"); + printf(" --rnafold Run as RNAFOLD default mode (version 1.8.5). \n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); @@ -126,7 +127,7 @@ void parse_options(int argc, char** argv) { help(); } else if (strcmp(argv[i], "-m") == 0) { T_MISMATCH = true; - } else if (strcmp(argv[i], "--unamode") == 0) { + } else if (strcmp(argv[i], "--unafold") == 0) { UNAMODE = true; } else if (strcmp(argv[i], "--rnafold") == 0) { RNAMODE = true; From 07ed2e69c852a2edbd7c235757b88ad365535d2f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 8 Jul 2011 12:46:52 -0400 Subject: [PATCH 093/187] added d2 option --- gtfold-mfe/include/global.h | 1 + gtfold-mfe/include/options.h | 1 + gtfold-mfe/include/traceback.h | 3 +- gtfold-mfe/src/algorithms.c | 300 ++++++++++++++--------- gtfold-mfe/src/global.c | 1 + gtfold-mfe/src/main.cc | 10 +- gtfold-mfe/src/options.cc | 28 ++- gtfold-mfe/src/traceback.c | 430 +++++++++++++++++---------------- 8 files changed, 435 insertions(+), 339 deletions(-) diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h index 1bdc31e..c452b2a 100644 --- a/gtfold-mfe/include/global.h +++ b/gtfold-mfe/include/global.h @@ -9,6 +9,7 @@ extern int* constraints; extern int g_nthreads; extern int g_unamode; +extern int g_dangles; extern int g_mismatch; extern int g_verbose; extern int g_prefilter_mode; diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 7c0cdbc..44de1ce 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -37,6 +37,7 @@ extern int nThreads; extern bool b_prefilter; extern int prefilter1; extern int prefilter2; +extern int dangles; extern bool LIMIT_DISTANCE; extern int contactDistance; diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h index f250058..ff654f4 100644 --- a/gtfold-mfe/include/traceback.h +++ b/gtfold-mfe/include/traceback.h @@ -26,7 +26,7 @@ #ifdef __cplusplus extern "C" { #endif - void trace(int len, int vv, int mode, int mismatch); + void trace(int len); //, int vv, int mode, int mismatch); #ifdef __cplusplus } #endif @@ -36,5 +36,6 @@ int traceV(int i, int j); int traceVM(int i, int j); int traceVBI(int i, int j); int traceWM(int i, int j); +int traceWMPrime(int i, int j); #endif diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index a0fe2ae..79425a5 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -30,7 +30,7 @@ along with this program. If not, see . #include "omp.h" #endif -//#define DEBUG 1 +#define DEBUG 1 void initializeMatrix(int len) { int i, j; @@ -120,134 +120,200 @@ int calcVBI2(int i, int j, int len) { return energy; } -int calculate(int len) { //, int nThreads, int unamode, int mismatch) { - int b, i, j; +int calculate(int len) { + int b, i, j; #ifdef _OPENMP - if (g_nthreads > 0) omp_set_num_threads(g_nthreads); + if (g_nthreads > 0) omp_set_num_threads(g_nthreads); #endif + #ifdef _OPENMP #pragma omp parallel #pragma omp master - fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); + fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif - initializeMatrix(len); - if (g_unamode || g_prefilter_mode) { - prefilter(len,g_prefilter1,g_prefilter2); - } - - for (b = TURN+1; b <= len-1; b++) { + initializeMatrix(len); + if (g_unamode || g_prefilter_mode) { + prefilter(len,g_prefilter1,g_prefilter2); + } + + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) #endif - for (i = 1; i <= len - b; i++) { - j = i + b; - int newWM = INFINITY_; - - if (PP[i][j]==1) { - int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack - - // Internal Loop BEGIN - if (g_unamode) - VBI(i,j) = calcVBI1(i,j); - else - VBI(i,j) = calcVBI(i,j); - // Internal Loop END - - // Multi Loop BEGIN - int VMij = WMPrime[i+1][j-1]; - int VMidj = WMPrime[i+2][j-1]; - int VMijd = WMPrime[i+1][j-2]; - int VMidjd = WMPrime[i+2][j-2]; - - int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; - int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; - VMij = MIN(VMij, (VMidj + d5 +Ec)) ; - VMij = MIN(VMij, (VMijd + d3 +Ec)); - - if (g_unamode || g_mismatch) { - VMij = MIN(VMij, (VMidjd + Estackm(i,j) + 2*Ec)); - } else { - VMij = MIN(VMij, (VMidjd + d5 + d3+ 2*Ec)); - } - - VMij = VMij + Ea + Eb + auPenalty(i,j); - VM(i,j) = canStack(i,j)?VMij:INFINITY_; - // Multi Loop END - - V(i,j) = MIN4(eh,es,VBI(i,j),VM(i,j)); - } - else V(i,j) = INFINITY_; - - int h; - for (h = i+TURN+1 ; h <= j-TURN-2; h++) { - // Added auxillary storage WMPrime to speedup multiloop calculations - WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); - //newWM = (!forcePair(i,j))?MIN(newWM, WMU(i,h-1) + WML(h,j)):newWM; - } - - //ZS: This sum corresponds to when i,j are NOT paired with each other. - //So we need to make sure only terms where i,j aren't pairing are considered. - newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; - - newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle - newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle - - if (g_unamode || g_mismatch) { - if (i1) energy += Ed3(j,i,i-1); + if (j ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj)); + } + } + fclose(file); + + file = fopen("Eh.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int eh = INFINITY_; + if (PP[ii][jj]) eh = eH(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh); + } + } + fclose(file); - file = fopen("WM.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = 1; jj <= len; ++jj) { - fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); - } - } - fclose(file); + file = fopen("Es.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int es = INFINITY_; + if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es); + } + } + fclose(file); + + file = fopen("BP.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]); + } + } + fclose(file); + + file = fopen("VM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj)); + } + } + fclose(file); + + file = fopen("WM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); + } + } + fclose(file); #endif - - return W[len]; + + return W[len]; } diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c index 1a64fe7..1c2d45b 100644 --- a/gtfold-mfe/src/global.c +++ b/gtfold-mfe/src/global.c @@ -9,6 +9,7 @@ int *structure; unsigned int chPairKey; int g_nthreads; +int g_dangles; int g_unamode; int g_mismatch; int g_verbose; diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 280ed9e..23e8380 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -78,6 +78,7 @@ void init_fold(string seq) { g_prefilter_mode = b_prefilter; g_prefilter1 = prefilter1; g_prefilter2 = prefilter2; + g_dangles = dangles; } void free_fold(int len) { @@ -226,19 +227,18 @@ int main(int argc, char** argv) { exit(-1); } - printRunConfiguration(seq); - // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); - init_fold(seq); + + printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); fflush(stdout); t1 = get_seconds(); - energy = calculate(seq.length()) ; //, nThreads, UNAMODE, T_MISMATCH); + energy = calculate(seq.length()) ; t1 = get_seconds() - t1; printf("Done.\n\n"); @@ -264,7 +264,7 @@ int main(int argc, char** argv) { } t1 = get_seconds(); - trace(seq.length(), VERBOSE, UNAMODE, T_MISMATCH); + trace(seq.length()); //, VERBOSE, UNAMODE, T_MISMATCH); t1 = get_seconds() - t1; printf("\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index a690bc1..e60c8b7 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -29,6 +29,7 @@ string outputDir = ""; string shapeFile = ""; string paramDir; // default value +int dangles=-1; int prefilter1=2; int prefilter2=2; @@ -52,6 +53,7 @@ void help() { printf(" limit is given, base pairs can be over any distance\n"); printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); printf(" -m Enable terminal mismatch calculations\n"); + printf(" -d2 Enable d2 calculations\n"); printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output NAME Name output files with prefix\n"); printf(" -w, --workDir DIR Path to directory for output files\n"); @@ -109,16 +111,19 @@ void parse_options(int argc, char** argv) { } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { NOISOLATE = true; } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) + if(i < argc) { outputPrefix = argv[++i]; + } else help(); } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) + if(i < argc) { outputDir = argv[++i]; + } else help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + } + else if (strcmp(argv[i], "--paramdir")== 0 || strcmp(argv[i], "-p") == 0) { if(i < argc) { paramDir = argv[++i]; PARAM_DIR = true; @@ -127,6 +132,10 @@ void parse_options(int argc, char** argv) { help(); } else if (strcmp(argv[i], "-m") == 0) { T_MISMATCH = true; + } else if (strcmp(argv[i], "-d2") == 0) { + dangles = 2; + } else if (strcmp(argv[i], "-d0") == 0) { + dangles = 0; } else if (strcmp(argv[i], "--unafold") == 0) { UNAMODE = true; } else if (strcmp(argv[i], "--rnafold") == 0) { @@ -202,8 +211,11 @@ void parse_options(int argc, char** argv) { // If output dir specified if (!outputDir.empty()) { outputFile += outputDir; + outputFile += "/"; suboptFile += outputDir; + suboptFile += "/"; bppOutFile += outputDir; + bppOutFile += "/"; } // ... and append the .ct outputFile += outputPrefix; @@ -225,8 +237,16 @@ void printRunConfiguration(string seq) { bool standardRun = true; printf("Run Configuration:\n"); + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } if (UNAMODE == true) { - printf("+ running in unamode\n"); + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 2) { + printf("+ running in -d2 mode\n"); standardRun = false; } if (T_MISMATCH == true) { diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 6cea549..508ed8f 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -30,20 +30,16 @@ #include "utils.h" #include "shapereader.h" -int verbose = -1; int total_en = 0; int total_ex = 0; -int unamode = 0; +int length = 0; -void trace(int len, int vv, int mode, int mismatch) { +void trace(int len) { + printf("traceback()\n"); int i; - verbose = vv; - unamode = mode; - if (mismatch) unamode = 1; - - for (i = 0; i < len+1; i++) - structure[i] = 0; + for (i = 0; i <= len; i++) structure[i] = 0; + length = len; if (W[len] >= MAXENG) { printf("- No Structure \n"); return; @@ -58,14 +54,11 @@ void trace(int len, int vv, int mode, int mismatch) { } void traceW(int j) { - int done, i, Wj; - int wim1, flag, Widjd, Wijd, Widj, Wij; - Wj = INFINITY_; - flag = 1; - done = 0; + int done = 0, i; + int wim1, flag = 1 ; + + assert(!(j == 0 || j == 1)); - if (j == 0 || j == 1) return; - for (i = 1; i < j && !done; i++) { if (j-i < TURN) continue; @@ -73,74 +66,95 @@ void traceW(int j) { flag = 1; if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0; - Widjd = Wijd = Widj = INFINITY_; - Wij = V(i,j) + auPenalty(i, j) + wim1; - - if (unamode) { - Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1; - } - else { - Widjd = V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1; - } - - Wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - Widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - - if ((W[j] == Wij && canStack(i,j)) || forcePair(i,j)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); - total_ex += auPenalty(i, j); - structure[i] = j; - structure[j] = i; - traceV(i, j); - if (flag ) traceW(i - 1); - break; - } else if ((W[j] == Widjd && unamode && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00); - total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1)); - structure[i + 1] = j - 1; - structure[j - 1] = i + 1; - traceV(i + 1, j - 1); - if (flag ) traceW(i - 1); - break; - } - else if ((W[j] == Widjd && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00); - total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); - structure[i + 1] = j - 1; - structure[j - 1] = i + 1; - traceV(i + 1, j - 1); - if (flag ) traceW(i - 1); - break; - } else if ((W[j] == Wijd && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); - total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j)); - structure[i] = j - 1; - structure[j - 1] = i; - traceV(i, j - 1); - if (flag ) traceW(i - 1); - break; - } else if ((W[j] == Widj && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){ - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); - total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i)); - structure[i + 1] = j; - structure[j] = i + 1; - traceV(i + 1, j); - if (flag ) traceW(i - 1); - break; + if (g_unamode||g_mismatch) { + if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); + total_ex += auPenalty(i, j); + traceV(i, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); + total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j)); + traceV(i, j - 1); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){ + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); + total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i)); + traceV(i + 1, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00); + total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1)); + traceV(i + 1, j - 1); + if (flag ) traceW(i - 1); + break; + } + } else if (g_dangles == 2) { + int e_dangles = 0; + if (i>1) e_dangles += Ed3(j,i,i-1); + if (j= j) - return 0; - else { - for (h = i; h < j && !done; h++) { - int aa = WM(i,h) + WM(h + 1,j); - if (aa == WM(i,j)) { - done = 1; - h1 = h; - break; - } + if (!done){ + if (g_unamode||g_mismatch) { + if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { + eWM += traceV(i, j); + done = 1; + } else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) { + eWM += traceV(i + 1, j); + done = 1; + } else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) { + done = 1; + eWM += traceV(i, j - 1); + } else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { + done = 1; + eWM += traceV(i + 1, j - 1); + } + } else if (g_dangles == 2) { + int energy = V(i,j) + auPenalty(i, j) + Eb; + energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + /*if (j Date: Fri, 8 Jul 2011 12:48:53 -0400 Subject: [PATCH 094/187] changed parameters for RNAfold mode --- gtfold-mfe/data/RNAParams/miscloop.DAT | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT index 3c000a5..69847f3 100644 --- a/gtfold-mfe/data/RNAParams/miscloop.DAT +++ b/gtfold-mfe/data/RNAParams/miscloop.DAT @@ -5,8 +5,8 @@ 10.10 -0.30 -0.30 0.50 0.0 -0.30 -1.60 -1.40 +0.0 +0.0 +0.0 4.10 0 From 9b11ef9650daff6cea3779bed9ba8f74cf7b80e5 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 8 Jul 2011 12:55:01 -0400 Subject: [PATCH 095/187] removed debug mode --- gtfold-mfe/src/algorithms.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 79425a5..bdf40c4 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -30,7 +30,7 @@ along with this program. If not, see . #include "omp.h" #endif -#define DEBUG 1 +//#define DEBUG 1 void initializeMatrix(int len) { int i, j; From 544254c80324c560f2cf0a8bff0a86a0375c29c2 Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Fri, 8 Jul 2011 15:28:20 -0400 Subject: [PATCH 096/187] Edited descriptions of --help message --- gtfold-mfe/src/options.cc | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index a690bc1..ec828de 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -48,17 +48,17 @@ void help() { printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); + printf(" -d, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); - printf(" -m Enable terminal mismatch calculations\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); - printf(" -o, --output NAME Name output files with prefix\n"); - printf(" -w, --workDir DIR Path to directory for output files\n"); - printf(" -t, --threads num Limit number of threads used\n"); - printf(" --unafold Run as UNAFOLD default mode (version 3.8). \n"); - printf(" --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n"); - printf(" --rnafold Run as RNAFOLD default mode (version 1.8.5). \n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -m Enable terminal mismatch calculations\n"); + printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" -t, --threads INT Limit number of threads used to INT\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); + printf(" --prefilter INT,INT Sets the prefilter mode similar to UNAfold\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5)\n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); @@ -68,7 +68,7 @@ void help() { printf(" --bpp Calculate base pair probabilities\n"); printf(" --subopt range Calculate suboptimal structures within 'range' kcal/mol\n"); printf(" of the mfe\n"); - printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE\n"); printf("\nConstraint syntax:\n"); printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); From f79902585d266ace2437440907cc08e89624b302 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 8 Jul 2011 15:44:40 -0400 Subject: [PATCH 097/187] merged Shel's changes --- gtfold-mfe/src/options.cc | 32 ++++++++++++++------------------ 1 file changed, 14 insertions(+), 18 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index e60c8b7..7238419 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -49,18 +49,17 @@ void help() { printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); + printf(" -d, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -p --paramdir DIR Path to directory from where parameters are to be read\n"); - printf(" -m Enable terminal mismatch calculations\n"); - printf(" -d2 Enable d2 calculations\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); - printf(" -o, --output NAME Name output files with prefix\n"); - printf(" -w, --workDir DIR Path to directory for output files\n"); - printf(" -t, --threads num Limit number of threads used\n"); - printf(" --unafold Run as UNAFOLD default mode (version 3.8). \n"); - printf(" --prefilter num1,num2 \n\t\t\tSets the prefilter mode similar to UNAfold\n"); - printf(" --rnafold Run as RNAFOLD default mode (version 1.8.5). \n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -m Enable terminal mismatch calculations\n"); + printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" -t, --threads INT Limit number of threads used to INT\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); + printf(" --prefilter INT,INT Sets the prefilter mode similar to UNAfold\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5)\n"); printf("\n"); printf(" -h, --help Output help (this message) and exit\n"); @@ -70,7 +69,7 @@ void help() { printf(" --bpp Calculate base pair probabilities\n"); printf(" --subopt range Calculate suboptimal structures within 'range' kcal/mol\n"); printf(" of the mfe\n"); - printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE\n"); printf("\nConstraint syntax:\n"); printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); @@ -111,19 +110,16 @@ void parse_options(int argc, char** argv) { } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { NOISOLATE = true; } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) { + if(i < argc) outputPrefix = argv[++i]; - } else help(); } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) { + if(i < argc) outputDir = argv[++i]; - } else help(); - } - else if (strcmp(argv[i], "--paramdir")== 0 || strcmp(argv[i], "-p") == 0) { + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { if(i < argc) { paramDir = argv[++i]; PARAM_DIR = true; From 7f6c3c618927f8ac8a520167f4d4cbb467198dfa Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 12:50:37 -0400 Subject: [PATCH 098/187] removed debug statement --- gtfold-mfe/src/traceback.c | 1 - 1 file changed, 1 deletion(-) diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 508ed8f..35c7c29 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -35,7 +35,6 @@ int total_ex = 0; int length = 0; void trace(int len) { - printf("traceback()\n"); int i; for (i = 0; i <= len; i++) structure[i] = 0; From 6cbc69ebea0603cfd752452143115a6c51689088 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 12:51:46 -0400 Subject: [PATCH 099/187] added options for dangles, mismatch --- gtfold-mfe/src/main.cc | 12 ++++++++++++ gtfold-mfe/src/options.cc | 30 ++++++++++++++++++------------ 2 files changed, 30 insertions(+), 12 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 23e8380..9e76e49 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -43,6 +43,8 @@ #include "subopt_traceback.h" #include "shapereader.h" +//#define DEBUG 1 + using namespace std; double get_seconds() { @@ -79,6 +81,16 @@ void init_fold(string seq) { g_prefilter1 = prefilter1; g_prefilter2 = prefilter2; g_dangles = dangles; + +#ifdef DEBUG + printf("g_nthreads = %d\n", g_nthreads); + printf("g_unamode = %d\n", g_unamode); + printf("g_mismatch = %d\n", g_mismatch); + printf("g_prefilter_mode = %d\n", g_prefilter_mode); + printf("g_dangles = %d\n", g_dangles); + +#endif + } void free_fold(int len) { diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 7238419..9282c22 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -49,10 +49,10 @@ void help() { printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); - printf(" -m Enable terminal mismatch calculations\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output NAME Write output files with prefix given in NAME\n"); printf(" -w, --workDir DIR Path of directory where output files will be written\n"); @@ -95,7 +95,7 @@ void parse_options(int argc, char** argv) { } else help(); - } else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-d") == 0) { + } else if(strcmp(argv[i], "--limitCD") == 0 || strcmp(argv[i], "-l") == 0) { if(i < argc){ contactDistance = atoi(argv[++i]); stringstream ss; @@ -126,16 +126,22 @@ void parse_options(int argc, char** argv) { } else help(); - } else if (strcmp(argv[i], "-m") == 0) { - T_MISMATCH = true; - } else if (strcmp(argv[i], "-d2") == 0) { - dangles = 2; - } else if (strcmp(argv[i], "-d0") == 0) { - dangles = 0; + } else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) { + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 1 || dangles == 2)) + help(); + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + if (!(dangles == 0 || dangles == 1 || dangles == 2)) + T_MISMATCH = true; } else if (strcmp(argv[i], "--unafold") == 0) { UNAMODE = true; + dangles = -1; } else if (strcmp(argv[i], "--rnafold") == 0) { RNAMODE = true; + dangles = 1; } else if (strcmp(argv[i], "--prefilter") == 0) { if(i < argc) { int value1 = -1, value2 = -1; @@ -233,7 +239,7 @@ void printRunConfiguration(string seq) { bool standardRun = true; printf("Run Configuration:\n"); - if (RNAMODE == true) { + if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; } @@ -241,8 +247,8 @@ void printRunConfiguration(string seq) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles == 2) { - printf("+ running in -d2 mode\n"); + if (dangles >= 0 && !RNAMODE) { + printf("+ running in dangles %d mode\n", dangles); standardRun = false; } if (T_MISMATCH == true) { From 3f2effa02f6f28e75b3da1ebb965612fd9a60bff Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 12:59:29 -0400 Subject: [PATCH 100/187] enabled precedence of -d over -m optiom --- gtfold-mfe/src/options.cc | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 9282c22..8a7e138 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -129,19 +129,20 @@ void parse_options(int argc, char** argv) { } else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) { if(i < argc) { dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 1 || dangles == 2)) - help(); + if (!(dangles == 0 || dangles == 1 || dangles == 2)) help(); + T_MISMATCH = false; } else help(); } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - if (!(dangles == 0 || dangles == 1 || dangles == 2)) - T_MISMATCH = true; + if (!(dangles == 0 || dangles == 1 || dangles == 2)) T_MISMATCH = true; } else if (strcmp(argv[i], "--unafold") == 0) { UNAMODE = true; dangles = -1; + T_MISMATCH = false; } else if (strcmp(argv[i], "--rnafold") == 0) { RNAMODE = true; dangles = 1; + T_MISMATCH = false; } else if (strcmp(argv[i], "--prefilter") == 0) { if(i < argc) { int value1 = -1, value2 = -1; From 57e86f4c414ef050b9886a9ad9e6c6a44e5ed91c Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 13:14:22 -0400 Subject: [PATCH 101/187] options.cc --- gtfold-mfe/src/options.cc | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 8a7e138..cd16136 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -127,21 +127,32 @@ void parse_options(int argc, char** argv) { else help(); } else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; if(i < argc) { dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 1 || dangles == 2)) help(); - T_MISMATCH = false; + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } else { + T_MISMATCH = false; + } } else help(); } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - if (!(dangles == 0 || dangles == 1 || dangles == 2)) T_MISMATCH = true; + std::string cmd = argv[i]; + if (!(dangles == 0 || dangles == 2)) + T_MISMATCH = true; + else { + printf("Ignoring %s option\n", cmd.c_str()); + T_MISMATCH = false; + } } else if (strcmp(argv[i], "--unafold") == 0) { UNAMODE = true; dangles = -1; T_MISMATCH = false; } else if (strcmp(argv[i], "--rnafold") == 0) { RNAMODE = true; - dangles = 1; + //dangles = 1; T_MISMATCH = false; } else if (strcmp(argv[i], "--prefilter") == 0) { if(i < argc) { From e8c7d3e288459b649b7a4208481e67bae067a0dd Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Mon, 11 Jul 2011 16:26:17 -0400 Subject: [PATCH 102/187] Edited descriptions of --help message --- gtfold-mfe/src/options.cc | 28 ++++++++++++++++++---------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index cd16136..7a2f446 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -48,22 +48,24 @@ void help() { printf("OPTIONS\n"); printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - + printf(" -d, --dangle INT Allow only one treatment of dangleing end energies in \n"); + printf(" mulit- and external loops (INT=0,2) see below for details\n"); + printf(" -h, --help Output help (this message) and exit\n"); printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); printf(" -m --mismatch Enable terminal mismatch calculations\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output NAME Write output files with prefix given in NAME\n"); - printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); printf(" -t, --threads INT Limit number of threads used to INT\n"); - printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); - printf(" --prefilter INT,INT Sets the prefilter mode similar to UNAfold\n"); + printf(" -v, --verbose Run in verbose mode\n"); + printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT\n"); printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5)\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); - printf("\n"); - printf(" -h, --help Output help (this message) and exit\n"); - printf(" -v, --verbose Run in verbose mode\n"); printf("\nBETA OPTIONS\n"); printf(" --bpp Calculate base pair probabilities\n"); @@ -75,6 +77,12 @@ void help() { printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n"); + printf("\tINT=2 dangling end energies are added for nucleotieds on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); exit(-1); } @@ -126,7 +134,7 @@ void parse_options(int argc, char** argv) { } else help(); - } else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) { + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { std::string cmd = argv[i]; if(i < argc) { dangles = atoi(argv[++i]); From 7959d2f46303b79a9af0fe784dd3b78cf5ac7d77 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 17:32:31 -0400 Subject: [PATCH 103/187] fixed commandline options --- gtfold-mfe/src/main.cc | 39 ++++- gtfold-mfe/src/options.cc | 321 ++++++++++++++++++-------------------- 2 files changed, 192 insertions(+), 168 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 9e76e49..86aee90 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -72,7 +72,41 @@ void init_fold(string seq) { if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + g_nthreads = nThreads; g_unamode = UNAMODE; g_mismatch = T_MISMATCH; @@ -82,7 +116,7 @@ void init_fold(string seq) { g_prefilter2 = prefilter2; g_dangles = dangles; -#ifdef DEBUG + #ifdef DEBUG printf("g_nthreads = %d\n", g_nthreads); printf("g_unamode = %d\n", g_unamode); printf("g_mismatch = %d\n", g_mismatch); @@ -238,12 +272,11 @@ int main(int argc, char** argv) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); } + init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); - init_fold(seq); - printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index cd16136..191fb5d 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -48,22 +48,24 @@ void help() { printf("OPTIONS\n"); printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - + printf(" -d, --dangle INT Allow only one treatment of dangleing end energies in \n"); + printf(" mulit- and external loops (INT=0,2) see below for details\n"); + printf(" -h, --help Output help (this message) and exit\n"); printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); - printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); printf(" -m --mismatch Enable terminal mismatch calculations\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); printf(" -o, --output NAME Write output files with prefix given in NAME\n"); - printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); printf(" -t, --threads INT Limit number of threads used to INT\n"); - printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); - printf(" --prefilter INT,INT Sets the prefilter mode similar to UNAfold\n"); + printf(" -v, --verbose Run in verbose mode\n"); + printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT\n"); printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5)\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); - printf("\n"); - printf(" -h, --help Output help (this message) and exit\n"); - printf(" -v, --verbose Run in verbose mode\n"); printf("\nBETA OPTIONS\n"); printf(" --bpp Calculate base pair probabilities\n"); @@ -75,6 +77,12 @@ void help() { printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n"); + printf("\tINT=2 dangling end energies are added for nucleotieds on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); exit(-1); } @@ -82,164 +90,148 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangles") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } else { - T_MISMATCH = false; - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - std::string cmd = argv[i]; - if (!(dangles == 0 || dangles == 2)) - T_MISMATCH = true; - else { - printf("Ignoring %s option\n", cmd.c_str()); - T_MISMATCH = false; - } - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - dangles = -1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - //dangles = 1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - int value1 = -1, value2 = -1; - std::stringstream ss; - ss << argv[++i]; - sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); - if (value1 <= 0 || value2 <= 0) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter1 = value1; - prefilter2 = value2; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; - - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -254,15 +246,15 @@ void printRunConfiguration(string seq) { if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; - } + } if (UNAMODE == true) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles >= 0 && !RNAMODE) { - printf("+ running in dangles %d mode\n", dangles); + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); standardRun = false; - } + } if (T_MISMATCH == true) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; @@ -271,7 +263,6 @@ void printRunConfiguration(string seq) { printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); standardRun = false; } - if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; From 93972e5372cbab03c46fef5b99a100636245031f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 11 Jul 2011 17:36:16 -0400 Subject: [PATCH 104/187] fixed a print statement --- gtfold-mfe/src/options.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 191fb5d..6886f65 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -260,7 +260,7 @@ void printRunConfiguration(string seq) { standardRun = false; } if (b_prefilter == true) { - printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); + printf("+ running with prefilter value = %d\n",prefilter1); standardRun = false; } if (NOISOLATE == true) { From 63fbc244a6315d204de8826fa14a12130bd09fca Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 12:47:02 -0400 Subject: [PATCH 105/187] merged changes --- gtfold-mfe/src/main.cc | 39 +---- gtfold-mfe/src/options.cc | 297 ++++++++++++++++++++------------------ 2 files changed, 160 insertions(+), 176 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 86aee90..9e76e49 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -72,41 +72,7 @@ void init_fold(string seq) { if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } - - if (UNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --unafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --unafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - if (RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --rnafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --rnafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - - if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); - T_MISMATCH = false; - } else { - if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); - dangles = -1; - } - g_nthreads = nThreads; g_unamode = UNAMODE; g_mismatch = T_MISMATCH; @@ -116,7 +82,7 @@ void init_fold(string seq) { g_prefilter2 = prefilter2; g_dangles = dangles; - #ifdef DEBUG +#ifdef DEBUG printf("g_nthreads = %d\n", g_nthreads); printf("g_unamode = %d\n", g_unamode); printf("g_mismatch = %d\n", g_mismatch); @@ -272,11 +238,12 @@ int main(int argc, char** argv) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); } - init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + init_fold(seq); + printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 6886f65..7a2f446 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -90,148 +90,164 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - T_MISMATCH = true; - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - prefilter1 = atoi(argv[++i]); - if (prefilter1 <= 0 ) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter2 = prefilter1; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } - - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } else { + T_MISMATCH = false; + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + std::string cmd = argv[i]; + if (!(dangles == 0 || dangles == 2)) + T_MISMATCH = true; + else { + printf("Ignoring %s option\n", cmd.c_str()); + T_MISMATCH = false; + } + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + dangles = -1; + T_MISMATCH = false; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + //dangles = 1; + T_MISMATCH = false; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + int value1 = -1, value2 = -1; + std::stringstream ss; + ss << argv[++i]; + sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); + if (value1 <= 0 || value2 <= 0) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter1 = value1; + prefilter2 = value2; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -246,23 +262,24 @@ void printRunConfiguration(string seq) { if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; - } + } if (UNAMODE == true) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles == 0 || dangles == 2) { - printf("+ running in dangle %d mode\n", dangles); + if (dangles >= 0 && !RNAMODE) { + printf("+ running in dangles %d mode\n", dangles); standardRun = false; - } + } if (T_MISMATCH == true) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } if (b_prefilter == true) { - printf("+ running with prefilter value = %d\n",prefilter1); + printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); standardRun = false; } + if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; From 3249482366ecfa4104a3cc90bece6b8724d2326b Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 12:49:48 -0400 Subject: [PATCH 106/187] fixed commanline options --- gtfold-mfe/src/main.cc | 39 ++++- gtfold-mfe/src/options.cc | 297 ++++++++++++++++++-------------------- 2 files changed, 176 insertions(+), 160 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 9e76e49..86aee90 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -72,7 +72,41 @@ void init_fold(string seq) { if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + g_nthreads = nThreads; g_unamode = UNAMODE; g_mismatch = T_MISMATCH; @@ -82,7 +116,7 @@ void init_fold(string seq) { g_prefilter2 = prefilter2; g_dangles = dangles; -#ifdef DEBUG + #ifdef DEBUG printf("g_nthreads = %d\n", g_nthreads); printf("g_unamode = %d\n", g_unamode); printf("g_mismatch = %d\n", g_mismatch); @@ -238,12 +272,11 @@ int main(int argc, char** argv) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); } + init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); - init_fold(seq); - printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 7a2f446..6886f65 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -90,164 +90,148 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } else { - T_MISMATCH = false; - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - std::string cmd = argv[i]; - if (!(dangles == 0 || dangles == 2)) - T_MISMATCH = true; - else { - printf("Ignoring %s option\n", cmd.c_str()); - T_MISMATCH = false; - } - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - dangles = -1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - //dangles = 1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - int value1 = -1, value2 = -1; - std::stringstream ss; - ss << argv[++i]; - sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); - if (value1 <= 0 || value2 <= 0) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter1 = value1; - prefilter2 = value2; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; - - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -262,24 +246,23 @@ void printRunConfiguration(string seq) { if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; - } + } if (UNAMODE == true) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles >= 0 && !RNAMODE) { - printf("+ running in dangles %d mode\n", dangles); + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); standardRun = false; - } + } if (T_MISMATCH == true) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } if (b_prefilter == true) { - printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); + printf("+ running with prefilter value = %d\n",prefilter1); standardRun = false; } - if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; From 58bc5a2605f11298c59430eb8328134a409bf48b Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 12:53:22 -0400 Subject: [PATCH 107/187] merged changes --- gtfold-mfe/src/main.cc | 39 +---- gtfold-mfe/src/options.cc | 297 ++++++++++++++++++++------------------ 2 files changed, 160 insertions(+), 176 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 86aee90..9e76e49 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -72,41 +72,7 @@ void init_fold(string seq) { if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } - - if (UNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --unafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --unafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - if (RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --rnafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --rnafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - - if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); - T_MISMATCH = false; - } else { - if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); - dangles = -1; - } - g_nthreads = nThreads; g_unamode = UNAMODE; g_mismatch = T_MISMATCH; @@ -116,7 +82,7 @@ void init_fold(string seq) { g_prefilter2 = prefilter2; g_dangles = dangles; - #ifdef DEBUG +#ifdef DEBUG printf("g_nthreads = %d\n", g_nthreads); printf("g_unamode = %d\n", g_unamode); printf("g_mismatch = %d\n", g_mismatch); @@ -272,11 +238,12 @@ int main(int argc, char** argv) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); } - init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + init_fold(seq); + printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 6886f65..7a2f446 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -90,148 +90,164 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - T_MISMATCH = true; - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - prefilter1 = atoi(argv[++i]); - if (prefilter1 <= 0 ) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter2 = prefilter1; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } - - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } else { + T_MISMATCH = false; + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + std::string cmd = argv[i]; + if (!(dangles == 0 || dangles == 2)) + T_MISMATCH = true; + else { + printf("Ignoring %s option\n", cmd.c_str()); + T_MISMATCH = false; + } + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + dangles = -1; + T_MISMATCH = false; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + //dangles = 1; + T_MISMATCH = false; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + int value1 = -1, value2 = -1; + std::stringstream ss; + ss << argv[++i]; + sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); + if (value1 <= 0 || value2 <= 0) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter1 = value1; + prefilter2 = value2; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -246,23 +262,24 @@ void printRunConfiguration(string seq) { if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; - } + } if (UNAMODE == true) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles == 0 || dangles == 2) { - printf("+ running in dangle %d mode\n", dangles); + if (dangles >= 0 && !RNAMODE) { + printf("+ running in dangles %d mode\n", dangles); standardRun = false; - } + } if (T_MISMATCH == true) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } if (b_prefilter == true) { - printf("+ running with prefilter value = %d\n",prefilter1); + printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); standardRun = false; } + if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; From 6b6b7badbb12bd0fa43828cadc13ab8697cbf732 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 12:54:43 -0400 Subject: [PATCH 108/187] fixed commanline options --- gtfold-mfe/src/main.cc | 39 ++++- gtfold-mfe/src/options.cc | 297 ++++++++++++++++++-------------------- 2 files changed, 176 insertions(+), 160 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 9e76e49..86aee90 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -72,7 +72,41 @@ void init_fold(string seq) { if (SHAPE_ENABLED) { readSHAPEarray(shapeFile.c_str(),len); } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + g_nthreads = nThreads; g_unamode = UNAMODE; g_mismatch = T_MISMATCH; @@ -82,7 +116,7 @@ void init_fold(string seq) { g_prefilter2 = prefilter2; g_dangles = dangles; -#ifdef DEBUG + #ifdef DEBUG printf("g_nthreads = %d\n", g_nthreads); printf("g_unamode = %d\n", g_unamode); printf("g_mismatch = %d\n", g_mismatch); @@ -238,12 +272,11 @@ int main(int argc, char** argv) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); } + init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); - init_fold(seq); - printRunConfiguration(seq); printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 7a2f446..6886f65 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -90,164 +90,148 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } else { - T_MISMATCH = false; - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - std::string cmd = argv[i]; - if (!(dangles == 0 || dangles == 2)) - T_MISMATCH = true; - else { - printf("Ignoring %s option\n", cmd.c_str()); - T_MISMATCH = false; - } - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - dangles = -1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - //dangles = 1; - T_MISMATCH = false; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - int value1 = -1, value2 = -1; - std::stringstream ss; - ss << argv[++i]; - sscanf(ss.str().c_str(),"%d,%d", &value1, &value2); - if (value1 <= 0 || value2 <= 0) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter1 = value1; - prefilter2 = value2; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; - - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** @@ -262,24 +246,23 @@ void printRunConfiguration(string seq) { if (RNAMODE == true) { printf("+ running in rnafold mode\n"); standardRun = false; - } + } if (UNAMODE == true) { printf("+ running in unafold mode\n"); standardRun = false; } - if (dangles >= 0 && !RNAMODE) { - printf("+ running in dangles %d mode\n", dangles); + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); standardRun = false; - } + } if (T_MISMATCH == true) { printf("+ enabled terminal mismatch calculations\n"); standardRun = false; } if (b_prefilter == true) { - printf("+ running with prefilter values = %d,%d\n",prefilter1,prefilter2); + printf("+ running with prefilter value = %d\n",prefilter1); standardRun = false; } - if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; From ef1b79b0e8cdce6d1cfb026f2e3ce87df595392a Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 13:27:09 -0400 Subject: [PATCH 109/187] fixed minor issue --- gtfold-mfe/configure | 2 +- gtfold-mfe/configure.in | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index c0dc675..e4e3fd1 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -5452,7 +5452,7 @@ if test "x$GXX" = "xyes"; then fi -If Sun cc is present, define appropriate compiler flags +#If Sun cc is present, define appropriate compiler flags { $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5 $as_echo_n "checking for Sun C compiler... " >&6; } cat >conftest.$ac_ext <<_ACEOF diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index 03441fc..0643019 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -99,7 +99,7 @@ fi dnl This is an example how to check for compiler characteristics that dnl are not a part of the standard Autoconf tests: -If Sun cc is present, define appropriate compiler flags +#If Sun cc is present, define appropriate compiler flags AC_MSG_CHECKING(for Sun C compiler) AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C #include "error: this is not a Sun C compiler." From 4bfd1f85ce99dca3d48320bade2114f513fcdc93 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 13:28:04 -0400 Subject: [PATCH 110/187] added new features list --- README | 13 ++++++++++++- gtfold-mfe/README | 13 ++++++++++++- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/README b/README index 34a28f1..3741de6 100644 --- a/README +++ b/README @@ -110,4 +110,15 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added beta options --subopt, --bpp, --useShape diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 34a28f1..3741de6 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -110,4 +110,15 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added beta options --subopt, --bpp, --useShape From 951612c2f739de63d4e4c2634731d9b141564bfa Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Tue, 12 Jul 2011 14:01:29 -0400 Subject: [PATCH 111/187] updated copyright information --- gtfold-mfe/src/main.cc | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 86aee90..32cc9ad 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -1,6 +1,7 @@ /* GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey http://www.cc.gatech.edu/~bader This program is free software: you can redistribute it and/or modify @@ -215,7 +216,7 @@ bool encodeSequence(string seq) { void print_header() { printf("GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n"); - printf("(c) 2007-2011 D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n"); + printf("(c) 2007-2011 D.A. Bader, C.E. Heitsch, S.C. Harvey\n"); printf("Georgia Institute of Technology\n\n"); } From 6c7bdb50ed28b05b6922eea8c068f50c8b352b79 Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Tue, 12 Jul 2011 14:45:31 -0400 Subject: [PATCH 112/187] corrected spelling errors in help message --- gtfold-mfe/src/options.cc | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 6886f65..b31d789 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -48,8 +48,8 @@ void help() { printf("OPTIONS\n"); printf(" -c, --constraints FILE\n"); printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --dangle INT Allow only one treatment of dangleing end energies in \n"); - printf(" mulit- and external loops (INT=0,2) see below for details\n"); + printf(" -d, --dangle INT Allow only one treatment of dangling end energies in \n"); + printf(" multi- and external loops (INT=0,2) see below for details\n"); printf(" -h, --help Output help (this message) and exit\n"); printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); printf(" limit is given, base pairs can be over any distance\n"); @@ -80,7 +80,7 @@ void help() { printf("\nDangle:\n"); printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n"); - printf("\tINT=2 dangling end energies are added for nucleotieds on either\n"); + printf("\tINT=2 dangling end energies are added for nucleotides on either\n"); printf("\tside of each branch in multi-loops and external loops.\n"); printf("\tAll other values for INT are ignored.\n"); exit(-1); From 01c1ecbcd7b02e71944a18ada38f23c65a240409 Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Tue, 12 Jul 2011 16:41:33 -0400 Subject: [PATCH 113/187] updated copyright info in README's and autor list in AUTHORS --- README | 48 ++++++++++++++++++++++++++++++---------------- gtfold-mfe/AUTHORS | 1 + gtfold-mfe/README | 48 ++++++++++++++++++++++++++++++---------------- 3 files changed, 63 insertions(+), 34 deletions(-) diff --git a/README b/README index 3741de6..56622c2 100644 --- a/README +++ b/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -111,14 +123,16 @@ Version History: Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. 2.0 11 July 2011 - Optimized the code to enable faster multiloop calculations - Added -d, --dangle to allow treatment of dangling end energies based on user input - Added -m --mismatch to enable terminal mismatch calculations - Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name - Added -p --paramdir to allow user to provide custom parameters - Added -t, --threads to limit number of threads used - Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides - such that it could be part of a helix of length INT - Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) - Added --unafold to run GTfold in UNAfold default mode (version 3.8) - Added beta options --subopt, --bpp, --useShape + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/AUTHORS b/gtfold-mfe/AUTHORS index 0f01d3b..0e9ed76 100644 --- a/gtfold-mfe/AUTHORS +++ b/gtfold-mfe/AUTHORS @@ -4,4 +4,5 @@ Amrita Mathuriya August 2007 - January 2009 Sainath Mallidi August 2009 - December 2010 Josh Anderson August 2010 - May 2011 Andrew Ash August 2010 - May 2011 +Zsuzsanna Sukosd February 2011 - June 2011 Prashant Gaurav August 2010 - diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 3741de6..56622c2 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -111,14 +123,16 @@ Version History: Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. 2.0 11 July 2011 - Optimized the code to enable faster multiloop calculations - Added -d, --dangle to allow treatment of dangling end energies based on user input - Added -m --mismatch to enable terminal mismatch calculations - Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name - Added -p --paramdir to allow user to provide custom parameters - Added -t, --threads to limit number of threads used - Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides - such that it could be part of a helix of length INT - Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) - Added --unafold to run GTfold in UNAfold default mode (version 3.8) - Added beta options --subopt, --bpp, --useShape + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data From 3b6010e3187489a7fa04a80a3b789c0c302cc42f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 16:56:51 -0400 Subject: [PATCH 114/187] added new header files --- gtfold-mfe/include/Makefile.am | 3 +-- gtfold-mfe/include/Makefile.in | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index a03865e..5a61bdd 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,2 @@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h - +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index 44a1859..607786e 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -93,7 +93,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -155,7 +154,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ all: all-am From c45defaea509bb30513ce46eda9060d4af64e407 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 16:57:54 -0400 Subject: [PATCH 115/187] removed TODO file --- gtfold-mfe/TODO | 7 ------- 1 file changed, 7 deletions(-) delete mode 100644 gtfold-mfe/TODO diff --git a/gtfold-mfe/TODO b/gtfold-mfe/TODO deleted file mode 100644 index 366385a..0000000 --- a/gtfold-mfe/TODO +++ /dev/null @@ -1,7 +0,0 @@ -Make single-letter options work - -Partition Function -================== - - - fast inner loops optimization - - factor in dangling energies From e09900940c1523b7e358ff041731ef786f4dd62a Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 17:16:54 -0400 Subject: [PATCH 116/187] removed TODO NEWS --- gtfold-mfe/Makefile.in | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in index 61df044..da3d87e 100644 --- a/gtfold-mfe/Makefile.in +++ b/gtfold-mfe/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -39,7 +39,7 @@ subdir = . DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ $(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \ - COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \ + COPYING ChangeLog INSTALL NEWS config.guess config.sub \ depcomp install-sh missing ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.in @@ -167,7 +167,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -320,7 +319,7 @@ uninstall-includeHEADERS: # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -345,7 +344,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -509,8 +508,7 @@ distdir: $(DISTFILES) fi; \ done -test -n "$(am__skip_mode_fix)" \ - || find "$(distdir)" -type d ! -perm -755 \ - -exec chmod u+rwx,go+rx {} \; -o \ + || find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ @@ -554,17 +552,17 @@ dist dist-all: distdir distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ - bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ + bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lzma*) \ - lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\ *.tar.xz*) \ xz -dc $(distdir).tar.xz | $(am__untar) ;;\ *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac From bbe5f6d75be54d93308a7bc2734aa06e7c42eb11 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 17:17:50 -0400 Subject: [PATCH 117/187] removing NEWS --- gtfold-mfe/NEWS | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 gtfold-mfe/NEWS diff --git a/gtfold-mfe/NEWS b/gtfold-mfe/NEWS deleted file mode 100644 index e69de29..0000000 From b68b49a30edeac2a927803a8757ff743df2d1e88 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 12 Jul 2011 17:22:10 -0400 Subject: [PATCH 118/187] removing NEWS --- gtfold-mfe/Makefile.in | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in index da3d87e..5f77d42 100644 --- a/gtfold-mfe/Makefile.in +++ b/gtfold-mfe/Makefile.in @@ -39,7 +39,7 @@ subdir = . DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ $(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \ - COPYING ChangeLog INSTALL NEWS config.guess config.sub \ + COPYING ChangeLog INSTALL config.guess config.sub \ depcomp install-sh missing ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.in From d8014e13df65de87d3f7065b0fa0fd054a0cf4d0 Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Wed, 20 Jul 2011 08:30:06 -0400 Subject: [PATCH 119/187] clarified help message --- gtfold-mfe/src/options.cc | 45 ++++++++++++++++++++------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index b31d789..5ef3802 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -43,44 +43,45 @@ int contactDistance = -1; void help() { printf("Usage: gtfold [OPTION]... FILE\n\n"); - printf(" FILE is an RNA sequence file. Single line or FASTA formats are accepted.\n\n"); + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); printf("OPTIONS\n"); printf(" -c, --constraints FILE\n"); - printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --dangle INT Allow only one treatment of dangling end energies in \n"); - printf(" multi- and external loops (INT=0,2) see below for details\n"); - printf(" -h, --help Output help (this message) and exit\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); - printf(" limit is given, base pairs can be over any distance\n"); + printf(" limit is given, base pairs can be over any distance.\n"); printf(" -m --mismatch Enable terminal mismatch calculations\n"); -// printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); printf(" -o, --output NAME Write output files with prefix given in NAME\n"); printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); - printf(" -t, --threads INT Limit number of threads used to INT\n"); - printf(" -v, --verbose Run in verbose mode\n"); - printf(" -w, --workDir DIR Path of directory where output files will be written\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); printf(" neighboring nucleotides such that it could be part of\n"); - printf(" a helix of length INT\n"); - printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5)\n"); - printf(" --unafold Run as UNAfold default mode (version 3.8)\n"); - + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); printf("\nBETA OPTIONS\n"); - printf(" --bpp Calculate base pair probabilities\n"); - printf(" --subopt range Calculate suboptimal structures within 'range' kcal/mol\n"); - printf(" of the mfe\n"); - printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE.\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); printf("\nConstraint syntax:\n"); - printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); - printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); printf("\nDangle:\n"); - printf("\tINT=0 ignores dangling end energies (mostly for debugging).\n"); - printf("\tINT=2 dangling end energies are added for nucleotides on either\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); printf("\tside of each branch in multi-loops and external loops.\n"); printf("\tAll other values for INT are ignored.\n"); exit(-1); From 4e11ae59062a8a66a56b94a587aa4e1426cc7ee2 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 20 Jul 2011 12:12:46 -0400 Subject: [PATCH 120/187] enable -d 2 when subopt is invoked --- gtfold-mfe/src/main.cc | 5 ++++- gtfold-mfe/src/options.cc | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 32cc9ad..4b016de 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -276,7 +276,10 @@ int main(int argc, char** argv) { init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) - readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + if (SUBOPT_ENABLED) + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH); + else + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); printRunConfiguration(seq); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 5ef3802..d893af6 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -175,6 +175,7 @@ void parse_options(int argc, char** argv) { BPP_ENABLED = true; } else if(strcmp(argv[i], "--subopt") == 0) { SUBOPT_ENABLED = true; + dangles = 2; if(i < argc) suboptDelta = atof(argv[++i]); else From 4656b8bc34f81f29768a83e054fdf7da21b73411 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 20 Jul 2011 12:13:33 -0400 Subject: [PATCH 121/187] new subopt algorithm using -d 2 mode --- gtfold-mfe/include/subopt_traceback.h | 6 +- gtfold-mfe/src/subopt_traceback.cc | 547 +++++++++----------------- 2 files changed, 186 insertions(+), 367 deletions(-) diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h index cccf44e..fd819b6 100644 --- a/gtfold-mfe/include/subopt_traceback.h +++ b/gtfold-mfe/include/subopt_traceback.h @@ -30,7 +30,7 @@ #include #include -enum label {lW=0, lV, lVBI, lVM, lWM}; +enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime}; extern const char* lstr[]; struct segment @@ -221,6 +221,8 @@ void traceV(int i, int j, ps_t & ps, ps_stack_t & gs); void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs); void traceW(int i, int j, ps_t & ps, ps_stack_t & gs); void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs); -void traceWM(ps_t& ps, ps_map_t& filter); +void traceWM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceWMPrime(int i, int j, ps_t & ps, ps_stack_t & gs); +//void traceWM(ps_t& ps, ps_map_t& filter); #endif diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index d5e4729..ccaa4a1 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -28,388 +28,205 @@ #include "global.h" #include "subopt_traceback.h" -const char* lstr[] = {"W", "V", "VBI", "VM", "WM"}; - -void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs); -int delta = 0; -int mfe = INFINITY_; - -void print_stack(ps_stack_t temp) -{ - std::cout << "{\n"; - while (!temp.empty()) - { - ps_t ps = temp.top(); - temp.pop(); - ps.print(); - std::cout << '\n' ; - } - std::cout << "}\n"; +#define DEBUG 1 + +const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"}; + +void (*trace_func[6]) (int i, int j, ps_t& ps, ps_stack_t& gs); +static int delta = 0; +static int mfe = INFINITY_; +static int length = -1; +static int gflag = 0; + +void process(ss_map_t& subopt_data, int len) { + int count = 0 ; + ps_stack_t gstack; + + // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} + ps_t first(0, len); + first.push(segment(1, len, lW, W[len])); + gstack.push(first); // initialize the partial structure stacka + + while (1) { + if (gstack.empty()) break; // exit + ps_t ps = gstack.top(); + gstack.pop(); + + if (ps.empty()) { + count++; + subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + continue; + } + else { + segment smt = ps.top(); + ps.pop(); + + gflag = 0; + if (smt.j_ - smt.i_ > TURN) { + (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); + } + + // discarded current segment, using remaining ones + if (!gflag) { + ps_t ps1(ps); + gstack.push(ps1); + } + } + } + +#ifdef DEBUG + printf("# SS = %d\n", count); +#endif } -void process(ss_map_t& subopt_data, int len) -{ - int count = 0 ; - ps_stack_t gstack; - - // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} - ps_t first(0, len); - first.push(segment(1, len, lW, W[len])); - gstack.push(first); // initialize the partial structure stacka +ss_map_t subopt_traceback(int len, int _delta) { + trace_func[0] = traceW; + trace_func[1] = traceV; + /* trace_func[2] = traceVBI;*/ + trace_func[3] = traceVM; + trace_func[4] = traceWM; + trace_func[5] = traceWMPrime; - while (1) - { - if (gstack.empty()) break; // exit + mfe = W[len]; + delta = _delta; + length = len; - ps_t ps = gstack.top(); - gstack.pop(); + ss_map_t subopt_data; + process(subopt_data, len); - if (ps.empty()) - { - //std::cout << ps.str << ' ' << ps.ae_/100.0 << std::endl; - ss_map_t::iterator it = subopt_data.find(ps.str); - if ( it == subopt_data.end()) - { - subopt_data.insert(std::make_pair(ps.str,ps.ae_)); - count++; - } - else - { - int energy = it->second; - if (ps.ae_ < energy && (ps.ae_ >= mfe && ps.ae_ <= mfe + delta)) { - subopt_data[it->first] = ps.ae_; - } - } - continue; - } - else - { - segment smt = ps.top(); - ps.pop(); - size_t s1 = gstack.size(); - - if (smt.j_ - smt.i_ >= TURN) - { - (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); - } - - // discard this segment, use remaining ones - if (gstack.size() == s1 && ps.total() <= mfe + delta) - { - ps_t ps1(ps); - gstack.push(ps1); - } - } - } + return subopt_data; } -ss_map_t subopt_traceback(int len, int _delta) -{ - trace_func[0] = traceW; - trace_func[1] = traceV; - trace_func[3] = traceVM; - - mfe = W[len]; - delta = _delta; - - ss_map_t subopt_data; - process(subopt_data, len); - - return subopt_data; +void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { + // Hairpin Loop + if (eH(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.accumulate(eH(i,j)); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Stack + if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); + ps1.accumulate(eS(i,j)); + ps1.update(i, j , '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Internal Loop + if (VBI(i,j) + ps.total() <= mfe + delta) { + traceVBI(i,j,ps,gstack); + } + + // Multiloop + if ( VM(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i, j, lVM, VM(i,j))); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } } -void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) -{ - // Hairpin Loop - if (eH(i,j) + ps.total() <= mfe + delta ) - { - //std::cout << "Hairpin " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.accumulate(eH(i,j)); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) - { - // std::cout << "Stack " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); - ps1.accumulate(eS(i,j)); - ps1.update(i, j , '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Internal Loop - if (VBI(i,j) + ps.total() <= mfe + delta ) - { - //std::cout << "Internal " << i << ' ' << j << std::endl; - //ps_t ps1(ps); - //ps1.push(segment(i, j, lVBI, VBI(i,j))); - //ps1.update(i, j, 'i', 'i'); - //push_to_gstack(gstack, ps1); - traceVBI(i,j,ps,gstack); - } - - // Multiloop - if ( VM(i,j) + ps.total() <= mfe + delta ) - { - //std::cout << "Multi " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVM, VM(i,j))); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - +void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int p,q; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { + if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(p, q, lV, V(p, q))); + ps1.update(i, j , '(', ')'); + ps1.accumulate(eL(i, j, p, q)); + push_to_gstack(gstack, ps1); + } + } + } } -void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) -{ - int p,q; - for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p) - { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==(i+1))?(j-2):(j-1); - - for (q = minq; q <= maxq; q++) - { - if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta && PP[p][q] == 1) - { - ps_t ps1(ps); - ps1.update(i, j, '(', ')'); - ps1.push(segment(p, q, lV, V(p, q))); - ps1.accumulate(eL(i, j, p, q)); - push_to_gstack(gstack, ps1); - } - } - } +void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack) { + for (int i = 1; i < j-TURN; ++i) { + int wim1 = MIN(0, W[i-1]); + int d3 = (i>1)?Ed3(j,i,i-1):0; + int d5 = (j 1) ps1.push(segment(1, i-1, lW, W[i-1])); - ps1.accumulate(auPenalty(i, j)); - push_to_gstack(gstack, ps1); - } - - - int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - if (wijd + ps.total() <= mfe + delta ) - { - ps_t ps3(ps); - ps3.push(segment(i, j-1, lV, V(i, j-1))); - if (wim1 <= 0 && i > 1) ps3.push(segment(1, i-1, lW, W[i-1])); - ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); - push_to_gstack(gstack, ps3); - } - - int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - if (widj + ps.total() <= mfe + delta ) - { - ps_t ps4(ps); - ps4.push(segment(i+1, j, lV, V(i+1,j))); - if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1])); - ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i)); - push_to_gstack(gstack, ps4); - } - - int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1; - if (widjd + ps.total() <= mfe + delta ) - { - ps_t ps2(ps); - ps2.push(segment(i+1, j-1, lV, V(i+1,j-1))); - if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1])); - ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); - push_to_gstack(gstack, ps2); - } - } - - if (W[j-1] + ps.total() <= mfe + delta ) - { - ps_t ps1(ps); - ps1.push(segment(1, j-1, lW, W[j-1])); - push_to_gstack(gstack, ps1); - } + +void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + int d5 = Ed5(j,i,j+1); + + if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5); + ps_new.push(segment(i,j, lV, V(i,j))); + push_to_gstack(gstack, ps_new); + } + + if (WMPrime[i][j] + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j])); + push_to_gstack(gstack, ps_new); + } + + if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i+1,j, lWM, WM(i+1,j))); + push_to_gstack(gstack, ps_new); + } + + if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i,j-1, lWM, WM(i,j-1))); + push_to_gstack(gstack, ps_new); + } } -void traceWM(ps_t& ps, ps_map_t& filter) -{ - ps_stack_t wm_stack; - wm_stack.push(ps); - - while (!wm_stack.empty()) - { - ps_t pss = wm_stack.top(); - wm_stack.pop(); - - // check if all segments in pss are Vs - if (pss.empty()) - { - std::string key = pss.str; - while (!pss.empty_v()) - { - segment ss = pss.top_v(); - pss.pop_v(); - - pss.push(ss); - key[ss.i_-1] = '*'; key[ss.j_-1] = '*'; - } - filter.insert(std::pair(key, pss)); - continue; - } - - segment wm_seg = pss.top(); - pss.pop(); - - int i1 = wm_seg.i_; int j1 = wm_seg.j_; - - if (wm_seg.label_ == lV) - { - ps_t ps1(pss); - ps1.push_v(wm_seg); - wm_stack.push(ps1); - continue; - } - int h = i1; int k = j1; - - int wmij = V(h,k) + auPenalty(h,k) + Eb; - if (pss.total() + wmij <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k,lV, V(h,k))); - ps1.accumulate(auPenalty(h,k) + Eb); - wm_stack.push(ps1); - } - - int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ; - if (pss.total() + wmijd <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k-1,lV, V(h,k-1))); - ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ; - if (pss.total() + wmidj <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k, lV, V(h+1,k))); - ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec ; - if (pss.total() + wmidjd <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1))); - ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec); - wm_stack.push(ps1); - } - - - if (pss.total() + WM(i1,j1-1) + Ec <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1))); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - if (pss.total() + WM[i1+1][j1] + Ec <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1))); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - for (int h = i1+1; h <= j1-1; ++h) - { - if (WM(i1,h) + WM(h+1,j1) + pss.total() <= mfe + delta ) - { - ps_t ps1(pss); - ps1.push(segment(i1, h, lWM, WM(i1,h))); - ps1.push(segment(h+1, j1, lWM, WM(h+1,j1))); - wm_stack.push(ps1); - } - } - } +void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) { + for (int h = i+TURN+1 ; h <= j-TURN-2; h++) { + if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,h-1, lWM, WM(i,h-1))); + ps_new.push(segment(h,j, lWM, WM(h,j))); + push_to_gstack(gstack, ps_new); + } + } } -void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) -{ - std::map filter; - int h; - - for (h = i+1; h <= j-1; ++h) - { - int dG; - int d5 = Ed5(i,j,i+1); - int d3 = Ed3(i,j,j-1); - int common = auPenalty(i,j) + Ea + Eb; - - dG = common + WM[i+1][h-1] + WM[h][j-1]; - if (dG + ps.total() <= mfe + delta ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common) ; - traceWM(ps1, filter); - } - - dG = common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec; - if (dG + ps.total() <= mfe + delta ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common + d5 + Ec); - traceWM(ps1, filter); - } - - dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec; - if (dG + ps.total() <= mfe + delta ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + Ec); - traceWM(ps1, filter); - } - - dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec; - if (dG + ps.total() <= mfe + delta ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + d5 + 2*Ec) ; - traceWM(ps1, filter); - } - } +void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int d3 = Ed3(i,j,j-1); + int d5 = Ed5(i,j,i+1); - ps_map_t::iterator it ; - for (it = filter.begin(); it != filter.end(); ++it) - { - push_to_gstack(gstack, it->second); - } + if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); + ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] )); + push_to_gstack(gstack, ps_new); + } } -void push_to_gstack(ps_stack_t& gstack , const ps_t& v) -{ - gstack.push(v); +void push_to_gstack(ps_stack_t& gstack , const ps_t& v) { + gflag = 1; + gstack.push(v); } From 462278d215babb250be4b2d39920b9cd0dadce2c Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 20 Jul 2011 12:16:37 -0400 Subject: [PATCH 122/187] removed debug statement --- gtfold-mfe/src/subopt_traceback.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index ccaa4a1..2d3d9ed 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -28,7 +28,7 @@ #include "global.h" #include "subopt_traceback.h" -#define DEBUG 1 +//#define DEBUG 1 const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"}; From 88591d68d2e08b3217b06a8cc41f4dc99a6a73ed Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Wed, 20 Jul 2011 12:28:07 -0400 Subject: [PATCH 123/187] clarified help message --- gtfold-mfe/src/options.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index d893af6..831bf5d 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -71,7 +71,7 @@ void help() { printf("\nBETA OPTIONS\n"); printf(" --bpp Calculate base pair probabilities.\n"); printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); - printf(" of the MFE.\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); printf("\nConstraint syntax:\n"); From 71817d1c43c35f0996d1fc8a4711bdd23c952514 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 20 Jul 2011 12:35:21 -0400 Subject: [PATCH 124/187] added NEWS --- gtfold-mfe/NEWS | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 gtfold-mfe/NEWS diff --git a/gtfold-mfe/NEWS b/gtfold-mfe/NEWS new file mode 100644 index 0000000..e69de29 From dc12e6a3ffd0b291ec4b3219899809b161e38994 Mon Sep 17 00:00:00 2001 From: Shel Swenson Date: Wed, 20 Jul 2011 13:19:23 -0400 Subject: [PATCH 125/187] fixed typos and spelling errors in README --- README | 5 +++-- gtfold-mfe/README | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/README b/README index 56622c2..0034999 100644 --- a/README +++ b/README @@ -126,13 +126,14 @@ Version History: Optimized the code to enable faster multiloop calculations Added -d, --dangle to allow treatment of dangling end energies based on user input Added -m --mismatch to enable terminal mismatch calculations - Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name Added -p --paramdir to allow user to provide custom parameters Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides such that it could be part of a helix of length INT Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) Added --unafold to run GTfold in UNAfold default mode (version 3.8) Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE - Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 56622c2..0034999 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -126,13 +126,14 @@ Version History: Optimized the code to enable faster multiloop calculations Added -d, --dangle to allow treatment of dangling end energies based on user input Added -m --mismatch to enable terminal mismatch calculations - Added -o, --output, , -w --workDir options to allow to write output files/directories with desired name + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name Added -p --paramdir to allow user to provide custom parameters Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides such that it could be part of a helix of length INT Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) Added --unafold to run GTfold in UNAfold default mode (version 3.8) Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE - Added --bpp (Beta only) which outputs basepair probabilities based on the partiaiton function + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data From 2170c3f7cd56f3e5c8ad3b813ffdc29801ff07a2 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 21 Jul 2011 16:41:43 -0400 Subject: [PATCH 126/187] added logic to read data from install dir, environ dir, current dir --- gtfold-mfe/src/loader.cc | 159 ++++++++++++++++++++++++++------------- 1 file changed, 106 insertions(+), 53 deletions(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 8ec31df..9af6e97 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -26,6 +26,11 @@ #include #include +#include +#include +#include +#include + #include "data.h" #include "utils.h" #include "constants.h" @@ -80,59 +85,101 @@ int init; int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ float prelog; -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, - int unamode = 0, int rnamode = 0, int mismatch = 0) { - - if (!userdatalogic && unamode) { - EN_DATADIR.assign(xstr(DATADIR)); - EN_DATADIR += "/"; - EN_DATADIR += "UNAParams"; - }else if (!userdatalogic && rnamode) { - EN_DATADIR.assign(xstr(DATADIR)); - EN_DATADIR += "/"; - EN_DATADIR += "RNAParams"; - } - else if (!userdatalogic) { - EN_DATADIR.assign(xstr(DATADIR)); - EN_DATADIR += "/"; - EN_DATADIR += "Turner99"; - } else { - EN_DATADIR.assign(userdatadir); - } - - //Handle the ending forward slash case - if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { - EN_DATADIR += "/"; - } - - initMiscloopValues("miscloop.DAT", EN_DATADIR); - initDangleValues("dangle.DAT", EN_DATADIR); - initStackValues("stack.DAT", EN_DATADIR); - initLoopValues("loop.DAT", EN_DATADIR); - initTstkhValues("tstackh.DAT", EN_DATADIR); - initTstkiValues("tstacki.DAT", EN_DATADIR); - initTloopValues("tloop.DAT", EN_DATADIR); - - if (unamode) { - initInt21Values("asint1x2.DAT", EN_DATADIR); - initInt22Values("sint4.DAT", EN_DATADIR); - initInt11Values("sint2.DAT", EN_DATADIR); - initTstkmValues("tstackm.DAT", EN_DATADIR); - initTstkeValues("tstacke.DAT", EN_DATADIR); - initTstk23Values("tstacki23.DAT", EN_DATADIR); - } else if (mismatch) { - initTstkmValues("tstackm.DAT", EN_DATADIR); - initTstkeValues("tstacke.DAT", EN_DATADIR); - initInt21Values("int21.DAT", EN_DATADIR); - initInt22Values("int22.DAT", EN_DATADIR); - initInt11Values("int11.DAT", EN_DATADIR); - - } - else { - initInt21Values("int21.DAT", EN_DATADIR); - initInt22Values("int22.DAT", EN_DATADIR); - initInt11Values("int11.DAT", EN_DATADIR); - } +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int rnamode = 0, int mismatch = 0) { + struct stat buf; + + if (!userdatalogic) { + std::string opt1, opt2, opt3; + char cwd[1024]; + bool found = false; + + opt1.assign(xstr(DATADIR)); + if (getenv("GTDATADIR") != 0) + opt2.assign(getenv("GTDATADIR")); + if (getcwd(cwd, sizeof(cwd)) != 0) { + opt3.assign(cwd); + opt3 += "/data"; + } + + if (stat(opt1.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt1); + fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str()); + } else { + if (found == false) fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str()); + } + + if (!found && stat(opt2.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt2); + fprintf(stdout,"Checking for environ variable 'GTDATADIR', found \n"); + } else { + if (found == false) fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n"); + } + + if (!found && stat(opt3.c_str(), &buf) == 0){ + found = true; + EN_DATADIR.assign(opt3); + fprintf(stdout,"Checking under current dir '%s', found.\n", opt3.c_str()); + + } else { + if (found == false) fprintf(stdout,"Checking under current dir '%s', not found.\n", opt3.c_str()); + } + + EN_DATADIR += "/"; + if (found == false) { + exit(-1); + } + + if (unamode) { + EN_DATADIR += "UNAParams"; + }else if (rnamode) { + EN_DATADIR += "RNAParams"; + } else { + EN_DATADIR += "Turner99"; + } + } + else { + EN_DATADIR.assign(userdatadir); + if (stat(EN_DATADIR.c_str(), &buf) == -1){ + fprintf(stdout,"Checking for parameter files in dir '%s', not found.\n\n", EN_DATADIR.c_str()); + exit(-1); + } + } + + //Handle the ending forward slash case + if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { + EN_DATADIR += "/"; + } + + initMiscloopValues("miscloop.DAT", EN_DATADIR); + initDangleValues("dangle.DAT", EN_DATADIR); + initStackValues("stack.DAT", EN_DATADIR); + initLoopValues("loop.DAT", EN_DATADIR); + initTstkhValues("tstackh.DAT", EN_DATADIR); + initTstkiValues("tstacki.DAT", EN_DATADIR); + initTloopValues("tloop.DAT", EN_DATADIR); + + if (unamode) { + initInt21Values("asint1x2.DAT", EN_DATADIR); + initInt22Values("sint4.DAT", EN_DATADIR); + initInt11Values("sint2.DAT", EN_DATADIR); + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initTstk23Values("tstacki23.DAT", EN_DATADIR); + } else if (mismatch) { + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + + } + else { + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + } } int initStackValues(const string& fileName, const string& dirPath) { @@ -142,6 +189,12 @@ int initStackValues(const string& fileName, const string& dirPath) { filePath = dirPath + fileName; cf.open(filePath.c_str(), ios::in); + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); + } + for (int i = 0; i < 4; i++) { for (int j = 0; j < 4; j++) { for (int k = 0; k < 4; k++) { From 5bc618a65e128e954708220ee79ab628b77d90fb Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 21 Jul 2011 16:50:26 -0400 Subject: [PATCH 127/187] renamed environ var to GTFOLDDATADIR --- gtfold-mfe/src/loader.cc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 9af6e97..b39796f 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -94,8 +94,8 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int bool found = false; opt1.assign(xstr(DATADIR)); - if (getenv("GTDATADIR") != 0) - opt2.assign(getenv("GTDATADIR")); + if (getenv("GTFOLDDATADIR") != 0) + opt2.assign(getenv("GTFOLDDATADIR")); if (getcwd(cwd, sizeof(cwd)) != 0) { opt3.assign(cwd); opt3 += "/data"; From 018827a03d8226c7ca9e6458757c5986b67d49e4 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 21 Jul 2011 16:51:56 -0400 Subject: [PATCH 128/187] renamed environ var to GTFOLDDATADIR --- gtfold-mfe/src/loader.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index b39796f..1043dc8 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -112,7 +112,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int if (!found && stat(opt2.c_str(), &buf) == 0) { found = true; EN_DATADIR.assign(opt2); - fprintf(stdout,"Checking for environ variable 'GTDATADIR', found \n"); + fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n"); } else { if (found == false) fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n"); } From 766e66f5e44a0b75ba84139d636076c55006cadc Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 21 Jul 2011 18:29:59 -0400 Subject: [PATCH 129/187] lookup environ var then install dir --- gtfold-mfe/src/loader.cc | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 1043dc8..1c39db9 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -100,8 +100,16 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int opt3.assign(cwd); opt3 += "/data"; } - - if (stat(opt1.c_str(), &buf) == 0) { + + if (stat(opt2.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt2); + fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n"); + } else { + if (found == false) fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', not found \n"); + } + + if (!found && stat(opt1.c_str(), &buf) == 0) { found = true; EN_DATADIR.assign(opt1); fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str()); @@ -109,14 +117,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int if (found == false) fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str()); } - if (!found && stat(opt2.c_str(), &buf) == 0) { - found = true; - EN_DATADIR.assign(opt2); - fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n"); - } else { - if (found == false) fprintf(stdout,"Checking for environ variable 'GTDATADIR', not found \n"); - } - if (!found && stat(opt3.c_str(), &buf) == 0){ found = true; EN_DATADIR.assign(opt3); From a8470e37d1bb4b5798bec19af1ffdb2d63f2b246 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 9 Sep 2011 11:04:34 -0400 Subject: [PATCH 130/187] Fixed pseudoknot detection logic in constraint pre-processing part of the code. --- gtfold-mfe/src/constraints.cc | 408 ++++++++++++++++++---------------- 1 file changed, 214 insertions(+), 194 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 08f67bc..f2ac801 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -5,11 +5,16 @@ #include #include #include +#include +#include #include "global.h" #include "options.h" #include "constraints.h" +using std::map; +using std::pair; + int* BP; int* ind; @@ -19,17 +24,17 @@ ZS: Explanation to BP array. BP(i,j) for i!=j can have one of the following values: 0: Nothing is required about a pair i,j in constraints 1: Force pairing between i and j. This implies also that - any non-nested pairings will be prohibited and any - other pairs i and j would be involved in are also prohibited. +any non-nested pairings will be prohibited and any +other pairs i and j would be involved in are also prohibited. 2: Prohibit pairing between i and j. (Nothing else is done) BP(i,i) can have one of the following values: 0: Nothing is known about position i at all 3: Position i is forced to be single-stranded. This implies also that - any pairs with i will be prohibited. +any pairs with i will be prohibited. 4: Position i is NOT single-stranded, it is forced to be in a pair. 5: Position i is prohibited from pairing with at least one nucleotide. -*/ + */ int** PBP; int** FBP; @@ -37,96 +42,111 @@ int** FBP; int nPBP; int nFBP; -bool compare_bp(const std::pair& o1, - const std::pair& o2) { - return o1.first < o2.first; -} - - static int load_constraints(const char* constr_file, int verbose=0) { - + fprintf(stdout, "- Running with constraints\n"); std::ifstream cfcons; cfcons.open(constr_file, std::ios::in); - if (cfcons == 0) { - fprintf(stderr, "Error opening constraint file\n\n"); - cfcons.close(); - return -1; - } - - char cons[100]; - - while (!cfcons.eof()) { - cfcons.getline(cons, 100); - if (cons[0] == 'F' || cons[0] == 'f') nFBP++; - if (cons[0] == 'P' || cons[0] == 'p') nPBP++; - } - cfcons.close(); - - //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP); - if (nFBP + nPBP == 0) { - fprintf(stderr, "No Constraints found.\n\n"); - return -1; - } - - FBP = (int**) malloc(nFBP*sizeof(int*)); - PBP = (int**) malloc(nPBP*sizeof(int*)); - - int fit = 0, pit = 0, it = 0; - - for (it = 0; it < nFBP; it++) { - FBP[it] = (int*) malloc(2* sizeof (int)); - } - for(it=0; it < nPBP; it++) { - PBP[it] = (int*)malloc(2*sizeof(int)); - } - cfcons.open(constr_file, std::ios::in); - - while(!cfcons.eof()) { - cfcons.getline(cons,100); - char *p=strtok(cons, " "); - p = strtok(0, " "); - if(cons[0]=='F' || cons[0]=='f') { - int fit1=0; - while(p!=0) { - FBP[fit][fit1++] = atoi(p); - p = strtok(0, " "); - } - fit++; - } - if(cons[0]=='P' || cons[0]=='p') { - int pit1=0; - while(p!=0) { - PBP[pit][pit1++] = atoi(p); - p = strtok(0, " "); - } - pit++; - } - } - - std::vector > v_fbp; + if (cfcons == 0) { + fprintf(stderr, "Error opening constraint file\n\n"); + cfcons.close(); + return -1; + } + + char cons[100]; + + while (!cfcons.eof()) { + cfcons.getline(cons, 100); + if (cons[0] == 'F' || cons[0] == 'f') nFBP++; + if (cons[0] == 'P' || cons[0] == 'p') nPBP++; + } + cfcons.close(); + + //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP); + if (nFBP + nPBP == 0) { + fprintf(stderr, "No Constraints found.\n\n"); + return -1; + } + + FBP = (int**) malloc(nFBP*sizeof(int*)); + PBP = (int**) malloc(nPBP*sizeof(int*)); + + int fit = 0, pit = 0, it = 0; + + for (it = 0; it < nFBP; it++) { + FBP[it] = (int*) malloc(2* sizeof (int)); + } + for(it=0; it < nPBP; it++) { + PBP[it] = (int*)malloc(2*sizeof(int)); + } + cfcons.open(constr_file, std::ios::in); + + while(!cfcons.eof()) { + cfcons.getline(cons,100); + char *p=strtok(cons, " "); + p = strtok(0, " "); + if(cons[0]=='F' || cons[0]=='f') { + int fit1=0; + while(p!=0) { + FBP[fit][fit1++] = atoi(p); + p = strtok(0, " "); + } + fit++; + } + if(cons[0]=='P' || cons[0]=='p') { + int pit1=0; + while(p!=0) { + PBP[pit][pit1++] = atoi(p); + p = strtok(0, " "); + } + pit++; + } + } + + map > all_bases; for(it=0; it< nFBP; it++) { - for(int k=1;k<= FBP[it][2];k++) - v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); + for(int k=1;k<= FBP[it][2];k++) { + pair base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1); + pair >::iterator, bool> retVal; + retVal = all_bases.insert(pair >(base_pair.first, base_pair)); + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + retVal = all_bases.insert(pair >(base_pair.second, base_pair) ); + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + } } - - if(v_fbp.size()>1){ - std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); - for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second - && v_fbp[ii].second >= v_fbp[ii+1].first) { + + vector > verify_stack; + for (map >::iterator it = all_bases.begin(); it != all_bases.end(); ++it) { + + pair > map_element = (*it); + int base = map_element.first; + pair base_pair = map_element.second; + if (base_pair.first == base) { + verify_stack.push_back(base_pair); + } else { + pair last_base_pair = verify_stack.back(); + if (last_base_pair.second == base) { + verify_stack.pop_back(); + } + else { fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(-1); + exit(1); } - } } - - return 0; + return 0; } int init_constraints(const char* constr_file,int length) { @@ -145,11 +165,11 @@ int init_constraints(const char* constr_file,int length) { BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int)); - if (BP == NULL) { - perror("Cannot allocate variable 'constraints'"); - exit(-1); - } - + if (BP == NULL) { + perror("Cannot allocate variable 'constraints'"); + exit(-1); + } + int LLL = length*(length+1)/2 + 1; @@ -158,7 +178,7 @@ int init_constraints(const char* constr_file,int length) { BP[i] = 0; } - + //ZS: for noncanonical bases (right now this only handles 'N'), force single-stranded. for(i = 1; i <= length; i++){ if(RNA[i]=='N'){ @@ -171,7 +191,7 @@ int init_constraints(const char* constr_file,int length) { } } - + //ZS: set prohibited basepairs if(nPBP != 0){ int temp; @@ -189,9 +209,9 @@ int init_constraints(const char* constr_file,int length) { printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; } - + for(k = 1; k <= PBP[it][2]; k++){ - + BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2; //Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out) @@ -265,7 +285,7 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][0]+k-1,i) = 2; BP(i,FBP[it][1]-(k-1)) = 2; } - + //mark that these two nucleotides are involved in a constrained pair //to avoid searching in O(N^2) time @@ -273,7 +293,7 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4; //force pairing BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1; - + } } } @@ -285,70 +305,70 @@ int init_constraints(const char* constr_file,int length) { int verify_structure(){ //ZS: This method returns true if the structure (global.h) is consistent with //the constraints, and false if it is not. - + if(CONS_ENABLED){ - int errorhappened = 0; - int it, k; - //Check prohibited constraints - if(nPBP != 0){ - for(it = 0; it < nPBP; it++){ - if(PBP[it][2] < 1 || PBP[it][1] == 0){ - //printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); - continue; - } - for(k = 1; k <= PBP[it][2]; k++){ - //correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1)) - if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){ - errorhappened = 1; - fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]); - break; + int errorhappened = 0; + int it, k; + //Check prohibited constraints + if(nPBP != 0){ + for(it = 0; it < nPBP; it++){ + if(PBP[it][2] < 1 || PBP[it][1] == 0){ + //printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); + continue; } - } - } - } - - //Check forced constraints - if(nFBP != 0){ - for(it = 0; it Date: Fri, 9 Sep 2011 22:07:01 -0400 Subject: [PATCH 131/187] Revert "Fixed pseudoknot detection logic in constraint pre-processing part of the code." Looks like I updated an older version of the constraints.cc file. Will do a new commit with the latest file. This reverts commit a8470e37d1bb4b5798bec19af1ffdb2d63f2b246. --- gtfold-mfe/src/constraints.cc | 408 ++++++++++++++++------------------ 1 file changed, 194 insertions(+), 214 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index f2ac801..08f67bc 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -5,16 +5,11 @@ #include #include #include -#include -#include #include "global.h" #include "options.h" #include "constraints.h" -using std::map; -using std::pair; - int* BP; int* ind; @@ -24,17 +19,17 @@ ZS: Explanation to BP array. BP(i,j) for i!=j can have one of the following values: 0: Nothing is required about a pair i,j in constraints 1: Force pairing between i and j. This implies also that -any non-nested pairings will be prohibited and any -other pairs i and j would be involved in are also prohibited. + any non-nested pairings will be prohibited and any + other pairs i and j would be involved in are also prohibited. 2: Prohibit pairing between i and j. (Nothing else is done) BP(i,i) can have one of the following values: 0: Nothing is known about position i at all 3: Position i is forced to be single-stranded. This implies also that -any pairs with i will be prohibited. + any pairs with i will be prohibited. 4: Position i is NOT single-stranded, it is forced to be in a pair. 5: Position i is prohibited from pairing with at least one nucleotide. - */ +*/ int** PBP; int** FBP; @@ -42,111 +37,96 @@ int** FBP; int nPBP; int nFBP; -static int load_constraints(const char* constr_file, int verbose=0) { +bool compare_bp(const std::pair& o1, + const std::pair& o2) { + return o1.first < o2.first; +} +static int load_constraints(const char* constr_file, int verbose=0) { + + fprintf(stdout, "- Running with constraints\n"); std::ifstream cfcons; cfcons.open(constr_file, std::ios::in); - if (cfcons == 0) { - fprintf(stderr, "Error opening constraint file\n\n"); - cfcons.close(); - return -1; - } - - char cons[100]; - - while (!cfcons.eof()) { - cfcons.getline(cons, 100); - if (cons[0] == 'F' || cons[0] == 'f') nFBP++; - if (cons[0] == 'P' || cons[0] == 'p') nPBP++; - } - cfcons.close(); - - //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP); - if (nFBP + nPBP == 0) { - fprintf(stderr, "No Constraints found.\n\n"); - return -1; - } - - FBP = (int**) malloc(nFBP*sizeof(int*)); - PBP = (int**) malloc(nPBP*sizeof(int*)); - - int fit = 0, pit = 0, it = 0; - - for (it = 0; it < nFBP; it++) { - FBP[it] = (int*) malloc(2* sizeof (int)); - } - for(it=0; it < nPBP; it++) { - PBP[it] = (int*)malloc(2*sizeof(int)); - } - cfcons.open(constr_file, std::ios::in); - - while(!cfcons.eof()) { - cfcons.getline(cons,100); - char *p=strtok(cons, " "); - p = strtok(0, " "); - if(cons[0]=='F' || cons[0]=='f') { - int fit1=0; - while(p!=0) { - FBP[fit][fit1++] = atoi(p); - p = strtok(0, " "); - } - fit++; - } - if(cons[0]=='P' || cons[0]=='p') { - int pit1=0; - while(p!=0) { - PBP[pit][pit1++] = atoi(p); - p = strtok(0, " "); - } - pit++; - } - } - - map > all_bases; + if (cfcons == 0) { + fprintf(stderr, "Error opening constraint file\n\n"); + cfcons.close(); + return -1; + } + + char cons[100]; + + while (!cfcons.eof()) { + cfcons.getline(cons, 100); + if (cons[0] == 'F' || cons[0] == 'f') nFBP++; + if (cons[0] == 'P' || cons[0] == 'p') nPBP++; + } + cfcons.close(); + + //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP); + if (nFBP + nPBP == 0) { + fprintf(stderr, "No Constraints found.\n\n"); + return -1; + } + + FBP = (int**) malloc(nFBP*sizeof(int*)); + PBP = (int**) malloc(nPBP*sizeof(int*)); + + int fit = 0, pit = 0, it = 0; + + for (it = 0; it < nFBP; it++) { + FBP[it] = (int*) malloc(2* sizeof (int)); + } + for(it=0; it < nPBP; it++) { + PBP[it] = (int*)malloc(2*sizeof(int)); + } + cfcons.open(constr_file, std::ios::in); + + while(!cfcons.eof()) { + cfcons.getline(cons,100); + char *p=strtok(cons, " "); + p = strtok(0, " "); + if(cons[0]=='F' || cons[0]=='f') { + int fit1=0; + while(p!=0) { + FBP[fit][fit1++] = atoi(p); + p = strtok(0, " "); + } + fit++; + } + if(cons[0]=='P' || cons[0]=='p') { + int pit1=0; + while(p!=0) { + PBP[pit][pit1++] = atoi(p); + p = strtok(0, " "); + } + pit++; + } + } + + std::vector > v_fbp; for(it=0; it< nFBP; it++) { - for(int k=1;k<= FBP[it][2];k++) { - pair base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1); - pair >::iterator, bool> retVal; - retVal = all_bases.insert(pair >(base_pair.first, base_pair)); - if (retVal.second == false) { - fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", - base_pair.first, base_pair.first, base_pair.second); - exit(1); - } - retVal = all_bases.insert(pair >(base_pair.second, base_pair) ); - if (retVal.second == false) { - fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", - base_pair.first, base_pair.first, base_pair.second); - exit(1); - } - } + for(int k=1;k<= FBP[it][2];k++) + v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); } - - vector > verify_stack; - for (map >::iterator it = all_bases.begin(); it != all_bases.end(); ++it) { - - pair > map_element = (*it); - int base = map_element.first; - pair base_pair = map_element.second; - if (base_pair.first == base) { - verify_stack.push_back(base_pair); - } else { - pair last_base_pair = verify_stack.back(); - if (last_base_pair.second == base) { - verify_stack.pop_back(); - } - else { + + if(v_fbp.size()>1){ + std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); + for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { + if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second + && v_fbp[ii].second >= v_fbp[ii+1].first) { fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(1); + exit(-1); } + } } - return 0; + + return 0; } int init_constraints(const char* constr_file,int length) { @@ -165,11 +145,11 @@ int init_constraints(const char* constr_file,int length) { BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int)); - if (BP == NULL) { - perror("Cannot allocate variable 'constraints'"); - exit(-1); - } - + if (BP == NULL) { + perror("Cannot allocate variable 'constraints'"); + exit(-1); + } + int LLL = length*(length+1)/2 + 1; @@ -178,7 +158,7 @@ int init_constraints(const char* constr_file,int length) { BP[i] = 0; } - + //ZS: for noncanonical bases (right now this only handles 'N'), force single-stranded. for(i = 1; i <= length; i++){ if(RNA[i]=='N'){ @@ -191,7 +171,7 @@ int init_constraints(const char* constr_file,int length) { } } - + //ZS: set prohibited basepairs if(nPBP != 0){ int temp; @@ -209,9 +189,9 @@ int init_constraints(const char* constr_file,int length) { printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; } - + for(k = 1; k <= PBP[it][2]; k++){ - + BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2; //Mark that these two nucleotides are involved in a prohibited pair (only used for for printing out) @@ -285,7 +265,7 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][0]+k-1,i) = 2; BP(i,FBP[it][1]-(k-1)) = 2; } - + //mark that these two nucleotides are involved in a constrained pair //to avoid searching in O(N^2) time @@ -293,7 +273,7 @@ int init_constraints(const char* constr_file,int length) { BP(FBP[it][1]-(k-1), FBP[it][1]-(k-1))=4; //force pairing BP(FBP[it][0]+k-1, FBP[it][1]-(k-1)) = 1; - + } } } @@ -305,70 +285,70 @@ int init_constraints(const char* constr_file,int length) { int verify_structure(){ //ZS: This method returns true if the structure (global.h) is consistent with //the constraints, and false if it is not. - + if(CONS_ENABLED){ - int errorhappened = 0; - int it, k; - //Check prohibited constraints - if(nPBP != 0){ - for(it = 0; it < nPBP; it++){ - if(PBP[it][2] < 1 || PBP[it][1] == 0){ - //printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); - continue; - } - for(k = 1; k <= PBP[it][2]; k++){ - //correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1)) - if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){ - errorhappened = 1; - fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]); - break; - } + int errorhappened = 0; + int it, k; + //Check prohibited constraints + if(nPBP != 0){ + for(it = 0; it < nPBP; it++){ + if(PBP[it][2] < 1 || PBP[it][1] == 0){ + //printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); + continue; + } + for(k = 1; k <= PBP[it][2]; k++){ + //correct answer: strcuture(PBP[it][0]+k-1) != structure(PBP[it][1]-(k-1)) + if(structure[PBP[it][0]+k-1] == PBP[it][1]-(k-1) || structure[PBP[it][1]-(k-1)] == PBP[it][0]+k-1){ + errorhappened = 1; + fprintf(stderr, "Constraint P %d %d %d is not fulfilled.\n",PBP[it][0], PBP[it][1], PBP[it][2]); + break; } - } - } + } + } + } + + //Check forced constraints + if(nFBP != 0){ + for(it = 0; it Date: Sat, 10 Sep 2011 13:49:26 -0400 Subject: [PATCH 132/187] Fix pseudoknot detection code. --- gtfold-mfe/src/constraints.cc | 76 +++++++++++++++++++++++++---------- 1 file changed, 55 insertions(+), 21 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 08f67bc..27ec4a7 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -5,6 +5,8 @@ #include #include #include +#include +#include #include "global.h" #include "options.h" @@ -13,6 +15,8 @@ int* BP; int* ind; +typedef pair basepair_t; + /* ZS: Explanation to BP array. @@ -37,13 +41,7 @@ int** FBP; int nPBP; int nFBP; -bool compare_bp(const std::pair& o1, - const std::pair& o2) { - return o1.first < o2.first; -} - - -static int load_constraints(const char* constr_file, int verbose=0) { +static int load_constraints(const char* constr_file, int seq_length, int verbose=0) { fprintf(stdout, "- Running with constraints\n"); @@ -107,30 +105,66 @@ static int load_constraints(const char* constr_file, int verbose=0) { } } - std::vector > v_fbp; + map all_bases; for(it=0; it< nFBP; it++) { - for(int k=1;k<= FBP[it][2];k++) - v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); + for(int k=1;k<= FBP[it][2];k++) { + basepair_t base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1); + pair::iterator, bool> retVal; + retVal = all_bases.insert(pair(base_pair.first, base_pair)); + if (base_pair.first < 1 || base_pair.first > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.first, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.second < 1 || base_pair.second > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.second, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.first >= base_pair.second - TURN) { + fprintf(stderr, "\nDistance between bases of base pair (%d,%d) is too small\n", + base_pair.first, base_pair.second); + exit(1); + } + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + retVal = all_bases.insert(pair(base_pair.second, base_pair) ); + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + } } - - if(v_fbp.size()>1){ - std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); - for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second!=0&&v_fbp[ii].second <= v_fbp[ii+1].second - && v_fbp[ii].second >= v_fbp[ii+1].first) { + + vector verify_stack; + for (map::iterator it = all_bases.begin(); it != all_bases.end(); ++it) { + + pair map_element = (*it); + int base = map_element.first; + basepair_t base_pair = map_element.second; + if (base_pair.first == base) { + verify_stack.push_back(base_pair); + } else { + basepair_t last_base_pair = verify_stack.back(); + if (last_base_pair.second == base) { + verify_stack.pop_back(); + } + else { fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(-1); + exit(1); } - } } - return 0; } int init_constraints(const char* constr_file,int length) { - load_constraints(constr_file); + load_constraints(constr_file, length); int i,j,it,k; @@ -177,7 +211,7 @@ int init_constraints(const char* constr_file,int length) { int temp; //Make sure smallest one is first for(it = 0; it < nPBP; it++){ - if(PBP[it][0] > PBP[it][1]){ + if(PBP[it][0] > PBP[it][1] && PBP[it][1] != 0){ temp = PBP[it][0]; PBP[it][0] = PBP[it][1]; PBP[it][1] = temp; From e9100f1da3609ebb4a06b2fee31fcb4456861d12 Mon Sep 17 00:00:00 2001 From: Manoj Soni Date: Sun, 11 Sep 2011 22:02:19 -0400 Subject: [PATCH 133/187] Corrected constraints code for handling single stranded constraints properly --- gtfold-mfe/src/constraints.cc | 100 +++++++++++++++++----------------- 1 file changed, 50 insertions(+), 50 deletions(-) diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 08f67bc..f6ee6b0 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -177,7 +177,7 @@ int init_constraints(const char* constr_file,int length) { int temp; //Make sure smallest one is first for(it = 0; it < nPBP; it++){ - if(PBP[it][0] > PBP[it][1]){ + if(PBP[it][0] > PBP[it][1] && PBP[it][1]!=0){ temp = PBP[it][0]; PBP[it][0] = PBP[it][1]; PBP[it][1] = temp; @@ -185,18 +185,33 @@ int init_constraints(const char* constr_file,int length) { } for(it = 0; it < nPBP; it++){ - if(PBP[it][2] < 1 || PBP[it][1] == 0){ + if(PBP[it][2] < 1){ printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; } for(k = 1; k <= PBP[it][2]; k++){ - BP(PBP[it][0]+k-1, PBP[it][1]-(k-1)) = 2; + if(PBP[it][1] == 0){ + //force single-stranded + BP(PBP[it][0]+k-1, PBP[it][0]+k-1) = 3; + //prohibit all pairs with that base + for(i = 1; i<=length; i++){ + if(i FBP[it][1] && FBP[it][1]!=0){ + if(FBP[it][0] > FBP[it][1]){ temp = FBP[it][0]; FBP[it][0] = FBP[it][1]; FBP[it][1] = temp; } } for(it = 0; it Date: Wed, 14 Sep 2011 11:04:58 -0400 Subject: [PATCH 134/187] adding partitition function header/src files --- gtfold-mfe/include/partition-func.h | 31 +++++++++++++++++++++++++ gtfold-mfe/src/partition-func.c | 36 +++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 gtfold-mfe/include/partition-func.h create mode 100644 gtfold-mfe/src/partition-func.c diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h new file mode 100644 index 0000000..ca2af33 --- /dev/null +++ b/gtfold-mfe/include/partition-func.h @@ -0,0 +1,31 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct partition_struct { + double ** u; + double ** up; + double ** upm; + double ** ud; + double ** u1d; + + double ** s1; + double ** s2; + double ** s3; + double ** u1; + + int length; +} partition_t; + +extern partition_t partition; + +void calculate_partition(); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c new file mode 100644 index 0000000..fe61d0c --- /dev/null +++ b/gtfold-mfe/src/partition-func.c @@ -0,0 +1,36 @@ +#include "partition-func.h" + +static void create_partition_arrays(); +static void init_partition_arrays(); +static void fill_partition_arrays(); +static void free_partition_arrays(); + +static void calc_u(int i, int j); +static void calc_ud(int i, int j); +static void calc_up(int i, int j); +static void calc_upm(int i, int j); +static void calc_u1(int i, int j); +static void calc_u1d(int i, int j); +static void calc_s1(int i, int j); +static void calc_s2(int i, int j); +static void calc_s3(int i, int j); + +void create_partition_arrays() +{ + +} + +void init_partition_arrays() +{ + +} + +void fill_partition_arrays() +{ + +} + +void free_partition_arrays() +{ + +} From 17bc05349ede27257f1ed42869776d09244d713d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 14 Sep 2011 11:14:50 -0400 Subject: [PATCH 135/187] added header energy.h --- gtfold-mfe/src/partition-func.c | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index fe61d0c..44de0ea 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -1,4 +1,6 @@ #include "partition-func.h" +#include "energy.h" + static void create_partition_arrays(); static void init_partition_arrays(); From 089d8d67459d83cdc28a2539783815ccc6638779 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 14 Sep 2011 11:41:41 -0400 Subject: [PATCH 136/187] added global vars --- gtfold-mfe/include/partition-func.h | 26 +++++++++++--------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index ca2af33..dcbea32 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -5,24 +5,20 @@ extern "C" { #endif -typedef struct partition_struct { - double ** u; - double ** up; - double ** upm; - double ** ud; - double ** u1d; +extern double ** u; +extern double ** up; +extern double ** upm; +extern double ** ud; +extern double ** u1d; - double ** s1; - double ** s2; - double ** s3; - double ** u1; +extern double ** s1; +extern double ** s2; +extern double ** s3; +extern double ** u1; - int length; -} partition_t; +extern int part_len; -extern partition_t partition; - -void calculate_partition(); +void calculate_partition(int len); #ifdef __cplusplus } From f96b75f866447ca6e40cf3b57d38a12360fd506d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Sep 2011 10:35:48 -0400 Subject: [PATCH 137/187] integrated partition func --- gtfold-mfe/include/options.h | 1 + gtfold-mfe/include/partition-func.h | 4 + gtfold-mfe/src/Makefile.am | 1 + gtfold-mfe/src/Makefile.in | 9 +- gtfold-mfe/src/main.cc | 11 +- gtfold-mfe/src/options.cc | 274 ++++++++++++++-------------- gtfold-mfe/src/partition-func.c | 236 +++++++++++++++++++++++- 7 files changed, 394 insertions(+), 142 deletions(-) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 44de1ce..5dbebf1 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -22,6 +22,7 @@ extern bool PARAM_DIR; extern bool T_MISMATCH; extern bool UNAMODE; extern bool RNAMODE; +extern bool CALC_PART_FUNC; extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index dcbea32..9761531 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -1,6 +1,9 @@ #ifndef _PARTITION_DANGLE_H #define _PARTITION_DANGLE_H + +#include + #ifdef __cplusplus extern "C" { #endif @@ -19,6 +22,7 @@ extern double ** u1; extern int part_len; void calculate_partition(int len); +void free_partition(); #ifdef __cplusplus } diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 428951a..c595933 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -18,6 +18,7 @@ gtfold_SOURCES = \ subopt_traceback.cc\ algorithms-partition.c\ partition-dangle.c\ + partition-func.c\ random-sample.cc\ shapereader.cc diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index e8e0471..bad351a 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -52,8 +52,8 @@ am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ - partition-dangle.$(OBJEXT) random-sample.$(OBJEXT) \ - shapereader.$(OBJEXT) + partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \ + random-sample.$(OBJEXT) shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -117,7 +117,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -195,6 +194,7 @@ gtfold_SOURCES = \ subopt_traceback.cc\ algorithms-partition.c\ partition-dangle.c\ + partition-func.c\ random-sample.cc\ shapereader.cc @@ -291,6 +291,7 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 4b016de..952aba1 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -38,7 +38,7 @@ #include "energy.h" #include "algorithms.h" #include "algorithms-partition.h" -#include "partition-dangle.h" +#include "partition-func.h" #include "constraints.h" #include "traceback.h" #include "subopt_traceback.h" @@ -283,6 +283,15 @@ int main(int argc, char** argv) { printRunConfiguration(seq); + if (CALC_PART_FUNC == true) + { + printf("\nComputing partition function...\n"); + calculate_partition(seq.length()); + free_partition(); + free_fold(seq.length()); + exit(0); + } + printf("\nComputing minimum free energy structure...\n"); fflush(stdout); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 831bf5d..7b4a4ee 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -18,6 +18,7 @@ bool T_MISMATCH = false; bool UNAMODE = false; bool RNAMODE = false; bool b_prefilter = false; +bool CALC_PART_FUNC = false; string seqfile = ""; string constraintsFile = ""; @@ -70,6 +71,7 @@ void help() { printf("\nBETA OPTIONS\n"); printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); @@ -91,149 +93,151 @@ void help() { * Parse the options from argc and argv and save them into global state. */ void parse_options(int argc, char** argv) { - int i; + int i; - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) - LIMIT_DISTANCE = true; - else - help(); - } - else - help(); - } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { - NOISOLATE = true; - } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { - if(i < argc) - outputPrefix = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { - if(i < argc) - outputDir = argv[++i]; - else - help(); - } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { - if(i < argc) { - paramDir = argv[++i]; - PARAM_DIR = true; - } - else - help(); - } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { - std::string cmd = argv[i]; - if(i < argc) { - dangles = atoi(argv[++i]); - if (!(dangles == 0 || dangles == 2)) { - dangles = -1; - printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); - } - } else - help(); - } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { - T_MISMATCH = true; - } else if (strcmp(argv[i], "--unafold") == 0) { - UNAMODE = true; - } else if (strcmp(argv[i], "--rnafold") == 0) { - RNAMODE = true; - } else if (strcmp(argv[i], "--prefilter") == 0) { - if(i < argc) { - prefilter1 = atoi(argv[++i]); - if (prefilter1 <= 0 ) { - printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); - help(); - } - b_prefilter = true; - prefilter2 = prefilter1; - } else - help(); - } - else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { - if(i < argc) - nThreads = atoi(argv[++i]); - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { - VERBOSE = true; - } - else if(strcmp(argv[i], "--bpp") == 0) { - BPP_ENABLED = true; - } else if(strcmp(argv[i], "--subopt") == 0) { - SUBOPT_ENABLED = true; - dangles = 2; - if(i < argc) - suboptDelta = atof(argv[++i]); - else - help(); - } - else if (strcmp(argv[i], "--useSHAPE") == 0){ - if( i < argc){ - shapeFile = argv[++i]; - SHAPE_ENABLED = true; - } - else - help(); - } - } else { - seqfile = argv[i]; - } - } + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + dangles = 2; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } else if (strcmp(argv[i],"--partition") == 0) { + CALC_PART_FUNC = true; + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // Must have an input file specified - if(seqfile.empty()) { - help(); - printf("Missing input file.\n"); - } + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - // If no output file specified, create one - if(outputPrefix.empty()) { - // base it off the input file - outputPrefix += seqfile; + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; - size_t pos; - // extract file name from the path - if ((pos=outputPrefix.find_last_of('/')) > 0) { - outputPrefix = outputPrefix.substr(pos+1); - } + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // and if an extension exists, remove it ... - if(outputPrefix.find(".") != string::npos) - outputPrefix.erase(outputPrefix.rfind(".")); - } + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } - // If output dir specified - if (!outputDir.empty()) { - outputFile += outputDir; - outputFile += "/"; - suboptFile += outputDir; - suboptFile += "/"; - bppOutFile += outputDir; - bppOutFile += "/"; - } - // ... and append the .ct - outputFile += outputPrefix; - outputFile += ".ct"; + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; - suboptFile += outputPrefix; - suboptFile += "_ss.txt"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; - bppOutFile += outputPrefix; - bppOutFile += "_bpp.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; } /** diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 44de0ea..5319eb8 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -1,7 +1,21 @@ #include "partition-func.h" #include "energy.h" +#include "algorithms-partition.h" +double ** u; +double ** up; +double ** upm; +double ** ud; +double ** u1d; + +double ** s1; +double ** s2; +double ** s3; +double ** u1; + +int part_len; + static void create_partition_arrays(); static void init_partition_arrays(); static void fill_partition_arrays(); @@ -16,23 +30,241 @@ static void calc_u1d(int i, int j); static void calc_s1(int i, int j); static void calc_s2(int i, int j); static void calc_s3(int i, int j); +static double f(int j, int h, int l); -void create_partition_arrays() +double f(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +} + + +void calculate_partition(int len) { + part_len = len; + create_partition_arrays(); + init_partition_arrays(); + fill_partition_arrays(); +} +void free_partition() +{ + free_partition_arrays(); } void init_partition_arrays() { - + int i, j; + int n = part_len; + for(i=1; i<=n-3; ++i){ + for(j=i; j<=i+3; ++j){ + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + } + for(i=1; i part_len-2) continue; + p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j])); + } + + u1d[l+1][j] = p_val; +} + +void calc_u(int i, int j) +{ + int uval = 1; + int h; + int ctr; + + for (h = i+1; h < j; ++h) { + uval = up[h][j] * exp( -(Ed5(h,j,h-1) + auPenalty(h,j)) / RT ); + } + + uval = uval + ud[i][j]; + + for (ctr = i+1; ctr < j-1; ++ctr) { + uval = uval + s1[ctr][j]; + } +} + +void calc_ud(int i, int j) +{ + int l; + + for (l = i+1; l < j; ++l) { + double val1, val2, val3; + val1 = up[i][l]; + val1 = val1 * exp(-auPenalty(i,l) / RT); + + val2 = u[l+2][j]; + val2 = val2 * exp(-Ed3(i,l,l+1)/RT); + + val3 = ud[l+1][j]; + val2 = val2 + up[l+1][j] * exp( -auPenalty(l+1,j) / RT ); + + ud[i][j] = ud[i][j] + (val1 * val2); + } +} + +void calc_up(int i, int j) +{ + double up_val = 0.0; + int h,l; + for (h = i+1; h < j-1; ++h) { + for (l = h+1; l < j; ++l) { + up_val = up[h][l] * exp(-eL(i,j,h,l)/RT); + } + } + up_val = up_val * exp(-Ed3(i,j,i+1)/RT); + up_val = up_val + exp(-eH(i,j)/RT ); + up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1]; + up_val = up_val + upm[i][j]; } From a922dc664c0aa5dbd9109354036461d6d6f5e9aa Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Sep 2011 11:21:57 -0400 Subject: [PATCH 138/187] boundary correction --- gtfold-mfe/src/partition-func.c | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 5319eb8..ae5ee53 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -73,12 +73,12 @@ void init_partition_arrays() s1[i][i+4] = 0; s2[i][i+4] = 0; } - for(i=1; i Date: Fri, 16 Sep 2011 11:37:30 -0400 Subject: [PATCH 139/187] more boundary correction --- gtfold-mfe/src/partition-func.c | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index ae5ee53..21d96ca 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -90,17 +90,21 @@ void fill_partition_arrays() for(b=TURN+1; b part_len-2) continue; p_val += (up[i][l]*exp((-1)*(c+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*b/RT) + exp((-1)*(Ed3(i,l,l+1)+b)/RT)*u1[l+2][j] + u1d[l+1][j])); } - u1d[l+1][j] = p_val; + u1d[i][j] = p_val; } void calc_u(int i, int j) From 91e95b88fe8365855504ae5110712d8213bc95c0 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Sep 2011 11:42:28 -0400 Subject: [PATCH 140/187] more boundary correction --- gtfold-mfe/src/partition-func.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 21d96ca..62a56d6 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -157,7 +157,7 @@ void create_partition_arrays() void free_partition_arrays() { - int len = part_len + 1; + int len = part_len + 2; freeTwoD(u,len,len); freeTwoD(up,len,len); freeTwoD(upm,len,len); From abcd9f532a8fc2788ea1717d2d16d151d1c580a4 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Sep 2011 17:30:32 -0400 Subject: [PATCH 141/187] more boundary correction --- gtfold-mfe/src/partition-func.c | 157 ++++++++++++++++++++++++-------- 1 file changed, 121 insertions(+), 36 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 62a56d6..e004a74 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -1,7 +1,37 @@ +#include #include "partition-func.h" #include "energy.h" #include "algorithms-partition.h" - +#include "global.h" +#include "utils.h" + +#ifdef _OPENMP +#include "omp.h" +#endif + +#define DEBUG_PF 1 + +#ifdef DEBUG_PF + #undef Ec + #undef Eb + #undef Ea + #define Ec 0 + #define Eb 0 + #define Ea 0 + #define eS StackE + #define eH HairE + #define eL ILoopE + #define Ed3 D3 + #define Ed5 D5 + #define auPenalty Etp +#endif + +int StackE(int i, int j) { return 0; } +int HairE(int i, int j) { return 0; } +int ILoopE(int i, int j, int ip, int jp) { return 0; } +int D3(int i, int j, int k) { return 0; } +int D5(int i, int j, int k) { return 0; } +int Etp(int i, int j) { return 0; } double ** u; double ** up; @@ -42,10 +72,20 @@ double f(int j, int h, int l){ void calculate_partition(int len) { + int i, j; part_len = len; create_partition_arrays(); init_partition_arrays(); fill_partition_arrays(); + + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } + + printf("%4.4f\n",u[1][part_len]); } void free_partition() @@ -53,8 +93,29 @@ void free_partition() free_partition_arrays(); } +void init_part_arrays_zeros(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=0; + up[i][j]=0; + upm[i][j]=0; + ud[i][j]=0; + u1d[i][j]=0; + + s1[i][j]=0; + s2[i][j]=0; + s3[i][j]=0; + u1[i][j]=0; + } + } +} + void init_partition_arrays() { + init_part_arrays_zeros(); + int i, j; int n = part_len; for(i=1; i<=n-3; ++i){ @@ -85,12 +146,12 @@ void init_partition_arrays() void fill_partition_arrays() { - int b,i; + int b,i,j; int n=part_len; for(b=TURN+1; b TURN) + { + for(l=i+2; l TURN) + { + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (canPair(p,q)==0) continue; + up_val += (up[p][q] * exp(-eL(i,j,p,q)/RT)); + } + } + + up_val = up_val * exp(-Ed3(i,j,i+1)/RT); + up_val = up_val + exp(-eH(i,j)/RT ); + up_val = up_val + exp(-eS(i,j)/RT ) * up[i+1][j-1]; + up_val = up_val + upm[i][j]; + + up[i][j] = up_val; + } + else { + up[i][j] = 0; + } } From badba13c72b4a9a0f833d81eb2a3dff6b18c5628 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Sep 2011 17:48:05 -0400 Subject: [PATCH 142/187] debug changes --- gtfold-mfe/src/partition-func.c | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index e004a74..215b1ba 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -268,7 +268,7 @@ void calc_u1(int i, int j){ int h; double quadraticSum = 0; - for(h=i+1; h Date: Mon, 26 Sep 2011 23:21:00 -0400 Subject: [PATCH 143/187] Test for single stranded constraint --- gtfold-mfe/src/test_ss_constraint.c | 155 ++++++++++++++++++++++++++++ 1 file changed, 155 insertions(+) create mode 100644 gtfold-mfe/src/test_ss_constraint.c diff --git a/gtfold-mfe/src/test_ss_constraint.c b/gtfold-mfe/src/test_ss_constraint.c new file mode 100644 index 0000000..e3bd2d3 --- /dev/null +++ b/gtfold-mfe/src/test_ss_constraint.c @@ -0,0 +1,155 @@ +/*This program is used for testing single stranded constraints. Functions written in this file can be used for other scripts as well +Author: Manoj Soni +Email: manoj6891@gmail.com +*/ +#include +#include +#include +//#include +#define LENGTH 10 +#define MAX_CONSTRS 10 + +void executeCommand(char* cmd){ + printf("Executing command: %s\n", cmd); + int returnVal = system(cmd); + printf("return value: %d\n", returnVal); + if(returnVal != 0){ + printf("Error: returnVal:%d, Exiting...\n", returnVal); + exit(-1); + } +} + +char* getToken(char* str, char* sep, int index){ + char * pch; + pch = strtok (str,sep); + char* fName = pch; + if(index==0) return fName; + if(index != -1){ + printf("Error: index can be only 0 or -1. 0 means first and -1 means last token\n"); + exit(-1); + } + while (pch != NULL) + { + //printf ("%s\n",pch); + fName=pch; + pch = strtok (NULL, sep); + } + printf("%s\n",fName); + return fName; +} + +char* getSeqName(char* seqFileName1){ + char* seqFileName = malloc(200); + strcpy(seqFileName,seqFileName1); + char* seq = getToken(seqFileName, "/", -1); + char* seqName = getToken(seq, ".", 0); + printf("seqName: %s\n",seqName); + return seqName; + +} + +void parseCtFileToFindForcedConstraintRegion(char* ctFileName, char* constrs[MAX_CONSTRS]){//printf("Entering parse method\n"); +//ct file contents are +//dG = -5.8 +//1 C 0 2 12 1 +//2 C 1 3 11 2 +//... ... ... +//then 1 is pairing with 12, 2 is pairing with 11 .. ? +//in other words, first column is i and 5th column is j for a pair (i,j) + //char* constrs[MAX_CONSTRS]; + int index=0; + FILE* ctFile = fopen(ctFileName, "r"); + char str[100]; + int arr[5]; + char c; + fscanf(ctFile, "%[^\n]", str);printf("first line: %s\n",str); + int start=-1, end=-1; + while(feof(ctFile)==0){ + fscanf(ctFile, "%d %c %d %d %d %d\n", &arr[0],&c,&arr[1],&arr[2],&arr[3],&arr[4]); + if(arr[3]!=0){ + if(start==-1){ start=arr[0]; end=arr[0];} + else end=arr[0]; + if (start!=-1 && end-start+1 >= LENGTH){ + //char* ss_constr; + char* ss_constr = (char*)malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + } + } + else{ + if(start==-1) continue; + // char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + + } + // printf("line is: %d %c %d %d %d %d\n", arr[0],c,arr[1],arr[2],arr[3],arr[4]); + } + if(index>=MAX_CONSTRS) return ;//constrs; + //char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + if(start!=-1){ + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + printf("constraint is: %s\n",ss_constr); + constrs[index++] = ss_constr; + } + fclose(ctFile); + return ;//ss_constr; +} + +char* createConstraintFile(char* constrs[MAX_CONSTRS]){ + char* constrFileName = "constraints.txt"; + FILE* constrFile = fopen(constrFileName, "w+"); + int i; + for(i=0; i Date: Mon, 26 Sep 2011 23:21:10 -0400 Subject: [PATCH 144/187] Test for single stranded constraint --- gtfold-mfe/src/test_ss_constraint.pl | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100755 gtfold-mfe/src/test_ss_constraint.pl diff --git a/gtfold-mfe/src/test_ss_constraint.pl b/gtfold-mfe/src/test_ss_constraint.pl new file mode 100755 index 0000000..60e7fc6 --- /dev/null +++ b/gtfold-mfe/src/test_ss_constraint.pl @@ -0,0 +1,11 @@ +#!/usr/bin/perl +use strict; +use warnings; +use File::Basename; + +die "Usage: ./test_ss_constraint.pl " if @ARGV < 1; + +my $seqName = $ARGV[0]; + +system("gcc -o test_ss_constraint test_ss_constraint.c"); +system("./test_ss_constraint $seqName"); From 0ffefa57394c34e0774589bccef51ab43037e063 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 30 Sep 2011 00:15:27 -0400 Subject: [PATCH 145/187] First version of test scripts: --- gtfold-mfe/tests/config/root-logger.conf | 7 ++ gtfold-mfe/tests/config/test-list.conf | 1 + gtfold-mfe/tests/config/test-params.conf | 22 +++++ .../data/16S_sequences/d.16.e.A.ambigua.seq | 2 + .../16S_sequences/d.16.e.A.baicalensis.seq | 2 + .../data/16S_sequences/d.16.e.A.bongranii.seq | 2 + .../data/16S_sequences/d.16.e.A.bracteata.seq | 2 + .../16S_sequences/d.16.e.A.capitellata.seq | 2 + .../16S_sequences/d.16.e.A.castellanii.seq | 2 + .../16S_sequences/d.16.e.A.connecticus.seq | 2 + .../data/16S_sequences/d.16.e.A.dasyae.seq | 2 + .../data/16S_sequences/d.16.e.A.ferocious.seq | 2 + .../data/16S_sequences/d.16.e.A.flavus.seq | 2 + .../data/16S_sequences/d.16.e.A.fundyense.seq | 2 + .../data/16S_sequences/d.16.e.A.hermannii.seq | 2 + .../data/16S_sequences/d.16.e.A.invadans.seq | 2 + .../data/16S_sequences/d.16.e.A.kariana.seq | 2 + .../16S_sequences/d.16.e.A.khaliulini.seq | 2 + .../16S_sequences/d.16.e.A.macrogynus.seq | 2 + .../data/16S_sequences/d.16.e.A.majus.seq | 2 + .../data/16S_sequences/d.16.e.A.michaelis.seq | 2 + .../data/16S_sequences/d.16.e.A.plicata.seq | 2 + .../data/16S_sequences/d.16.e.A.scoticae.seq | 2 + .../data/16S_sequences/d.16.e.A.thaliana.seq | 2 + .../d.16.e.A.verticilliflorum.seq | 2 + .../data/16S_sequences/d.16.e.B.bigemina.seq | 2 + .../data/16S_sequences/d.16.e.B.bovis.seq | 2 + .../data/16S_sequences/d.16.e.B.canis.seq | 2 + .../data/16S_sequences/d.16.e.B.coli.seq | 2 + .../data/16S_sequences/d.16.e.B.emersonii.seq | 2 + .../16S_sequences/d.16.e.B.gelatinosum.seq | 2 + .../data/16S_sequences/d.16.e.B.gibsoni.seq | 2 + .../data/16S_sequences/d.16.e.B.hamifera.seq | 2 + .../16S_sequences/d.16.e.B.investiens.seq | 2 + .../16S_sequences/d.16.e.B.macrosporum.seq | 2 + .../16S_sequences/d.16.e.B.mandrillaris.seq | 2 + .../16S_sequences/d.16.e.B.mediterranea.seq | 2 + .../data/16S_sequences/d.16.e.B.microti.1.seq | 2 + .../data/16S_sequences/d.16.e.B.microti.2.seq | 2 + .../data/16S_sequences/d.16.e.B.microti.3.seq | 2 + .../data/16S_sequences/d.16.e.B.microti.4.seq | 2 + .../data/16S_sequences/d.16.e.B.microti.5.seq | 2 + .../16S_sequences/d.16.e.B.moritziana.seq | 2 + .../data/16S_sequences/d.16.e.B.ostreae.seq | 2 + .../data/16S_sequences/d.16.e.B.pacifica.seq | 2 + .../16S_sequences/d.16.e.B.plumatellae.seq | 2 + .../data/16S_sequences/d.16.e.B.rodhaini.seq | 2 + .../data/16S_sequences/d.16.e.G.vagum.seq | 2 + .../data/16S_sequences/d.16.e.G.vavrai.seq | 2 + .../tests/scripts/Scoregtwithunafold.pm | 60 ++++++++++++ gtfold-mfe/tests/scripts/start_test.pm | 94 +++++++++++++++++++ gtfold-mfe/tests/scripts/test_utils.pl | 84 +++++++++++++++++ 52 files changed, 360 insertions(+) create mode 100644 gtfold-mfe/tests/config/root-logger.conf create mode 100644 gtfold-mfe/tests/config/test-list.conf create mode 100644 gtfold-mfe/tests/config/test-params.conf create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq create mode 100644 gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq create mode 100755 gtfold-mfe/tests/scripts/Scoregtwithunafold.pm create mode 100755 gtfold-mfe/tests/scripts/start_test.pm create mode 100755 gtfold-mfe/tests/scripts/test_utils.pl diff --git a/gtfold-mfe/tests/config/root-logger.conf b/gtfold-mfe/tests/config/root-logger.conf new file mode 100644 index 0000000..7fa2cc7 --- /dev/null +++ b/gtfold-mfe/tests/config/root-logger.conf @@ -0,0 +1,7 @@ +#root-logger.conf +log4perl.rootLogger = INFO, myFILE +log4perl.appender.myFILE = Log::Log4perl::Appender::File +log4perl.appender.myFILE.filename = ../logs/error_log +log4perl.appender.myFILE.mode = append +log4perl.appender.myFILE.layout = Log::Log4perl::Layout::PatternLayout +log4perl.appender.myFILE.layout.ConversionPattern = [%p] (%F line %L) %m%n diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf new file mode 100644 index 0000000..b339d8d --- /dev/null +++ b/gtfold-mfe/tests/config/test-list.conf @@ -0,0 +1 @@ +Scoregtwithunafold diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf new file mode 100644 index 0000000..2922a50 --- /dev/null +++ b/gtfold-mfe/tests/config/test-params.conf @@ -0,0 +1,22 @@ +# Important directory variables +G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ +G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/ +G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/ +G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf + +#Sequence Inclusion Filters +#G_INCLUDE_SEQUENCES=rad +#G_INCLUDE_SEQUENCES=d.16.e.B.g* +#G_INCLUDE_SEQUENCES=d.16.e.B.m* +#G_INCLUDE_SEQUENCES=d.16.e.B.h* +G_INCLUDE_SEQUENCES=d.16.e.G.va* +#G_EXCLUDE_SEQUENCES=d.16.e.A.* +#G_EXCLUDE_SEQUENCES=d.16.e.B.ma* +#G_INCLUDE_SEQUENCES=acc1 +#G_INCLUDE_SEQUENCES=a.*j +#G_INCLUDE_SEQUENCES=a..tb* + diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq new file mode 100644 index 0000000..53be3ef --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ambigua +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGACUAAGCCAUGCAUGUGUAAGUAUAAGAAGUACUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUUGUAUUUAUUAGGUUACAAAACCAACCCUCUCUCGGGAGGUUCUUUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCAGGGCUUUACGCCGGCGACGGAUCAUGUAAGUUCCUGCCCUAUCAGCUUCGGAUGGUAGGGUAUUGGCCUACCAUGGCAUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUCUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAASACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUACGUGACUGUAUCUCUGCCCUCCUUGGUUGGAUCCAGUGCUGGCAUUUGGUUGUCGGUCUGGGGACGGCCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUCGUUGGUUUGCGCGCCGAAACAAUGAUUAAUAGGGACAGUUUGGGGAUAUUCCUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACCAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGBGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAACGUGCAUCGUGAUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGCGGUCCGUUCCUUUACUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq new file mode 100644 index 0000000..6dbbac3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.baicalensis +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGGACUAAGCCAUGCAUGUGUAAGUAUAAGAACUUUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUCGUAUUUAUUAGGUUACAAAACCAACCCUCUUUCGGGAGGUUCUCUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCACGGCUUUAUGCCGGCGUCGGAUCAGGUAAGUUCCUGCCCCAUCAGCUUCGGAUGGUAGAGUAUUGGCCUACCAUGGCGUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAAUACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUUCGUGACUGUAUCUCUGCCCUCCUUGGUUGGAGCCAGUGUUGGCAUUCAGUUGUUGGGCUGGGGACAAUCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUUGUUGGUUUGCGCGCCAAAAUAAUGAUUAACAGGGACAGUUUGGGGAUAUUCGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACAGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGUGAGGCCUGGGUAAUCUUAUGAACGUGCAUCGUGCUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGUCCGUUCCUUCAGUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq new file mode 100644 index 0000000..bd0b78d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bongranii +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAACUCUUUUACUUGAAAACUGCGAACGGCUCAUUAUAUCAGUUAUAGUUUAUUGGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCGAUACCCUUCUGGGGUAGUAUUUAUUAGAUAGAAACCAACCCCUUCGGGGUGAUGUGGUGAUUCAUAAUAAGUUUACGAAUCGCAUGCCUUCGGGCGGCGAUGGAUCUUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUGUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUGUGGCUGUUGCGGGAGGCCUGGCACGUGCCAGCGCUCUUCCUGCGACGCCAUCCUUGGGUUGAAAGUGGGUGGCAUUAGGUUGUCGCCUAUGGGAAGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAGAUUAGCAUGGAAUAAUAAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGUACUUAGGUAAUGAUUAACAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGAGUUUCUUUAUGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGUUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGCUUGGUUAGUGAAUCUUCACUGGCUGAAGCUUCUUAGAGGGACGUGCAUUCUAUCAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUCUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAUUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGCUAGCUCCCUUCAUUGUGGGUUGGCCGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq new file mode 100644 index 0000000..ddb3562 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bracteata +CACCAGGUUGAUUCUGCCUGACACACACGCUCGUCCCAAAGAUUAAGCCAUGCAUGCUUGUGAAGGAAGCGGAACGGCGUACGGCUCAGUAGGACGGACCUAAUCUAUCCAGCACGGGAGGGAUAACCACGGGAAACUGUGGCUAAGACCGGGAUCUGCCGUGCCCUCGGGUGCUGAAGAGCGGCGGUGUGCUGGGCGAGAGUCUGACCUAUUAGCUUGAUGGCGCGGUAAGGGCGGGCCAUGGCGACGAUGGGUGACGGGGAAUCGGGGUUUGAUUCCGGAGAAGGAGGCUGAGAGACGGCUCCUACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCACUCGAGCGGAGGUAGUGACGGGACGUCUAUGGGGAGCUCUUGAUAACUGCGAGGGGCCUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUGUGUGGUGAUUGCUGCAGUUAAAAGGUCCGUAGUCGACGUGUCUGGCGGGGUCUUGAGGUGCGCUCAACGUGCUAGGACCUCCGCGAGUUGCGUUCCGGAGCACUUGGGGGUGAGGGUAUUCCUGCGUGAGAGGUGAAAUUCGGUGAUCGCGGGGGGACCGACGGGGGCGCAGGCGCUCAUCCAGACUGUGUCCUAUGAUCAAGGGCGGAAGCCGUGGUAGCGAAGGUGAUUAGUGACCACUGUAGUCGCGGCCGCAAACGAUGCGUUCCCGCCUGCUGGGCGGAGGGAAACCGAGAGAGCUCUGGGGAUAGUACGAGCGCAAGCCUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAUCAUGCGGGUUAAUUUGACUCAACGCGGGGCAGCUUACCAGGGCACGCGCGGGUGCGAUCGCGAUGCGAGAUUCUGCGGCGAGUGGUGCAUGGCCGUUUCUAACACGUGGGGUGACCAGUCUGGUUAAGUCCGAUAACGCGUGCCGCCCCGGCCCUGUGCGAAUGGGGGACGACUGCCGACGAGGCAGGGGAAGAGGGGCGAAAACAGGUCCGUAAUGCCCUCCGAAGCCCUGGGCGCCACGCGUGAUACAAUAGCUGCGUCGCGGUUGGGGUCGGGACUGCGGGCUGCGAGGCCAGCACGAACGCGGAAUUCCUAGUAAGCGUGCGUCACCAUUGCGUGCUGAAUGCGUCCCUGUCCUUUGUACACACCGCCCGUCGUUAUUUGAGAUGGUAGUGCGGCCGAGCGGCUGUCCUCGGGCGGCCGCGAGUCCGCCCUGCUAGAUCGAAUACAAGUCGUAACAAGGUAACCANNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq new file mode 100644 index 0000000..3de621e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.capitellata +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUCACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAUACCCUUCUGGGGUAGUAUUUAUUAGAUGGAAACCAACCCCUUCGGGGUGAUGUGGUGAAUCAUAAUAAGCUUGCGGAGYCCGGUGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGACGGUAAGGUAUUGGCUUACCGUGGCUUUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCUUGACACAAGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAACCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGCGGUUCCUGUGGUCCGAUUUCGGUACUUUCUGGGACUGCCAUCCUUGGGUGGAUCCUGUGUGGCAUUAGGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUUGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGUGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUAAUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGGUUUCGUUACGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUCCUUUGAGUGAUUUUCACUGAUUCGGGCUUCUUAGAGGGACGUGCAUUCUAUUAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUUUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGGAUGGUCCGGUGAAGCCUCGGGAUUGUGACCGGUGCCUUUAUUGGUGUCGGUCGCGAGAACUUGUCUAAACCUUAUCAUCUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq new file mode 100644 index 0000000..aee7873 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.castellanii +CGACUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUGUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGGUUAUUUGAUGGUCUCUUUUGUCUUUUUUUACCUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCGCAAGGUCCCGAGCGCGGGGGGCGGGGCUUCACGGCCUCGUCCUCGCAUGCGCAGAGGGAUGUAUUUAUUAGGUUAAAAACCAGCAGCCGGCAACGGCUUCAACUCCUGGUGAUUCAUAGUAACUCUUUCGGAUCGCAUUCAUGCCCUCCUUGUGGGGGCGGCGACGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGCGCUCGAUAAGAGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUAGGGACGCGCAUUUCAAGCGCCCGUGUCGUCGGGUCAAACCGGCGACUGCGUUGGCGUUGCGGGCUCGGUCCGUCGGUGCCCCACAAAGGGCUACUGGCGUGUCAACCGGCCCGCCCGUCCCCUCCUUCUGGAUUCCCGUUCCUGCUAUUGAGUUAGUGGGGACGUCACAGGGGGCUCAUCGUCGUGCGGCGUCAAAACCGUGGCGGCGGUGGGUCCCUGGGGCCCAGAUCGUUUACCGUGAAAAAAUUAGAGUGUUCAAAGCAGGCAGAUCCAAUUUUCUGCCACCGAAUACAUUAGCAUGGGAUAAUGGAAUAGGACCCUGUCCUCCUAUUUUCAGUUGGUUUUGGCAGCGCGAGGACUAGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUCUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUAGGAGACGUUGAAUACAAAACACCACCAUCGGCGCGGUCGUCCUUGGCGUCGGUCCUUCACGGGGCCGGCGCGAGGGCGGCUUAGCCCGGUGGCACCGGUGAAUGACUCCCCUAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAUGCCGCGCUAGCCCGUCCAUCAAAACCCAUGCGUGGCUCACGCGGUCCGCUGCGGGGUGGUGUCACUUCGCGGCGACGUCAUCCCGCCGGCAGGGCCCGGGUCCGUGUGGGCGGUAGGGUUCGGCGUCCGUGCUUCUUAGAGGGACUGCUGCGCGCCUAGCCAGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUCCAACGAGUCCGCUUCAAUCGAGGCGCGAUGCCGUUGGGGUCAAACCCAACUGCGUCGCUGUCCUCGAUCGCGCCUGGGCCGAUAGGUCCGGGUAAUCUUUGCAAAUUUAAUCGUGCUGGGGAUAGAUCAUUGUAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCCUCGGAGCCGUGGCCUCUACGCAAUCCGGGCAACCGGGUUGUGAGGUCUCCCCUUUUGGCGGCGAAGUCGAUUGAACCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCGAAAGGAUCAGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq new file mode 100644 index 0000000..accfe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.connecticus +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGCCUUGAAGAUUAAGCCAUGCAAGCUUGUGAAUAUUAUAUAUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCCAUAUUAUUUAUAACCACGGGAAACUGUGGCUAAGUAUUAGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAUUAUUAGUGUAUAUGGUGUGUAUAAACAGCACACCGAAGUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAAUGUGCGUAGUCUGGUUAGUGGUCUGGAGUAAAUCUUUUGUAUCUAACAACAGGGUAUUCUAGAGACUUAUACCUUGAGACAGGGAAGAGGCGAUGAUAUUUGGUAGCGAGAGGUGAAAAUCGAUGACCUACCAAGGAGCACCGGAGGCGAAAGCGAUCGCCGAGAACUGUUCUGACGAUCAAGCGCGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGGUAUUUACCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGAGGGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUGGUUGCUUUUGUGACUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGGUGGUAGUAUUAGUAAAGUGUAGCUAGCCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGCGAGCAGUCAGGUGAUGGGGAUAAGUGUUUGUGAGUAAUGAAUGCUUGGAACUGUUGCUGGUAAAUGAUUGUGAGUGUAAGAACCCGUGCAGCUAAAUUGGAUGUAAGUCGUAACAAGGUAACCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq new file mode 100644 index 0000000..c3ebfab --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.dasyae +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGAGGUAACUCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCUCGUAAGAGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGGGCAGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGAUGUUCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGGGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGAGCCGUUACCAUUGUGUAGCUGUUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAACGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCUAAAUCCGUUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq new file mode 100644 index 0000000..4352cb6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ferocious +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUGAAGAUUAAGCCAUGCAAGCCUGUGAAUACUUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCACNAACCCUAAUAACCACGGUAAACUGUGGCUAAGGUAGUGGAUGAGGAUGUGACCUAUCAGCUUUGUCGGUACGAUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAAGUUAUAUUGAGUGAAUAAAAUACACUCAUAAAUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCUGGUUUAUAGCCUGAGUUAAAUACGUGUGCUUUAAGCAUGAAGUAUGUCAGGGACUUAGACCUUGGGAUAGGGACGGGGCAAUGAUAUUCGGCAGCGAGAGGUGAAAAUCGAUGACCUGCUGAGGAGCAACAGAGGCGAAAGCGGUUGUCCAGAACUAGUCCGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCCUAGCAGUAAACGAUGCCAACACUGUGGUGGAAUGUCACUGCAGAAGCGAAAGCUAGUGUGUAGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCUGAGGCAGGCUGUUAGUAGGAGAUUGCUUAGCAAGAUACUGCAGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGGAUUCUAUUGUAAAAGGUAGAGACGGUGUAUGUAAGUACAAGGAAGCACCACCCAAUAACAAGUCUGUGAUGCCCGUAGAUGUCCAGGGCUCCACGCGCACUACAGUUUAGUGAAGUGUGUGGAGAGUGAUUUGCUAGGUAGUUGGGAUUGAUGUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACCAACGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGUGGGUNAANUCCAUAGCGAGCUUAGCGAGGUAGUGAUUAUGCACGAGUUAGGUUAGUUAUGGAAAGAACCCAUGCAGCUAGAUUGGAUGUAAGUCGUAACAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq new file mode 100644 index 0000000..b35efec --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.flavus +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACAUGGAUACCUGUGGUAAUUCUAGAGCUAAUACAUGCUAAAAACCUCGACUUCGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGCCCUUCGGGGCUCCUUGGUGAUUCAUAAUAACUUAACGAAUCGCAUGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACGGGGCUCUUUUGGGUCUCGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGUCUGGCUGGCCGGUCCGCCUCACCGCGAGUACUGGUCCGGCUGGACCUUUCCUUCUGGGGAACCUCAUGGCCUUCACUGGCUGUGGGGGGAACCAGGACUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGAUAGUCGGGGGCGUCAGUAUUCAGCUGUCAGAGGUGAAAUUCUUGGAUUUGCUGAAGACUAACUACUGCGAAAGCAUUCGCCAAGGAUGUUUUCAUUAAUCAGGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGCGGUGUUUCUAUGAUGACCCGCUCGGCACCUUACGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACAAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUCUUUUGGAUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUCGGCCCUUAAAUAGCCCGGUCCGCGUUUGCGGGCCGCUGGCUUCUUAGGGGGACUAUCGGCUCAAGCCGAUGGAAGUGCGCGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGGGCCAGCGAGUACAUCACCUUGGCCGAGAGGUCCGGGUAAUCUUGUUAAACCCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUGCCUAGUAGGCACGAGUCAUCAGCUCGUGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCGGUGAGGCCUUCGGACUGGCCCAGGAGGGUUGGCAACGACCCCCCAGGGCCGGAAAGUUGGUCAAACCCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq new file mode 100644 index 0000000..cd73918 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq @@ -0,0 +1,2 @@ +>d.16.e.A.fundyense +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUCAAUUUUGUGAAACUGCAAAUGGCUCAUUAAAACAGUCACAAYGCAUUUGGCGAUCAAUUCUAAAUGGAUAUCUGUGGRAAUUCUAUAGUUAAUACAUGCACUAAAACUUAUCUUUGGGGAAAGGUUGUGGUCGUUAGUUACAGAACCAAUUCAAGCUAUGCUUGGACACUUGAAUGAUUCACAAUGACAAAUGAAUUACAUGGCAACAGCUGGUGAUAAUUCAUUCCAGUUUCUGACCUAUCAGCUUUCGACGGUAAGGUAUUGGCUUACCGUGGCAAUGACAGGUGACGGAGGAUUAGGGUUUGAUUCCGGAGAGGGAGCUUGAGAAAUGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGGCACAGGGAGGUAGUGACAAGAAAUAACAAUACAAGGCAUCCAUGUCUUGUACUUGGAAUGAAUGGAUUUUAAACCUUUCUAUAAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGAGGAUGGCUGGUCCGCCCUCUGGGUGAGUAUUUGGCACAGCCUGAGCAUUUAUCUUGAAAGUACAACUGCACUUGACUGUGUGGUGUGUUAUUGAGAACAUUUACUUUGAGGAAAUCAGAGUGUUUCAAGCAGGUGUUUGGCCUUGAAUACAUUAGCAUGGAAUAAUAAUCAAGAUCGUGGUUCUUUUUUGUUGGUUUCUAGAAUUGAGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCGUAUUUGAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACGGACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAAGGGAUCGAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACCAUGCCAACUAGAGAUUGGAGGUUGUUACUUGUAUGACUUUUUCAGCACCCUAUGCGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAAUGAGGAUUGACAGAUUGAUAGCUUUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUUACAUGUAAUUUCGAUUAUGUGGGCAACUUCUUAGAGGGACKUUGUGUGUAUAAUGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGUGUUCAACGAGUUUUCAACCUUGCCUGGAAAGGUUUGGUAAUUCUUGAACAGGCAUCGUGAUGGGGAUUGUUUAUUGCAAUUAUUAACCUUCAACGAGGAAUUCCUAGUAAGCUUGAGUCAUCAGCUUGUGCUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGARUGAUCCGGUGAAUAAUUUGGACUGUAGCAAUGUUCAGUUCUUGAACAAUGCAAUGGCAAAUUUAAUGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCUGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq new file mode 100644 index 0000000..1eb2af9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.hermannii +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGCAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCAUUUAUAUGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUACGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGCUUGUCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq new file mode 100644 index 0000000..52c4664 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq @@ -0,0 +1,2 @@ +>d.16.e.A.invadans +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUGUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUCUACUCGACAGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUAAAUACCCAACUGCUUGUCGGACGGGUAGCAUUUAUUAGAUUGAAACCAAUUCACUUCGGUGAUUUUGUGUUGAAUCAUAAUAACUGUGCUGAUCGCUCUAAGCGAUAAGUCGAUUGAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGAUAUGGGCCUACCAUGGCGUUAACGGGUAACGGGGAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUUAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCUAAUUUAGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUUUGAGCGUCCGGUCGACGAAAUGUCAGUACUAUGGAUGUUUGGGCCAUAUUUUGUGAGGAUGCCUUUCUGCCAUUGAGUUGGUGGUUGGGUGGACUUGCAUCGUUUACUGUGAAAAAAUUAGAGUGUUUAAAGCAGGCGUUUGCUCAUUUGAAUACAUUAGCAUGGAAUAAUAAGAUACGACCUUGGUGGUCUAUUUUGUUGGUUUGCACGCCAGGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCAUAUUUCAACGUCAGAGGUGAAAUUCUUGGAUCGUUGAAAGAUGAGCUUAGGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUCAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUGACCAUAAACUAUGCCGACUCGGGAUUGGCAGUCGUUUAAUUAGAAUGACCUUGUCAGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCCGCGUGCUAAAUAGUCCUGCUUACCAAUUUGGUAGGUAAGGACUUCUUAGAGGGACUUUCAGUGACUAACUGAAGGAAGUUGGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGGUACGCUCAACGAGUAUAUAACCUUGAUCGAUAGGUCUGGGUAAUCUUUUGAAUACGUAUCGUGCUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAAGUCAUCAGCUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGACUCGGUGAGAAAUUGGGACCGCUGUUUCGCUUGCUUCAUUGUGAGUGAAACGGUGGGAACUUUUUCUAACCUCGCCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq new file mode 100644 index 0000000..9e4029d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.kariana +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAAUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUCAAUACUCGACUCACGAAGAGUAGUAUUUAUUAGAUUGAAACCAACCGCUUCGGCGUGAUGUGGUGAUUCAUAAUAACUUUGCGAAUCGCAUGGUUUAACACCGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGUUGGAGAGCUCCUCCGUUCGCUUAGSUUCGUGCUGGAGCUUCUCCGUCCAUCCUUGGGUGGAUCCUGUGUGGCAUUCAGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUUUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGUUGUUCGUUUUGACUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUUGGGUGAAUGACUCGUUCAUUGACUACAGCUUCUUAGAGGGACGUUCAUCUCUUAAGAUGAAGGAGGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUGUUCCUUGGCCGAGAGGCCUGGGGAAUCUUGUUAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGACUGUUCUGCUUUAUUGUGGUCGGUUGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq new file mode 100644 index 0000000..e28f2e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq @@ -0,0 +1,2 @@ +>d.16.e.A.khaliulini +UCCACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUCGAAGAUUAAGCCAUGCAAGUCUGUGAAUCUUUAUAGAGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCAUCGUGUGAACAUAACCAUGGUAAACUAUGGCUAAAUUGAUGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCGAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAGCAUUUAUAUGUGGUAUGUUUAAAUAGCAUAUCGAAGUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGNGGUUAAAACGUGCGUAGUCUGGUUAAUGGCCUGAAGGUAACAUGCAUUUUCAUAGUGUAGGAUAUUUCAGGAACUUAUGCCUUGAGANAGGGAAGGGGUAAUGUUAUUUGGUAGCGAGAGGUGACAAUCGAUGACCUACCAAGGAGCGACAGAGGCGAAAGCGAUUACCAAUAACUGAUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGAUACUUGUCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUANUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCNGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGUGAGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUAUUUGGUUGAGAGACCAAAUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGAUGGUAGUUUUUAUAAGCGGUAACCAUUCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGUGAGUGUAGACCAAUGGGAGGAUCAGUAUACUUGUGUGAGUUGAUUACGCUUGUGUAUUGUGACUGUUGUUAGCAUGAGCAUAAGAACCCGUGCAACUAGAUUGGAUGUAAGUCGUAACAAGGUAANCAUNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq new file mode 100644 index 0000000..cd1bf7e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.macrogynus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCUUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACAAAAGUCCUGACCUUUACGGAAGGGAUGCAGUUAUUAGAUACAAAACCAACCCGGGCAACCGGUUUUUUGGUGAUUCAUGAUAACUUUGCGGACCGCAUGGCCCUGCCGGCGGCGGGUCAUUCAAAUUUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUGAUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCAGGACCUUUUGGUCUUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAAGGGUUUUUUUCGUAGCUAGCCAUUGUUCCCUUUGCGGUCAAUGUGCAUUUGGCUACAGGCCCUUUUUUUCUGCUAGGAGAUGCGGCUCUUCUGCUUGUCAGCGGGGCUGCAGUUUUCCUAGCACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUCUUUGCCUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUUUGGUUCUAUUUUGUUGGUUUCUAGGACUAGAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGCUUGUAGUUUUUCCAAAAAGACACGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUUUCCUACUCGUUACUUGCUCAUGGGUUUUAUCUCAUGGCACGCAAGUUCUUAGCGGGACUGCUGGCGUUUAGCCAGAGGAAGUUCGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGCAGUCAGCAAGUUUUUUAACUGGCUGUAGUUCUUUCGGGAGCUAUGGUCGAUUUCCUUGCCCGAAAGGGUUGGGUAAUCUUUUGAAACUGCAUCGUGAUGGGGAUCGACCUUUGUAAUUAUCGGUCGUGAACGAGGAAUUCCUAGUAAGUGUGGGUCAUCAGCCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGUUGAGCGAUUGCAGCAAUGUGAACGCCCGACGAGAAAUUGAUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq new file mode 100644 index 0000000..8d7d7a0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.majus +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACCUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACACGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACUAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUACGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUCAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGUUGGGCCGGCCGGUCCGCCUCUGGUGUGCACCGGUCGUCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGGCCUYAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUUCGGUCCUAUUACGUUGGCCUUCGGGAUYGGAGUAAUGAUUAACAGGGACAGUYGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGGUAUCCCUCCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUGAGAGGAAGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq new file mode 100644 index 0000000..8870493 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.michaelis +NNNNNGGUUGAUUCUGCCUGACGUAGAACGCUAGUCUCACAGAUUCAGCCAUGCAAGUAGUAUGUAUGUAAUACACAAUGGCUCAGUAUCGAGUAUAGCUUUGCUCUCCAAGAUGUGAUACUUUCAGGAAACAGAAAAUAAAGCAUCUAUCUUCUAAAGUUUUUUAGAGGAGAGGAGAAGAAGCACUCACCUAUCAGUUAGUAGGUAUGGUAAGGGCAUACCUAGACGAAGACGGGUACGGGGAAGGCAACUUCGAUUCCGGAGAGGGCGCCUUUAGAGAUGGCGACCAGUUCUAAGGAGUGCAGCAGGCUCGAAACUUACCGAAUUAUAGAAUAGAGGUAGUGAUGGAAACGUUUAUAUAGAAAUACUGGUAAAGCAAGUAUUAUUAACUGAGGAAAGCUGGUGCCAGCAGCCGCGGUAAUACUUGCUCCAGGAGCUUAUUCGAUAUGUUGCGGUUAAAACGUCCGUAGUCGCGGCUGGGACUGACCUGUAAUCUAUUUGGUCAACAGAUAGAUAGGGGCAGUAGCAAGUUGGAAAAGAGCAAUUUGGUGUCAGCUAAUGGUAUGGGGAGGGGUAAAGUCUGAGGAUCCUGCAGGAGGAGCAAAGGCGUAAGCACUGACAAAGAUUGAUUCUGUUGAUCAAGGACAGAGGCUAGAGGAUCGAAUACGAUUAGAUACCGUAGUAGUUCUAGCAGUGACCGAUGAUGAUUUUGCCUUAUGCAAUAGAGAAAUCAAAAUAGAUCUCCGGGGAGUACAUGCGCACAGGAACUUAAGAAUUGACGGAAGCUAGCCACAAGGGUUGGAUUGUGCGGCUUAAUUUGACUCAAAGCGGAAAAGCUUACCAAGCUUAUUUAUUCAACGAGUAUUUAUCCGAGAGUAAAAUGGUGUGCAUGGCCGUUCCUAACACAUGGAGUGAUUUUGUGAUUAACCUUCCGUAAUCUGUGUAAAUCCUCAUAAUAGCUUGUUUGAAAAGAACAAUUCGAGCAAGAACAGGUCAGUGAUGUCCUUUGAUAGCUUGGGCUGCACGCGCAAUACAAUUUUUAUGUAGUAAGAUAUAGAUAGGGAUUGAGGGCUGAAAGCGCUCAUGAACACGGAAUAGCUAGUAACGUGAGUUCAAUAUACGGCGAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUGAUUUUUGAGUCAAUUAUAAUUGGCUACUUGAAUGAGUUAUUCUAAAACCGGUACAAGUCGUAACAAGGCUACGGUUGAAGAAUCAGCAGUAGGAUUAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq new file mode 100644 index 0000000..f9edb71 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.plicata +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUCGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAGUUAGAUAACAGGCCGACGCUUGACGAUUCAUAACUUUUUUUCUGAUCGCGCCUUGUGCGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGACGUGAAGGUAUUGUCUUCACGUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAAUAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGCUUGCGUAUGUCACCGAUGAUGCGGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGGGCGUCUGGCGGAGAGUAAAUCUUUGUCGGUCGCGCCUGCUUUUGUGGAGGGCGCGAGCGGGCGGCUUUACUGUCGCGCGUUCGCGGCGCCACCGUUUACUGUGAAUAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUUGUCCUUUUUGUUGGUUUGUGAGGCCGAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAGACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGACUGAAUUUGGCCCGCCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGGCGGGCUAUCGCUUGAUAGUACUGACCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAACCCCCAAACCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUAUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGGGUCAUCAUCCCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUCGGGACCGCGCCGACUAGCGCGUCUAACGCGUUGGUUGUUGUGGAAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq new file mode 100644 index 0000000..88f7469 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.scoticae +CACCAGGUUGAUUCUGCCUGACGUGUGUGCUAGUCUUGGGGACUUAGCCAUGCAAGCUAGCGAAGCGGAGCGGAGCGGCGGACGGCUCAGUAGGACGGCGAUAAUUCACCCGCGGCAGAAGAGGGAUAACCGCGGCAAGCUGCGGCUAAGACAAGGGAGGCUGUGUUGCGGGGAGGCGCACGCAGCGGACACGGCGGCGAAGAUGCCGACCUAUCAGCUAGUAGGUAGGGUAAGGGCCUACCUAGGCGACGACGGGUGACGGGGGGUGAGAGCCUGAUACCGGAGAGGGAGCCUGAGAAACAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGCCCAAUCCCUACGGGGGGAGGCAGCUACAAGACGUGGGGAAGCCCCGGAAAGCACGGCAAAGGAGUGCGUAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGCACAUGUGUGUUGCUGCAGUUAAAACGUCCGUAGUCGGCCAUGAGGGGCAGUGAGGAAAGGGCUGUGCUCAAGGCGGUGUGCAGCGCGGGACCCGGGGCGAGAGGAACGGACGACGGGCGCGGGAUCUGGGGGCGAGAGGUGAAAAUCGGGGACCCUCUGGGGACGAGCGGAAGCGAAGGCGGCGCCCGAGGACGUGUCCGUUGAUCAAGGACGAAGGCCGGAGGAUCAAAGAUGAUUAGAGACCGUCGUAGUUCCGGCAGUAAACGAUGCCAACGGGGCGAAGCCAAGGGGCUGUGUCCGGGAGAAAUUGGAGUGUUUAGGCUCUGGGGAUAGUACGGUCGCAAGACAGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAGCUUACCAGUGCCGCAUGCGCGGGAGAUUGGCGGCGGAGCGCCCCCGAGAUUGCGCAGGGAGUGGUGCAUGGCCGUUUGCAACACGUGGGGUGACCUGUCUGGUUGAUUCCGACAACGCGUGAGGCCUAGGGCGCAGGGCUGUGCGACGGGCCGCGGCAAGCGGCAGGAAGGGAGGCGAUAACAGGUCAGUGAUGCCCUCAGAUGCACUGGGCUGCACGCGCACUACAAUGGCGGGGCGAGACGGAGUGCCGAGAGGUGCGAAGGAGGCCUGGCUGCAGCGGGGAUGGGUGCCUGGAAGGGCGCCCUGAACGAGGAAUUCCUAGUAGCCGCGGGUCACCAAGCCGCGGCGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUACCUAAGAUGGAUGUGCAGGCGAGGUGGCUGGAGGGAAGGCAGCCGAGCCGGUGCAACUAGAUAAGGUAUAAGUCGUAACAAGGCUACGGUUGANNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq new file mode 100644 index 0000000..54b1917 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.thaliana +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACUGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAUUGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAAUGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUCGCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq new file mode 100644 index 0000000..2598366 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq @@ -0,0 +1,2 @@ +>d.16.e.A.verticilliflorum +NNNNNNNNNGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUAAGAUGGUGAUACUGUGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUUUUUUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAAUAAAUCUUGACUUUUGGAAGAGGAGCAUUUAUUAGAUAAGAGGUCAAUGCAAGCUUUGCUUGUUGCACUGAUGAUUCAUGAUAAUAGACGGAUCGCAUGGCCCCUGUGUCGGCGAUGCAUCAUUCAAGUUUCUGCCCUAUNAACUUUCGAUGGUAAGAUAUUGGCCUACUAUGGUGUUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUGCGGGGAGGUAGUGACAAAAAAUAACAAUACCGGGCUUUAACGAGUUUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAUGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGGUUGGGUUUGAUCGGUCUACCUUUGGGUGUGUACCGGUUACCUCGUCCCUCCUACCCAUGAUGCGCUUCUGGCCUUAAUUGGUCGGGUCGUGCCUUGGGUGCUGUUACUUUGAAGAAAUUAGUGUGCUCAAAGCAAGUUUGUGCUCUGGAUACAUUAGCAUGGGAUAACGUCAUAGGAUUUUGAUCCUAUUUGGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGUGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUACUUUUAGGACUCCGUUGGUACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCGUUAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGUGGAGGUACACCUUCAUGGGUAGCUUCUUAGAGGGACUAUGCCAACUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGACUAUUAGGUCUGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUUAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUAUGGCGACGUNNNNGCUUUGCUGUCGGCGAUGUUGUGAGAAGUUCAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq new file mode 100644 index 0000000..f2d9e72 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bigemina +UGAAUAGCAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCGUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAAGUUCGAGGCCUUUUGGCGGCGUUUAUUAGUUCGUUAACCACUUUUUCUGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUGCGAUGUUCCAUUCAAGUUUCUGCCCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUCGUCUUGUAAUUGGAAUGAUGGUGAUGUACAACCUCACCAGAGUACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUCAGCCUCGCGUUUUUUCCCUUUUGUUGGGUCUUUUCGCUGGCUUUUUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUUCAGCAUGGAAUAAUAGAGUAGGACCUUGGUUCUAUUUUGUUGGUUUUGAGCCUUGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACCACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGGGAUUGGAGGUCGUCAUUUUCCGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCUGCUUGGAUGUUGUCCUCGUUUGCUUCUUAGAGGGACUCCUGUGCUUCAAGCGUGGGGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAUCGAGUUUGUCCUGUCCCGAAAGGGUUGGGUAAUCUUUAGUGUGCAUCGUGUCGGGGAUUGAUUUUUGCAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUUUUCCGAUUCGUCGGUUUUGCCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq new file mode 100644 index 0000000..2c3855a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bovis +NNNNNNNNNNNNNNNNNNNNNNNNNNNNUAGUCAUAUGCUUGUCUUAAAGACUAAGCCAUGCAUGUCUAAGUACCAGCUUGUUACGGUGAGACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCACUUUGCUAUGGAUAACCGCGCUAAUUGUGUGGCUAAUACACGUUUGAGGUUAUUACCGCGUUUACUGGUCUUGUGAUUUACAGUAACCUGCGACUCGCUUUUUGCGAUAUUCCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUCCCGAGGCAUCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGCGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUACCAAUACGGGGCUACUGCUCUGUAAUUGGCAUGGGGGCGACCUUCACCCUCGCCCGAGUACCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUACUUCACGUCCCCCGCUUGGUCCUUUCCUCGCCGGGACGCCUCGUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGUUUCGCCUGUAUAAUUGAGCAUGGAAUAACCUUGUAUGACCCUGUCGUACCGUUGGUUGACUUUGGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUACUCGACUGUCAGAGGUGAAAUUCUUAGAUUUGUCGAUGACGCACGACUGCGAAAGCAUUUGCCAAGGACGCUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCUUAAACUAUGCCGACUAGGGAUUGGUGGUCGUCGCCUCGACUCCGUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGCGUAAGGAUUGACAGGUUGAUUGUCCUUUCUUGAUUCUCUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAUUUAGUCGCUCGGUCUCCGUCCGUGCGCACUUCAUAGAGGGACUCUGCGGCGUCAAGCUGCGGUGAGGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCUUGCCUCGUGUUUACCCUCGGCCGAUAGGCCUGGUAACCCCUAGUCUGCAUCGUGUUUGGGAUUGAUCUUUGCAAUUCUAGAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGAACCUGCUUGCGCGAUCCGUCGCCGCUCGCGGCCAGGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq new file mode 100644 index 0000000..2699b8a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.canis +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGGUAUUCUUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACACGUUGGAGGCCUUUUGGCCGCGUUUAUUAGUUGUAAACCUCCGCUUGGUUUUCGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUAGCGAUGGACCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUAAUGUCUUGUAAUUGGAAUGAUGGUGACUUAAACCCUCACCAGAGUAGCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUUUGCUUGGCGGUUUGUUGCCUUUGUGGCUUGAUUCCGCUUGGCUUUUGGCUUUUUGCCUUAUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUGUAGCAUGGAAUAAUAGAGUAGGACUUUGGUUCUAUUUUGUUGGUUUGGGAACCUUGGGUAAUGGUUANUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGACGUUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGUGAUUGGAGGUCGUCGUUUGUUUGACCCCUUCAGGAGCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAACGGUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCGCUGGUUACUUGGUUUCCCGCUGCUUCUUAGAGGGACUUUGGGGCUUGAAGCUCCAAGGAAGAUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUGUUGCCCCUGGCCGAGAGGUCUGGGUAAUCUUUAGUAUGCAUCGUGACGGGGAUUGAUUUUUGUAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUAUUCCGAUUCGUCGGUUUUGCCGUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq new file mode 100644 index 0000000..dc4b931 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq @@ -0,0 +1,2 @@ +>d.16.e.B.coli +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUAACUACACAGUAAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUACAUUAAAUGGAUAACUGUAGAAAAACUAGAGCUAAUACAUGCCGAGGCCGUAAGGUCGUAUUUAUUAGAUAUUCCAAUUAAGGUGAAUCAUAAUAACUUCGCAAAUCGCGAUUUUGUCGCGAUAAAUCAUCCAAGUUUCUGCCCUAUCAUGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCUACGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUGGUGACAAGAUAUAACGACGCAAUUUAUUUUGUGAUUGUAGUGAGGGUAUUCCAAACCGAACCACUAGUACGAUUAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCAAGGCGUGUAUACUCUUUUUGAGUAUGCUACCUACUAGUCUCUGACUGUUACUGUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCAAGAAUACAUUAGCAUGGAAUAACGAAUGUGUCUAGAAUCUUGGUUAAUUCUAGAUUGCGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACUAACGUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGAUAGGGGAUCAAAGACAAUCAGAUACUGUCGUAGUCCUAUCUAUAAACUAUGCCGACUAGGGAUUGGAAUGGUUAUAACGCCGUUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGACUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAACUAGUCUAAUCCAUUUUAUGGAAUAUGACUUCUUAGAGGGACUAUGUAUUUAAAUACAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAUAUGUCCUGGGCUGCACGCGUGCUACACUGAUGCAUACAACAAGUGCCUAGCCCGCCAGGGUAUGGCAAUCUCGAAUAUGCAUCGUGAUGGGGAUAGAUCUUUGCAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGUGCAAGUCAUCAUCUUGCAUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUACCGGGUGAUCCGGUGAACCUUUUGGACCGCGAUGCGGAAAAAUAAGUAAACCAUAUCACCUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq new file mode 100644 index 0000000..16f916b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq @@ -0,0 +1,2 @@ +>d.16.e.B.emersonii +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCCAUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACUCAAGUCCUGACCGCUUGUCGGAAGGGAUGCAGUUAUUAGAUACAAAACCAGCCCCGGGCAACCGGGUUUUCUGUUGGUGAUUCAUGCUAACUUUGCGGAUCGCAUAGCCUUUGUGCUGGCGACGGGUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGUAGGAUAGAGGCCUACCGUGGUGAUAACGGGUAACGGGGAAUAAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCGGGGCCUUUUGGCCAUCGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAGGGCUGUCUUUGUCACCUGGCCACUGAGCCUUURCGGCCAGUGUUGCUUUCGGGUGCGGGCCCUUUAUUUCUGCUGGGUGCUCCUUUGGGUUGGCUUUUGCUAGCUCGGGGGAUGUCUGCCCAGCACGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUUUAAGCUUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUCUGGUUCUAUUUUGUUGGUUUCUGGGACUGGAGUAAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGUCAUGUAGUUAUUCACAUAAAAGACGCGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGAUCUGCUAAUUAGUUGGGCUUGCAUUUAUGCAAGUAAUCCAACUUCUUAGAGAGACUGCUGGCGUUUAGCCAGAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUAAGGUCAGCGAGUUUCAACUUGCUGGCUUAAGUUGAGUUUCGGCUCGGCUUAAGCUGGGAUUCCUUGGCCGUGAGGUCUGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUUGACCUUUGUAAUUAUCGGUCAUGAACGAGGAAUACCUAGUAAGUGUGGGUCAUCAACCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGCCGGGUGAUUGCAGCAAUGCGAACACUUGGCGAGAAAUUGCUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq new file mode 100644 index 0000000..3c16027 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gelatinosum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUACGACAAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAAAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGUGCGCGCCGGGCUGUGCGCGUAAUGCGUGUGGCGCGGGGCGUGCUUUUGUGGAGGGCGGCCGCUCGUGGCUUAACUGUUGCGGGUGUGCCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGUACCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUUGGGACUGCUGCGAUCGGGGUUCAUUCUCUGGCCGCGGUGGGAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq new file mode 100644 index 0000000..76f7cfc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gibsoni +NNNNNNNNNNNNNNNNNNNNNNNNNCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUUUUAUAUGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAAAUUCGUUUCUACAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAUGAUCGAGGUCCUUCUGGACUGCGUUUAUUAGACUCGAAACCUUCCCGCUUCGGCGGUUCCCGGUGAUUCAUAAUAAACAGCGAAUCGCAUGGCUUUUGCCGGCGAUAAUUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCAGCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACGGACACCGUGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUAAGCUUUGUAAUUGGAAUGAUGGGAAUCCAAACCCCUUCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGCCGCCGGGACUUCGUUCCCUUCGGGCUUCGUUUUCUCGGUGGCAUCCCUCUGGUUAAUUUGGGCCUCGGCCCUCUUUUUCCAGUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCCUUGAAUACUUCAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUCAGGACCAAAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAUUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAUAGUUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGCAGCUGAGAAUAAACUUUGUUGUUUCAGCAUUGCUUCUUAGAGGGACUUUGCGGUCAUAAAUCGCAAGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUUUUAUCCUUGCCCGAAAGGGUUAGGUAAUCUUUAGUAUGCAUCGUGAUGGGGAUUGAUUAUUGCAAUUAUUAAUCAUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGACGUUUCUAAUUCGUUAGCAACGUCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq new file mode 100644 index 0000000..ee77a35 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq @@ -0,0 +1,2 @@ +>d.16.e.B.hamifera +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAACUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGGAACGCCGUGGUACAAAUUGGAUAUACAAACCAAUGUUUGGUGAUUCACAAUUUAUUUUCUGAUCGCACUUAUGUGCGACGCAUCGUUCAAAUUUCCGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCCAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGCUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCGGCGCGGGGCGUCCUCACGGACGGUUCUGCGGCGGCCGCCUUUGUGGAUGGGGGCUAGAGCGAUGUUUCAUUACAUUGCACUAGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAGUAAAUUAGCAUGGAGUAAUAGAAUAGGACCUGUGUUCUGUUUUGUUGGUUUGUGAGGCGCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCGGUUACCGAUUUCUGGUAGCCAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGGGCGAAAGCUUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGACAGACUGUGUUUCACGGACUGUCUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq new file mode 100644 index 0000000..f71fd58 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq @@ -0,0 +1,2 @@ +>d.16.e.B.investiens +NNNNNNNNNNNNNNNNNNNNNNNUAUAUGCUUGUCUAAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGAACGCAAGUUCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGGGCCCGGUGCUGUGCGCGUAAUGCGUGCGGCGCUUGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUUGCUGUCGCGGUGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUGUCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGCUUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUUAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGAUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq new file mode 100644 index 0000000..d4c4c9b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.macrosporum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGUUAUAGUUUCUUCGAUGUUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAUCACGCGGGGCAACCCGUGGUACGAAUCAGAUAUCAAACCAAUGUAUGGUGAUUCAUGAAUAUUUUUCGGAUCGCACUGUAUGGUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUAUCAUGGUUGUGACAGGUGACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGCAUAUGCGUCUUCUAAUUGGAAUGAGAACACGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUGUUGGCACGGGCCGGGCUGUGCGCGUCAUGCGUGCGGCCACGGGACGUGCUUUUGUGGAUGGCGGCCGCACGUGGCUUAAUUGUUGCGGGCGUGCCGGCGCCACCAUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACGUUAGCAUGGAAUAAUAGAAUAGGACUCGUUUCUAUUUUGUUGGUUUGUCAGUGGCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUCUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACUGCUGCGAAAGCGUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCGGGUACCCGUGUGGUAGCUGCUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGGCCAACGGGUGAGGAUACGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGACCGCCACGACCGGGGUUUACUCUCUGGCCGCAGUGGAAACUUAUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq new file mode 100644 index 0000000..2225903 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mandrillaris +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUUCCUUUAUUUUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCCCAAAGUCCCGACUGGGGGUCGCAAGGCUCUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCGAUGCAGGGUGGCUUGCUGCCCUGACCCAACGGUGAUUCAUAAUAACUCUAUCGAAUCGCACCAUGGUCCCCUCGUGGGAUCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGUCUUGCAAAAAGACUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUCGGAGUGUUUGGCAGGGCUGGUCCGCCGAAAUAGGUGAGCACCGUCCUGCCCGCUCCUCUUGUCCGGGUUCUCAUCCCUGCUAUUCACUUAGUGGGGAACCAAAGGUUCUGUUCCCGCCCUCGGGUGGGGCAGGACUGGAGGCCCGGACCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGACAAGUCAAAACUGUCAUUGAAUAUAUUAGCAUGGGAUAAUGGAAUAAGCCUCUCUGCUUAUUUUGUUGGUUUCUAAGUAGGGAGAAAUGAUUGAUAGGGACAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUGGGAGACGUUACACAUGCUGCCCAAAAGGCAGCAUGGAGGACUCCCCCAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUCAUGCCAAUCCUGCUAUUCAAAACCAGGGGGUGAGCGCGGUGCGGUCGGCUCCAAUCUUCGGGUUGGGGUCGGUUCGUGCCCCUUGCCUUCUGGCGGUUGGAUUGGUAGAAGUACUUCUUAGAGGGACAAUCGGUGAUUAGCCGAGGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUUCAACGAGUGCCACACCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAAUUUAAUCGUGAUGGGGAUAGAUUAUUGUAAUUGUUAAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUCUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCUUCGGAGCUCGACCUCUCCGCGAUCCGGGCAACUGGGUCGUGAGGUUGGGCAAAGUCGAUUAAAUCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq new file mode 100644 index 0000000..5e88cb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mediterranea +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAACCUGCGGAUGGAUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACCUCUGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAUGCUUCGGCAUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUUGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGACACGGCGUGGUCGUCUCAAUGAGUCUGUACCGUCGCAUGUGUCGCCAUCCUUGGUUAAAACUUGUCUGGCAUUAGGUUGUCGGGCUUGGGGAUAGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAAGACCCAGGUUCUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCCGACUCCGUCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGGCGUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGUAAUGAAUUUCAUUGCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGACCGAGAGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGACUUUAGGUUGAUUUAUUUCGACUUAAGGUUGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGUGAACCNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq new file mode 100644 index 0000000..341c71c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.1 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUAUUUUACGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAAUUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUUCCCUUCGGGGUUCUAUUUUCCGGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGUACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq new file mode 100644 index 0000000..e6f2747 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.2 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCAUCUGGAUUUGGUGCCUUCGGGUACUGUUUCCAGGGUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAACCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAGCGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq new file mode 100644 index 0000000..21c1754 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.3 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUACGCGUGGCGUUUAUUAGACUUUAACCAGCCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUUCGAGCGUUAUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUAUCCUUAAUUGGUUACUAUCUUCCAGUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUAUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUAGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAGAAACGUGGAUUCGUCCUUCGUUUUUCGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq new file mode 100644 index 0000000..e92416b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.4 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq new file mode 100644 index 0000000..ac524f3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.5 +NNNNNNNNNNNNNNNNNNNNNCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUCGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq new file mode 100644 index 0000000..f694c36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq @@ -0,0 +1,2 @@ +>d.16.e.B.moritziana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCCUGCAAGUGCCUGUAUGAGUGUUUAUAUAACGAAACUGCGAAUGGCUCGGUAAAACAGUAAAAAUUUUUUCGGAGAAAAUACUACUCGGAUAACCGUAGUAAAGCUAGAGCUAAUACGUGCUACAAAAUGAGGCGAGCAAUCGUUCUCGUGGUACAAAAUAGAGAUACAACCCAGUUUUUACUGGUGAUUCAUACUUUUUUCUGAUCACACUUUUAUGUGUGUGACGCUCCGAUCAAAUUUCUGACCUAUCAACUAUGAUGGUAAGGUAGUGGCUUACCAUAGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGAACUUCGGGAGGUAGUGACAAGAAAUAGCAAUAGGGGGACCAAUGGUCUCUCUAAUUGGAAUGAAAACAAUGUAAACUCCUUAUUGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAACUUUGGCGAUGGUUGCUGAAACUCCGUAAGGAGAUUGAUGUAGCCUCGUCCUUGUGGAUUUUUGGGGGUGUGGUGGUACUUUAUUGUAUUGCUGCAUUUCCGCCACUGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAAGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUAUUGGUUUGUCUGUAUCAGGUAAUGAUUAACAGGGACGGUCGGGGGCAUUUGUAUUCCAGCGUUAGAGGUGAAAUUCUUGGAUCGUUGGAAGACAAACAGCUGCCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUGUAAACUAUGAGGCCUGGGGAUCGGGCGUGGCCUAUUGGUACGUUCGGCACCCUCCGGGAAACCAAAGCUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGAAAAUGCUAUUAAACUGCGGUAGCAUCGAAAAUUUAAUCUUCUUAGACGGACUGUAGGCGUAUAGUCUAUGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAAUGGCUCAACGGGUGAGGUAGUGCGAAAGCAUGACCCAAUCUCUAAAUCCAUUCGUGCUGGGGAUAGAAGCUUGCAAUUAUCCUUCUUGAACGAGGAAUACCUUGUAAGCGCGAGUCAUCAUCUCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGAGCUGGGCGAAUUAGUGUUUAUUCACGAAUUUCCUGGUUUAAACUUGGUCAAACCUUACUACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq new file mode 100644 index 0000000..e9dcbc1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.ostreae +NNNNNGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCCAAGUAUAAACACGUUUGUACUGUGAAACUGCAGAUGGCUCAUUAUAACAGUUAUAGUUUAUUUGACAUUGAACUGUUACACGGAUAACCGUAGUAACCUAGGGCUAAUACGUGACAAACCCUGCCUCGGCGGGAGUGCAUAUUAGCUGAAAACCAACUUUGGUUGAAUAAUAAUAUUUGUCGGAUCGCGUUGGCUUCGCCAGCGACAUGUCAUUCAAGUUUCUGACCUAUCAGCUUGACGGUAGGGUAUUGGCCUACCGUGGCUUUGACGGGUAACGGGGAAUGCGGGUUCGAUUCCGGAGAGGCAGCCUGAGAAACGGCUACCACAUCCACGGGAGGCAGCAGGUGCGCAAAUUACCCAAUUCUGACUCAGAGAGGUAGUGACAAGAAAUAACGAUAUGCGGCCAACUGGUUGCUUAUCCGGAAUGAGAACAAUGUAAAAACCUUAUCGAAUUCCAGCGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCGCUAGCGUAUACUAAAGUUGUUGCUGUUAAAACGCUCGUAGUUGGAUAUCUGCCCCCGGGCCGGCCCGGUCGUCCGCGACCGCACACACGUGCAGAGCGGCCGCCCGGGGGCAUAAUUCAGGAACGCCGGUCUGGCCAUUUAAUUGGUCGGGCCGCUGGUCCUGAUCCUUUACUUUGAGAAAAUUAAAGUGCUCAAAGCAGGCUCGCGCCUGAAUGCAUUAGCAUGGAAUAAUAAGACACGACUUCGGCGCCGCCUCGGCGGUUGUUUUGUCGGUUUUGAGCUGGAGUAAUGAUUGAUAGAAACAAUUGGGGGUGCUAGUAUCGCCGGGCCAGAGGUAAAAUUCUUUAAUUCCGGUGAGACUAACUUAUGCGAAAGCAUUCACCAAGCGUGUUUUCUUUAAUCAAGAACUAAAGUUGGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCCAACCAUAAACGAUGUCAACUAAGCAUUGGGCUAUCAAACUUCCUCAGCACUUUUCGAGAAAUCAAAGUUUUCGGACUCAGGGGGAAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGAAGGGCACCACAAGUUGUGGAGCCUGCGGCUUAAUUUGAUUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUAAAGUUCUUUCUUGAUUCUAUGCAUGGUGGUGCAUGGCCGUUCUUAGUCCCUAGGGUGACCCCUCUGGUUAAUUCCGAUAACGGACGAGACCCCACCCAUCUAACUAGCCGGCGCUAACCCGGCGCUCGGCGCCAGUUAGCGGGGUGCAGCAUUGCGCGCCCGGCUUCUUAGAGGGACUAUCUGUGUCUCCAGCAGAUGGAAGAUUGGGGCAAUAACAGGUCAGGAUGCCCUUAGAUGCUCUGGGCUGCACGCGCGCUACAAUGGUGCGUUCAACGAGUUUGACCCGGCUUGACAAGGCCGGGUAAUCUUCAACGCGCACCCAAGUUGGGAUAGAUGAUUGCAAUUGUUCAUCUUGAACAAGGAAUAUCUAGUAAACGCAAGUCAUCAACUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUUCUACCGAUUGAAUAAUGAGGUGAAUUAGGUGGAUAAGAGCGCUCCGCGUUCUUAGAAGCUUCGUGAACCUUGUUAUUUAGAGGAAGGAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq new file mode 100644 index 0000000..86d81a3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq @@ -0,0 +1,2 @@ +>d.16.e.B.pacifica +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACUGUUCGCGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAAGCUUCGGCUUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUCGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGAGUUCGUUUGGCCGGCCGUAAAGGUCUGUGCCGAAAUGUUAUUCGCCAUCCUUGGUGUAAUCUUGUCCGCCAUUAAGUUGUGUGGGCUUGAGGAUGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAGGACCCUGGUACUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCUGACUCCGCCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGCGAAUGAAUUUCAUUCCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGCUCGAGAGGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGAUCGUUUGGUGGUUCAUUCUGCCUUACGAUCGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq new file mode 100644 index 0000000..8e89a0b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.plumatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCCAGUGACCGUAAGGAACGGCAGACAGCUCAGUAAUACAGUUAUAAUUUACUCGUAGGAUAUGGAUAACCAUGGAAAACUAUGGCUAAAACAUAGGGAAAAUACCGUCACAGGGAAUUUUGAGGUACUUGAUACGAUUAAGUUUCUGACCUAUUAGCUAGAUGGUAAGGUAAAGGCUUACCAUGGCUGUGAUGGGUAACGGGGGAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAUCGGGAGAGGUAGUGAAGAGACGUGGAAUAUAAUUUAGCGAGGGCAUAUUAAAUGGCAGCCUGUAAACUGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAACUAUUGUUGCUGUUAAAACGUCCGUAGUAGAUUAUGCUGUUACUAUGACAAAAAUGUAUAUCUCAAAUGAAAUAUAUAGCAUAGUACAAAGUAAAGAUAGGAACAGAUGAUGGCAGCAGUAUUUAAUAGUUAGAGGUGAAAAUCGAAGACCUAUUAAGGACUAUCAGAAGCGAAAGCGGCUGUCAAGGAUGUCUCCGUUUAUCAAGGACUCAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACCAUGCCAACUAGGUGAGGCCAUUAGGCUACGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCAGGGGAUAGUACGAAAGCAAUUUUGAAACUUAAAGAGAUUGACGGAAGGAUACCACAAGGAUUGGAUUGUGCGGCUUAAUUUGACUCGACGCGGGACAACUUACCAGGGCCGAAUGUCUAUGAGAUUGGCGAUUUGAGAGAAUUCCCGAGAUUAGACAAAGGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUUCCGAUAACGCGUGAGGCCCUAAAUGCAACAGUGUUGUAUGACGGACAGUGCAAACUGUAGGAAGGAGGGCGAUAACAGGUCAGUGAUGCCCCCAGAUGUUCUGGGCUGCACGCGCAAUACAAUAUAUGAAAUAGAAUAGAGUGUGAAAACACAUCAUUAAAUUCAUAUGUACCAGGGAUAAGCGCUUGUAAAUGCGUUUUGAACAUGGAAUUCCUAGUAAUCGCAGGUCAUUAUGCUGCGAUGAAUGUGUCCCUGUUCUUCGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUAUAGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq new file mode 100644 index 0000000..0f910b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq @@ -0,0 +1,2 @@ +>d.16.e.B.rodhaini +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUUUUAUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCAUGUGCGUUUACGCAGCGUUUAUUAGACUAAACCAUCCCCUUUGGGUACCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUAACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUCAAAGCUUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUCGUCGUUUAUGCUCGCUUCCAAGCGUUUGUAAUUGACUUGGCAUCUUUGUGGAUUAGUGCGCAAGCAUUUUUCCACUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAAUUGCCUUGAAUACUACAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUUUGAGCCAUAGUAAUGGUUAAUAGGAGCAGUAGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAAAUGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUAUGGGACUACAUUUCAGUCUCAUUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGGAAGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAAGAACUUAGAUUCGUCUAAAGUUUUUUGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq new file mode 100644 index 0000000..7343a20 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vagum +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGGCAACUUUUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACGAUUUCUUUUCUGAUCGCACUAUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACGCAGGGCGUCUUUGCGGACGGUUCUGUAUCGGCCGCCUUUGUGGAGGGGGGCUUAGCGGUGCUUUAUUGCCUUGCUAAGUCGCUGCCACCGUUUACUGUGAAAAAAUUGGAGUGUUCAAAGCAGGCGUUUGCCUUGUACACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUGUUGGUUUGUGAGAAUUAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCUGCCGUCAGAGGUGAAAUUCUUAGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGCGCUGCUUUAUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCUCUUUCGGUAGCGAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUAGGCGAGAGCCUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGUCGGACUGUGUUUUACAGACCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGACCCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq new file mode 100644 index 0000000..acaa018 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vavrai +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUAAAGAUUAAGCCAUGCAAGCCAGCGAAGGUAACGGAGCGGCGAACGGCUCAGUAGGACAGGGUUAUCUGACCACCGAACAGGAUAACCGCGGUAAUCUGUGGCUAAUACGUGUGUGGGUGAGACUCUGCCCUAUCAGCUUGGGGGUACGGUAAGUGCGUACCCUUGCGACGACGGGUAACGGGAAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCACGUCCAAGGAUGGCAGCAGGCGCGGAAAUUACCCACUUGGAGGACCAGAGGUAGUGACGAGGCGUUUUUAAUGAGAAUAGUGUAAAAAGCUGUUCGAAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUCUGCGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCGGGUUAUUUGCCAGCAAUAAAGGUGCAGUCUCUAACUGUAUAUUGUGCUGGUACUUUGAUCUAGGAACUGGAUAAAGGUUAUGGUAUUCGACAGCGAGGGGUGAAAAUUAAUGACCUGUUGAGGAGCGACUGAUGCGAAAGCGGUAAUCUAUGACGGGUUUGACGAUAAAGCGCGUAGGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCUUUGCAGUAAACGAUGCCAACAGGAAUGCAAGUGCUGUGUUCCUAGGGAAACUGAGUGUAUGGGCUCUGGGGAUAGUACAGGCGCAAGCUAGAAACUUGAGGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGACAACUUACCAGGGUAUGUGACAUUGAGCGAAGAGCAUGGAUGCGAUCUGUGUUCUGAUGAUGUUACGUGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAUCCGAUAACGCGUGAGACCCUGGAUAAUGACGAUACUUGACAAGAGUAGGGAAGCUCGGGUCGAUAACAGGUCUGUGAUGCCCAUAGAUAUUUUGGGCGCCACGCGCACUACAUUGGGGAUGGUUACGUGAAACGGAACAUCCUUUCGGUUGGGAUUGACGUUUGUAAAUACGUCAUGAACUCGGAAUUCCUAGUAAUUUGUUGUCAUUAACGACAUAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGAAUGUGCGGAUGAAGUUGGUUAGGUCAAAAGAAUCCGUGCGAUUAGAUUGGAUACAAGUCGUAACAAGGUUACUGUAGGAGAACCUGCAGUAGGAUCAAUAA diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm new file mode 100755 index 0000000..41ffe28 --- /dev/null +++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm @@ -0,0 +1,60 @@ +#!/usr/bin/perl +package Scoregtwithunafold; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[3]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + my $gtfold_energy = `head -1 $gtoutfilename`; + my $unafold_energy = `head -1 $unaoutfilename`; + + if ($gtfold_energy =~ m/([0-9.-]+$)/) { + $gtfold_energy = $1; + } + if ($unafold_energy =~ m/dG = ([0-9.-]+)/) { + $unafold_energy = $1; + } + + if ($gtfold_energy eq $unafold_energy) { + $logger->info("TEST PASSED: $seqname: Energy Value matched for MFE -> $gtfold_energy"); + } + else { + $logger->error("TEST FAILED: $seqname: Energy Value Not Matched for MFE -> gtfold = $gtfold_energy, unafold = $unafold_energy"); + } + #my $ctcmd1 = "/usr/local/bin/ct-energy $gtoutfilename"; + #my $ctcmd2 = "/usr/local/bin/ct-energy -s DAT $unaoutfilename"; + #system("$ctcmd1"); + #print "ct-energy = "; + #system("$ctcmd2"); + } +} +1; diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm new file mode 100755 index 0000000..16e53c3 --- /dev/null +++ b/gtfold-mfe/tests/scripts/start_test.pm @@ -0,0 +1,94 @@ +#!/usr/bin/perl +use strict; +use warnings; +use Module::Load; + +use File::Basename; +use File::Path; +use Log::Log4perl qw(:easy); + +require 'test_utils.pl'; + +my $configdir="../config"; +Log::Log4perl::init( "$configdir/root-logger.conf" ); +my $logger = Log::Log4perl->get_logger; + +$logger->info("Starting Tests..."); + +# Read Parameter File +my $paramfile = "$configdir/test-params.conf"; + +# Create Work Directory +my $workdir = "../work"; +$logger->info("Deleting directory $workdir"); +rmtree($workdir, 0, 1); +$logger->info("Creating work directory $workdir"); +mkdir $workdir; + +my %Config; + +%Config = load_config_file($paramfile); + +###### Prepare a Hashmap of Sequences ###### + +my %Sequences; +my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}}; + +my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"}; +my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"}; + +foreach (@seqdir_arr) { + + opendir(DIR, $_) || die $!; + while (my $seqfile = readdir(DIR)) { + + my $seqname; + my $path; + my $suffix; + ($seqname,$path,$suffix) = fileparse($seqfile); + + if (-d $seqfile) { + next; + } + + $seqfile = "$_$seqname"; + my $seq_include = (not defined($seq_include_regex)) || ($seqname =~ /$seq_include_regex/); + + my $seq_exclude = (not defined($seq_exclude_regex)) || ($seqname !~ /$seq_exclude_regex/); + if ( $seq_include && $seq_exclude ) { + $Sequences{$seqname} = $seqfile; + $logger->info("Selected Sequence ... $seqname"); + } + } +} + +my $test_include_regex = $Config{"G_INCLUDE_TESTS"}; +my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"}; + +my $test_list_file = $Config{"G_TEST_LIST_FILE"}; + +open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file"); + + while () { + + my $testname = $_; + chomp($testname); + + $testname =~ s/^\s*//; # Remove spaces at the start of the line + $testname =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($testname !~ /^#/) && ($testname ne "") ) { # Ignore lines starting with # and blank lines + + my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/); + + my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/); + + if ( $test_include && $test_exclude ) { + my $module = $testname; + load($module); + $module->test(\%Config, \%Sequences, $logger); + } + + } + + } + diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl new file mode 100755 index 0000000..2191bdf --- /dev/null +++ b/gtfold-mfe/tests/scripts/test_utils.pl @@ -0,0 +1,84 @@ +#!/usr/bin/perl +use strict; +use File::Path; + +sub load_config_file() +{ + my $paramfile = $_[0]; + my %Config; + my $Name; + my $Value; + my $line; + my $orig_value; + open(PARAMFILE, $paramfile) || die("Could not open file: $paramfile"); + + while () { + + my $line = $_; + chomp($line); + + $line =~ s/^\s*//; # Remove spaces at the start of the line + $line =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($line !~ /^#/) && ($line ne "") ) { # Ignore lines starting with # and blank lines + ($Name, $Value) = split (/=/, $line); # Split each line into name value pairs + + if ($Name =~ /G_INCLUDE_SEQUENCES|G_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) { + $orig_value= %Config->{$Name}; + $Value =~ s/[.]/\\./g; + $Value =~ s/[*]/.\*/g; + if ($orig_value ne "") { + $Value = $orig_value."|".$Value; + } + } + + if ($Name eq "G_SEQUENCE_DIR") { + my @seqdir_arr = %Config->{$Name}; + push (@{%Config->{$Name}}, $Value); + next; + } + + %Config->{$Name} = $Value; # Create a hash of the name value pairs + + } + } + + $Value = %Config->{"G_INCLUDE_SEQUENCES"}; + +# printf($Value."\n"); +# if ("rad" =~ /\G$Value/) { +# printf("matched1\n"); +# } +# printf($Value."\n"); +# if ("a.a.dvdsf" =~ /\G(rad|a\..*)/g) { +# printf("matched2\n"); +# } +# printf($Value."\n"); +# if ("daf" =~ /\G$Value/) { +# printf("matched3\n"); +# } +# printf($Value."\n"); +# if ("d.afdsf" =~ /\G$Value/) { +# printf("matched4\n"); +# } +# printf($Value."\n"); +# if ("acc1" =~ /\G$Value/) { +# printf("matched5\n"); +# } +# printf($Value."\n"); +# if ("acc11" =~ /\G$Value/) { +# printf("matched6\n"); +# } +# printf($Value."\n"); +# if ("a..afjlhfj" =~ /\G$Value/) { +# printf("matched7\n"); +# } +# printf($Value."\n"); +# if ("afdjs" =~ /\G$Value/) { +# printf("matched8\n"); +# } + +# printf ("@{%Config->{'G_SEQUENCE_DIR'}}\n"); + + return %Config; +} +1; From f7923e671690bbe3cf7561a8304c18f1e7ba0d1d Mon Sep 17 00:00:00 2001 From: Manoj Soni Date: Sat, 1 Oct 2011 17:46:55 -0400 Subject: [PATCH 146/187] Partition Function calculation implementation completed --- gtfold-mfe/src/partition-func.c | 443 ++++++++++++++++++++++++++++++-- 1 file changed, 423 insertions(+), 20 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 215b1ba..23ff1c9 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -1,4 +1,6 @@ #include +#include +#include #include "partition-func.h" #include "energy.h" #include "algorithms-partition.h" @@ -9,7 +11,7 @@ #include "omp.h" #endif -#define DEBUG_PF 1 +//#define DEBUG_PF 0 #ifdef DEBUG_PF #undef Ec @@ -62,6 +64,58 @@ static void calc_s2(int i, int j); static void calc_s3(int i, int j); static double f(int j, int h, int l); +static double get_u(int i, int j); +static double get_ud(int i, int j); +static double get_up(int i, int j); +static double get_upm(int i, int j); +static double get_u1(int i, int j); +static double get_u1d(int i, int j); +static double get_s1(int i, int j); +static double get_s2(int i, int j); +static double get_s3(int i, int j); + + +static void set_u(int i, int j, double val); +static void set_ud(int i, int j, double val); +static void set_up(int i, int j, double val); +static void set_upm(int i, int j, double val); +static void set_u1(int i, int j, double val); +static void set_u1d(int i, int j, double val); +static void set_s1(int i, int j, double val); +static void set_s2(int i, int j, double val); +static void set_s3(int i, int j, double val); + + +void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){ + printf(msg); + printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal); + printf("\nprogram is exiting now due to above error\n"); + exit(-1); +} + +double get_u(int i, int j) {if(u[i][j]==-1) errorAndExit("get_u entry is -1.",i,j,-1,0); return u[i][j];} +double get_ud(int i, int j) {if(ud[i][j]==-1) errorAndExit("get_ud entry is -1.\n",i,j,-1,0); return ud[i][j];} +double get_up(int i, int j) {if(up[i][j]==-1) errorAndExit("get_up entry is -1.\n",i,j,-1,0); return up[i][j];} +double get_upm(int i, int j) {if(upm[i][j]==-1) errorAndExit("get_upm entry is -1.\n",i,j,-1,0); return upm[i][j];} +double get_u1(int i, int j) {if(u1[i][j]==-1) errorAndExit("get_u1 entry is -1.\n",i,j,-1,0); return u1[i][j];} +double get_u1d(int i, int j) {if(u1d[i][j]==-1) errorAndExit("get_u1d entry is -1.\n",i,j,-1,0); return u1d[i][j];} +double get_s1(int i, int j) {if(s1[i][j]==-1) errorAndExit("get_s1 entry is -1.\n",i,j,-1,0); return s1[i][j];} +double get_s2(int i, int j) {if(s2[i][j]==-1) errorAndExit("get_s2 entry is -1.\n",i,j,-1,0); return s2[i][j];} +double get_s3(int i, int j) {if(s3[i][j]==-1) errorAndExit("get_s3 entry is -1.\n",i,j,-1,0); return s3[i][j];} + + +void set_u(int i, int j, double val) {if(u[i][j]!=-1 && u[i][j]!=val) errorAndExit("set_u entry is not -1.\n",i,j,u[i][j],val); u[i][j]=val;} +void set_ud(int i, int j, double val) {if(ud[i][j]!=-1 && ud[i][j]!=val) errorAndExit("set_ud entry is not -1.\n",i,j,ud[i][j],val); ud[i][j]=val;} +void set_up(int i, int j, double val) {if(up[i][j]!=-1 && up[i][j]!=val) errorAndExit("set_up entry is not -1.\n",i,j,up[i][j],val); up[i][j]=val;} +void set_upm(int i, int j, double val) {if(upm[i][j]!=-1 && upm[i][j]!=val) errorAndExit("set_upm entry is not -1.\n",i,j,upm[i][j],val); upm[i][j]=val;} +void set_u1(int i, int j, double val) {if(u1[i][j]!=-1 && u1[i][j]!=val) errorAndExit("set_u1 entry is not -1.\n",i,j,u1[i][j],val); u1[i][j]=val;} +void set_u1d(int i, int j, double val) {if(u1d[i][j]!=-1 && u1d[i][j]!=val) errorAndExit("set_u1d entry is not -1.\n",i,j,u1d[i][j],val); u1d[i][j]=val;} +void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAndExit("set_s1 entry is not -1.\n",i,j,s1[i][j],val); s1[i][j]=val;} +void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;} +void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;} + + + double f(int j, int h, int l){ if(j - 1 == l) return 1; @@ -69,6 +123,37 @@ double f(int j, int h, int l){ return exp(-Ed3(h,l,l+1)/RT); } +void printMatrix(double** u, int part_len){ + int i,j; + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } +} + +void printAllMatrixes(){ + printf("\n\nAfter calculation, u matrix:\n\n"); + printMatrix(u,part_len); + printf("\n\nAfter calculation, ud matrix:\n\n"); + printMatrix(ud,part_len); + printf("\n\nAfter calculation, up matrix:\n\n"); + printMatrix(up,part_len); + printf("\n\nAfter calculation, upm matrix:\n\n"); + printMatrix(upm,part_len); +printf("\n\nAfter calculation, u1 matrix:\n\n"); + printMatrix(u1,part_len); +printf("\n\nAfter calculation, u1d matrix:\n\n"); + printMatrix(u1d,part_len); +printf("\n\nAfter calculation, s1 matrix:\n\n"); + printMatrix(s1,part_len); +printf("\n\nAfter calculation, s2 matrix:\n\n"); + printMatrix(s2,part_len); +printf("\n\nAfter calculation, s3 matrix:\n\n"); + printMatrix(s3,part_len); + +} void calculate_partition(int len) { @@ -76,15 +161,21 @@ void calculate_partition(int len) part_len = len; create_partition_arrays(); init_partition_arrays(); - fill_partition_arrays(); - for (i = 0; i <= part_len+1; ++i) + /*printf("\nAfter initialization but before calculation, u matrix:\n\n"); + for (i = 0; i <= part_len+1; ++i) { for (j = 0; j <= part_len+1; ++j) printf("%0.1f ",u[i][j]); printf("\n"); } + printf("%4.4f\n",u[1][part_len]);*/ + + fill_partition_arrays(); + + //printAllMatrixes(); + printf("%4.4f\n",u[1][part_len]); } @@ -112,9 +203,95 @@ void init_part_arrays_zeros(){ } } +void init_part_arrays_ones(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=1; + up[i][j]=1; + upm[i][j]=1; + ud[i][j]=1; + u1d[i][j]=1; + + s1[i][j]=1; + s2[i][j]=1; + s3[i][j]=1; + u1[i][j]=1; + } + } +} + + +void init_part_arrays_negatives(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=-1; + up[i][j]=-1; + upm[i][j]=-1; + ud[i][j]=-1; + u1d[i][j]=-1; + + s1[i][j]=-1; + s2[i][j]=-1; + s3[i][j]=-1; + u1[i][j]=-1; + } + } +} + +void init_partition_arrays() +{//ERROR_FOUND first nested for loop was wrongly written and iterated + //init_part_arrays_zeros(); + //init_part_arrays_ones(); + init_part_arrays_negatives(); + + int i, j; + int n = part_len; + for(i=1; i<=n; ++i){ + for(j=i; j<=i+TURN && j<=n; ++j){ //if(j>n)continue; + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; (i+TURN)<=n; ++i){ + //s1[i][i+TURN] = 0; + //s2[i][i+TURN] = 0; + } + + for(i=1; (i+TURN+1)<=n; ++i){//ERROR no need to do this as it will already be calculated as zero only + //s1[i][i+TURN+1] = 0; + //s2[i][i+TURN+1] = 0; + } + + /*for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + }*/ + for(i=1; i<=n; ++i){ + u[i+1][i] = 1; + u1[i+1][i] = 0; + u1d[i+1][i] = 0; + } + for(i=1; i<=n-1; i++){ + u1[i+2][i] = 0; + } + +} + +/* void init_partition_arrays() { - init_part_arrays_zeros(); + //init_part_arrays_zeros(); + init_part_arrays_negatives(); int i, j; int n = part_len; @@ -142,8 +319,8 @@ void init_partition_arrays() for(i=1; i<=n-1; i++){ u1[i+2][i] = 0; } -} - +}*/ +/* void fill_partition_arrays() { int b,i,j; @@ -165,13 +342,46 @@ void fill_partition_arrays() calc_upm(i,j); calc_up(i,j); + calc_ud(i,j); + calc_u(i,j); + } + } +}*/ +void fill_partition_arrays() +{ + int b,i,j;//printf("TURN=%d\n",TURN); + int n=part_len; + for(b=TURN+1; bTURN) + { + /*for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (canPair(p,q)==0) continue; + up_val += (get_up(p,q) * exp(-eL(i,j,p,q)/RT)); + } + }*/ + int h,l; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + //if((l-h)<=TURN) continue; + up_val += (get_up(h,l) * exp(-eL(i,j,h,l)/RT)); + } + } + + //ERROR below line should not be there + //up_val = up_val * exp(-Ed3(i,j,i+1)/RT); + up_val = up_val + exp(-eH(i,j)/RT ); + up_val = up_val + (exp(-eS(i,j)/RT ) * get_up(i+1,j-1)); + up_val = up_val + get_upm(i,j); + + set_up(i, j, up_val);//up[i][j] = up_val; + } + else { + set_up(i, j, 0.0);//up[i][j] = 0; + } +//printf("Exiting calc_up: i=%d, j =%d, val=%.3f\n",i,j,up[i][j]); } + + From c3fb23c438ba82453664c6d36fb05ef1c31dcce8 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Sat, 1 Oct 2011 18:46:32 -0400 Subject: [PATCH 147/187] added stochastic sampling --- gtfold-mfe/include/stochastic-sampling.h | 87 ++++ gtfold-mfe/src/stochastic-sampling.cc | 559 +++++++++++++++++++++++ 2 files changed, 646 insertions(+) create mode 100644 gtfold-mfe/include/stochastic-sampling.h create mode 100644 gtfold-mfe/src/stochastic-sampling.cc diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h new file mode 100644 index 0000000..e318296 --- /dev/null +++ b/gtfold-mfe/include/stochastic-sampling.h @@ -0,0 +1,87 @@ +#ifndef __STOCHASTIC_SAMPLING__ +#define __STOCHASTIC_SAMPLING__ + +#include +#include +#include "partition-func.h" +#include "energy.h" + +enum {U=0,UP,UD,U1,U1D}; + +double randdouble(); +double U_0(int i, int j); +double U_ij(int i, int j); +double U_hj(int i, int h, int j); +double U_il(int i, int j); +double U_s1h(int i, int h, int j); +double U_ihlj_case1(int i, int h, int l, int j); +double U_ihlj_case2(int i, int h, int l, int j); +double U_ihlj_case3(int i, int h, int l, int j); +double UD_il_case1(int i, int l, int j); +double UD_il_case2(int i, int l, int j); +double UD_il_case3(int i, int l, int j); +double Q_ijH(int i, int j); +double Q_ijS(int i, int j); +double Q_ijM(int i, int j); +double UPM_ip1l_case1(int i, int l, int j); +double UPM_ip1l_case2(int i, int l, int j); +double UPM_ip2l_case1(int i, int l , int j); +double UPM_ip2l_case2(int i, int l , int j); +double UPM_ijs2h(int i, int h , int j); +double UPM_ijhl_case1(int i, int h, int l, int j); +double UPM_ijhl_case2(int i, int h, int l, int j); +double U1D_ij_il_case1(int i, int l, int j); +double U1D_ij_il_case2(int i, int l, int j); +double U1D_ij_il_case3(int i, int l, int j); +double U1_ij(int i, int j); +double U1_ij_s3h(int i, int h, int j); +double U1_j_hl_case1(int h, int l, int j); +double U1_j_hl_case2(int h, int l, int j); +double U1_j_hl_case3(int h, int l, int j); + +struct base_pair +{ + int i; + int j; + int t; + + base_pair(int i_, int j_, int t_) : i(i_), j(j_), t(t_) {} + base_pair(const base_pair& bp) :i(bp.i), j(bp.j), t(bp.t) { } + base_pair& operator = (const base_pair& bp) + { + if (this != &bp) + { + i = bp.i; + j = bp.j; + t = bp.t; + } + return *this; + } + + int type() const { return t ;} + + bool isPaired() const + { + return t == UP; + } + + friend std::ostream& operator << (std::ostream& out, const base_pair& bp) + { + out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.isPaired() << std::endl; + return out; + } +}; + +void set_single_stranded(int i, int j, int* structure); +void set_base_pair(int i, int j, int* structure); + +void rnd_upm(int i, int j, int* structure); +void rnd_u1d(int i, int j, int* structure); +void rnd_u1(int i, int j, int* structure); +void rnd_up(int i, int j, int* structure); +void rnd_ud(int i, int j, int* structure); +void rnd_u(int i, int j, int* structure); + +void rnd_structure(int* structure, int len); + +#endif diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc new file mode 100644 index 0000000..137cb09 --- /dev/null +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -0,0 +1,559 @@ +#include "stochastic-sampling.h" + +#include +#include +#include + +std::stack g_stack; + + +double randdouble() +{ + return rand()/(double(RAND_MAX)+1); +} + +double U_0(int i, int j) +{ + return 1.0/u[i][j]; +} + +double U_ij(int i, int j) +{ + return up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]; +} + +double U_hj(int i, int h, int j) +{ + return up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]; +} + +double U_il(int i, int j) +{ + return ud[i][j]/u[i][j]; +} + +double U_s1h(int i, int h, int j) +{ + return s1[h][j]/u[i][j]; +} + +double U_ihlj_case1(int i, int h, int l, int j) +{ + return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]; +} + +double U_ihlj_case2(int i, int h, int l, int j) +{ + return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]; +} + +double U_ihlj_case3(int i, int h, int l, int j) +{ + return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]; +} + +double UD_il_case1(int i, int l, int j) +{ + return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]; +} + +double UD_il_case2(int i, int l, int j) +{ + return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]; +} + +double UD_il_case3(int i, int l, int j) +{ + return up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]; +} + +double Q_ijH(int i, int j) +{ + return exp(-eH(i,j)/RT)/up[i][j]; +} + +double Q_ijS(int i, int j) +{ + return exp(-eS(i,j)/RT)*up[i+1][j-1]/up[i][j]; +} + +double Q_ijM(int i, int j) +{ + return upm[i][j]/up[i][j]; +} + +double UPM_ip1l_case1(int i, int l, int j) +{ + return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]; +} + +double UPM_ip1l_case2(int i, int l, int j) +{ + return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]; +} + +double UPM_ip2l_case1(int i, int l , int j) +{ + return up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]; +} + +double UPM_ip2l_case2(int i, int l , int j) +{ + return (up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]; +} + + +double UPM_ijs2h(int i, int h , int j) +{ + return exp((-1)*Ed3(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j]; +} + + +double UPM_ijhl_case1(int i, int h, int l, int j) +{ + return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]; +} + +double UPM_ijhl_case2(int i, int h, int l, int j) +{ + return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]; +} + +// u1d : case 1 +double U1D_ij_il_case1(int i, int l, int j) +{ + return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]; +} + +// u1d : case 2 +double U1D_ij_il_case2(int i, int l, int j) +{ + return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]; +} + +// u1d : case 3 +double U1D_ij_il_case3(int i, int l, int j) +{ + return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]; +} + +// u1 +double U1_ij(int i, int j) +{ + return u1d[i][j]/u1[i][j]; +} + +// u1 : sample h +double U1_ij_s3h(int i, int h, int j) +{ + return (s3[h][j] * exp((-1)*(Ec+(h-i)*Eb)/RT))/u1[i][j]; +} + +// u1 : sample l +double U1_j_hl_case1(int h, int l, int j) +{ + return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]; +} + +double U1_j_hl_case2(int h, int l, int j) +{ + return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]; +} + +double U1_j_hl_case3(int h, int l, int j) +{ + return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]; +} + +void rnd_u(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + + cum_prob += U_0(i,j); + if (rnd <= cum_prob) + { + set_single_stranded(i,j, structure); + return; + } + + cum_prob += U_ij(i, j); + if (rnd <= cum_prob) + { + base_pair bp(i,j,UP); + g_stack.push(bp); + return; + } + + for (int h = i+1; h < j; ++h) + { + cum_prob += U_hj(i,h,j); + if (rnd <= cum_prob) + { + base_pair bp(h,j,UP); + set_single_stranded(i,h-1,structure); + g_stack.push(bp); + return; + } + } + + cum_prob += U_il(i,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,j,UD); + g_stack.push(bp1); + return; + } + + int h1 = -1; + for (int h = i+1; i < j-1; ++h) + { + cum_prob += U_s1h(i,h,j); + if (rnd <= cum_prob) + { + h1 = h; + break; + } + } + assert (h1 != -1) ; + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += U_ihlj_case1(i,h1,l,j); + if (rnd <= cum_prob) + { + set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case2(i,h1,l,j); + if (rnd <= cum_prob) + { + set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case3(i,h1,l,j); + if (rnd <= cum_prob) + { + set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + } + assert(0); +} + +void rnd_ud(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + + for (int l = i+1; l < j ; ++l) + { + cum_prob += UD_il_case1(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case2(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case3(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } +} + +void rnd_up(int i, int j, int* structure) +{ + double rnd = randdouble(); + +// printf("%d %d %d %d\n",i, structure[i], j, structure[j]); + +// if (structure[i] > 0){ +// printf("ERROR\n"); +// } +// if (structure[j] > 0) { +// printf("ERROR\n"); +// } + + set_base_pair(i,j,structure); + + rnd -= Q_ijH(i,j); + if (rnd <= 0) + { + set_single_stranded(i+1,j-1,structure); + return ; + } + + rnd -= Q_ijS(i,j); + if (rnd <= 0) + { + base_pair bp(i+1,j-1,UP); + g_stack.push(bp); + return ; + } + + rnd -= Q_ijM(i,j); + if (rnd <= 0) + { + assert(0); + rnd_upm(i,j,structure); + } +} + +void rnd_u1(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + cum_prob += U1_ij(i,j); + if (rnd <= cum_prob) + { + base_pair bp(i,j,U1D); + g_stack.push(bp); + return; + } + + int h1 = -1; + for (int h = i+1; h < j-1; ++h) + { + cum_prob += U1_ij_s3h(i,h,j); + if (rnd <= cum_prob) + { + h1 = h; + break; + } + } + + // sample l given h1 + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l <= j ; ++l) + { + cum_prob += U1_j_hl_case1(h1,l,j); + if (rnd <= cum_prob) + { + base_pair bp(h1,l,UP); + g_stack.push(bp); + return; + } + + cum_prob += U1_j_hl_case2(h1,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1_j_hl_case3(h1,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } +} + +void rnd_u1d(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + for (int l = i+1; i <= j; ++j) + { + cum_prob += U1D_ij_il_case1(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + set_single_stranded(l+1,j,structure); + g_stack.push(bp1); + return; + } + + cum_prob += U1D_ij_il_case2(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1D_ij_il_case3(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } +} + +void rnd_upm(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + for (int l = i+2; l < j; ++l) + { + cum_prob += UPM_ip1l_case1(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i+1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip1l_case2(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i+1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp2); + g_stack.push(bp1); + } + } + + for (int l = i+3; l < j; ++l) + { + cum_prob += UPM_ip2l_case1(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i+2,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip1l_case2(i,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(i+2,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + } + + int h1 = -1; + for (int h = i+3; h < j-1; ++j) + { + cum_prob += UPM_ijs2h(i,h,j); + if (rnd <= cum_prob) + { + h1 = h; + break; + } + } + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += UPM_ijhl_case1(i,h1,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UPM_ijhl_case2(i,h1,l,j); + if (rnd <= cum_prob) + { + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } +} + +void rnd_structure(int* structure, int len) +{ + srand(rand()); + base_pair first(1,len,U); + g_stack.push(first); + + while (!g_stack.empty()) + { + base_pair bp = g_stack.top(); + // std::cout << bp; + g_stack.pop(); + + if (bp.type() == U) + rnd_u(bp.i,bp.j,structure); + else if (bp.type() == UD) + rnd_ud(bp.i,bp.j,structure); + else if (bp.type() == UP) + rnd_up(bp.i,bp.j,structure); + else if (bp.type() == U1) + rnd_u1(bp.i,bp.j,structure); + else if (bp.type() == U1D) + rnd_u1d(bp.i,bp.j,structure); + + } +} + +void set_single_stranded(int i, int j, int* structure) +{ + for(;i<=j;++i) + structure[i] = 0; +} + +void set_base_pair(int i, int j, int* structure) +{ + assert(j-i > TURN); + // printf("PAIRING %d %d\n",i,j); + structure[i] = j; + structure[j] = i; +} From 947fa1850cf9d0bdd9a314f19fb9b04bba7bf79f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Sat, 1 Oct 2011 18:47:06 -0400 Subject: [PATCH 148/187] added stochastic sampling files --- gtfold-mfe/src/Makefile.am | 4 ++-- gtfold-mfe/src/Makefile.in | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index c595933..62cedca 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -16,10 +16,10 @@ gtfold_SOURCES = \ algorithms.c\ traceback.c\ subopt_traceback.cc\ - algorithms-partition.c\ + stochastic-sampling.cc\ + algorithms-partition.c\ partition-dangle.c\ partition-func.c\ - random-sample.cc\ shapereader.cc gtfold_LDFLAGS = diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index bad351a..d36b292 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -53,7 +53,7 @@ am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \ - random-sample.$(OBJEXT) shapereader.$(OBJEXT) + shapereader.$(OBJEXT) stochastic-sampling.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -193,9 +193,9 @@ gtfold_SOURCES = \ traceback.c\ subopt_traceback.cc\ algorithms-partition.c\ + stochastic-sampling.cc\ partition-dangle.c\ partition-func.c\ - random-sample.cc\ shapereader.cc gtfold_LDFLAGS = @@ -283,6 +283,7 @@ distclean-compile: -rm -f *.tab.c @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@ @@ -292,7 +293,6 @@ distclean-compile: @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/random-sample.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ From 6bf57630f9f29236a1edf842cfdb1026843025e1 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Sat, 1 Oct 2011 18:48:31 -0400 Subject: [PATCH 149/187] changes related to stochastic sampling --- gtfold-mfe/include/options.h | 2 ++ gtfold-mfe/include/partition-func.h | 1 + gtfold-mfe/src/main.cc | 34 +++++++++++++++++++++++++++++ gtfold-mfe/src/options.cc | 8 +++++++ gtfold-mfe/src/partition-func.c | 20 +++++------------ 5 files changed, 50 insertions(+), 15 deletions(-) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 5dbebf1..f0499a9 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -23,6 +23,7 @@ extern bool T_MISMATCH; extern bool UNAMODE; extern bool RNAMODE; extern bool CALC_PART_FUNC; +extern bool RND_SAMPLE; extern string seqfile; extern string constraintsFile; @@ -39,6 +40,7 @@ extern bool b_prefilter; extern int prefilter1; extern int prefilter2; extern int dangles; +extern int num_rnd; extern bool LIMIT_DISTANCE; extern int contactDistance; diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index 9761531..e87fc45 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -21,6 +21,7 @@ extern double ** u1; extern int part_len; +double f(int j, int h, int l); void calculate_partition(int len); void free_partition(); diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 952aba1..77a23a5 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -43,6 +43,7 @@ #include "traceback.h" #include "subopt_traceback.h" #include "shapereader.h" +#include "stochastic-sampling.h" //#define DEBUG 1 @@ -291,6 +292,39 @@ int main(int argc, char** argv) { free_fold(seq.length()); exit(0); } + if (RND_SAMPLE == true) + { + printf("\nComputing partition function...\n"); + calculate_partition(seq.length()); + + int* structure = new int[seq.length()+1]; + srand(time(NULL)); + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + for (int count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (seq.length()+1)*sizeof(int)); + rnd_structure(structure, seq.length()); + + std::string ensemble(seq.length()+1,'.'); + for (int i = 1; i <= (int)seq.length(); ++ i) { + // printf("%d %d\n",i,structure[i]); + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } + std::cout << ensemble.substr(1) << std::endl; + } + } + + free_partition(); + free_fold(seq.length()); + delete [] structure; + exit(0); + } printf("\nComputing minimum free energy structure...\n"); fflush(stdout); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 7b4a4ee..b600088 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -19,6 +19,7 @@ bool UNAMODE = false; bool RNAMODE = false; bool b_prefilter = false; bool CALC_PART_FUNC = false; +bool RND_SAMPLE = false; string seqfile = ""; string constraintsFile = ""; @@ -30,6 +31,7 @@ string outputDir = ""; string shapeFile = ""; string paramDir; // default value +int num_rnd = 0; int dangles=-1; int prefilter1=2; int prefilter2=2; @@ -184,6 +186,12 @@ void parse_options(int argc, char** argv) { help(); } else if (strcmp(argv[i],"--partition") == 0) { CALC_PART_FUNC = true; + } else if (strcmp(argv[i],"--sample") == 0) { + RND_SAMPLE = true; + if(i < argc) + num_rnd = atoi(argv[++i]); + else + help(); } else if (strcmp(argv[i], "--useSHAPE") == 0){ if( i < argc){ diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 215b1ba..b59bd2e 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -1,4 +1,5 @@ #include + #include "partition-func.h" #include "energy.h" #include "algorithms-partition.h" @@ -9,7 +10,7 @@ #include "omp.h" #endif -#define DEBUG_PF 1 +#define DEBUG_PF 0 #ifdef DEBUG_PF #undef Ec @@ -60,7 +61,6 @@ static void calc_u1d(int i, int j); static void calc_s1(int i, int j); static void calc_s2(int i, int j); static void calc_s3(int i, int j); -static double f(int j, int h, int l); double f(int j, int h, int l){ if(j - 1 == l) @@ -72,20 +72,10 @@ double f(int j, int h, int l){ void calculate_partition(int len) { - int i, j; part_len = len; create_partition_arrays(); init_partition_arrays(); fill_partition_arrays(); - - for (i = 0; i <= part_len+1; ++i) - { - for (j = 0; j <= part_len+1; ++j) - printf("%0.1f ",u[i][j]); - printf("\n"); - } - - printf("%4.4f\n",u[1][part_len]); } void free_partition() @@ -176,7 +166,7 @@ void calc_s1(int h, int j) int l; for (l = h; l < j; ++l) { - s1[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* + s1[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+ up[l+1][j]*exp(-(auPenalty(l+1,j)/RT)))); } @@ -187,7 +177,7 @@ void calc_s2(int h, int j) int l; for (l = h; l < j; ++l) { - s2[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* + s2[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1]+u1d[l+1][j-1]); } } @@ -197,7 +187,7 @@ void calc_s3(int h, int j) int l; for (l = h; l < j; ++l) { - s3[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* + s3[h][j] += up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j] + u1d[l+1][j]); } From 69d1e003e51a9df8e558f1dd9ab7d68b7caa51bb Mon Sep 17 00:00:00 2001 From: Manoj Soni Date: Sat, 1 Oct 2011 23:43:19 -0400 Subject: [PATCH 150/187] Partition Func overflow error due to int value resolved --- gtfold-mfe/src/partition-func.c | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 23ff1c9..2086252 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -11,7 +11,7 @@ #include "omp.h" #endif -//#define DEBUG_PF 0 +//#define DEBUG_PF 1 #ifdef DEBUG_PF #undef Ec @@ -174,7 +174,7 @@ void calculate_partition(int len) fill_partition_arrays(); - //printAllMatrixes(); + printAllMatrixes(); printf("%4.4f\n",u[1][part_len]); } @@ -348,7 +348,7 @@ void fill_partition_arrays() } }*/ void fill_partition_arrays() -{ +{//printf("RT=%d\n",RT);return; int b,i,j;//printf("TURN=%d\n",TURN); int n=part_len; for(b=TURN+1; b Date: Sun, 2 Oct 2011 00:23:23 -0400 Subject: [PATCH 151/187] added checks --- gtfold-mfe/src/partition-func.c | 2 +- gtfold-mfe/src/stochastic-sampling.cc | 143 +++++++++++++++----------- 2 files changed, 83 insertions(+), 62 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index f21d4cb..9a2e691 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -173,7 +173,7 @@ void calculate_partition(int len) fill_partition_arrays(); - printAllMatrixes(); + //printAllMatrixes(); printf("%4.4f\n",u[1][part_len]); } diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index 137cb09..b89bad7 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -1,5 +1,6 @@ #include "stochastic-sampling.h" +#include "global.h" #include #include #include @@ -12,6 +13,11 @@ double randdouble() return rand()/(double(RAND_MAX)+1); } +bool feasible(int i, int j) +{ + return j-i > TURN && canPair(RNA[i],RNA[j]); +} + double U_0(int i, int j) { return 1.0/u[i][j]; @@ -19,12 +25,12 @@ double U_0(int i, int j) double U_ij(int i, int j) { - return up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]; + return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]:0; } double U_hj(int i, int h, int j) { - return up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]; + return (feasible(h,j) == true)?up[h][j]*exp(-(Ed5(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0; } double U_il(int i, int j) @@ -39,32 +45,32 @@ double U_s1h(int i, int h, int j) double U_ihlj_case1(int i, int h, int l, int j) { - return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]; + return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0; } double U_ihlj_case2(int i, int h, int l, int j) { - return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]; + return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0; } double U_ihlj_case3(int i, int h, int l, int j) { - return up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]; + return feasible(h,l)?up[h][l]*exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0; } double UD_il_case1(int i, int l, int j) { - return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]:0; } double UD_il_case2(int i, int l, int j) { - return (up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]:0; } double UD_il_case3(int i, int l, int j) { - return up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]; + return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]:0; } double Q_ijH(int i, int j) @@ -82,24 +88,29 @@ double Q_ijM(int i, int j) return upm[i][j]/up[i][j]; } +double Q_ijhlBI(int i, int j, int h, int l) +{ + return feasible(h,l)?exp(-1*eL(i,j,h,l)/RT)*up[h][l]/up[i][j]:0; +} + double UPM_ip1l_case1(int i, int l, int j) { - return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]; + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(Ed3(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0; } double UPM_ip1l_case2(int i, int l, int j) { - return (up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]; + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; } double UPM_ip2l_case1(int i, int l , int j) { - return up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]; + return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(Ed3(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0; } double UPM_ip2l_case2(int i, int l , int j) { - return (up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]; + return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+Ed3(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; } @@ -111,30 +122,30 @@ double UPM_ijs2h(int i, int h , int j) double UPM_ijhl_case1(int i, int h, int l, int j) { - return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]; + return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-Ed3(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0; } double UPM_ijhl_case2(int i, int h, int l, int j) { - return up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]; + return feasible(h,l)?up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0; } // u1d : case 1 double U1D_ij_il_case1(int i, int l, int j) { - return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]:0; } // u1d : case 2 double U1D_ij_il_case2(int i, int l, int j) { - return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]:0; } // u1d : case 3 double U1D_ij_il_case3(int i, int l, int j) { - return (up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]:0; } // u1 @@ -152,17 +163,17 @@ double U1_ij_s3h(int i, int h, int j) // u1 : sample l double U1_j_hl_case1(int h, int l, int j) { - return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]; + return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0; } double U1_j_hl_case2(int h, int l, int j) { - return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]; + return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(Ed3(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0; } double U1_j_hl_case3(int h, int l, int j) { - return (up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]; + return feasible(h,l)?(up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0; } void rnd_u(int i, int j, int* structure) @@ -171,14 +182,14 @@ void rnd_u(int i, int j, int* structure) double cum_prob = 0.0; cum_prob += U_0(i,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { set_single_stranded(i,j, structure); return; } cum_prob += U_ij(i, j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp(i,j,UP); g_stack.push(bp); @@ -188,7 +199,7 @@ void rnd_u(int i, int j, int* structure) for (int h = i+1; h < j; ++h) { cum_prob += U_hj(i,h,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp(h,j,UP); set_single_stranded(i,h-1,structure); @@ -198,7 +209,7 @@ void rnd_u(int i, int j, int* structure) } cum_prob += U_il(i,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,j,UD); g_stack.push(bp1); @@ -206,10 +217,10 @@ void rnd_u(int i, int j, int* structure) } int h1 = -1; - for (int h = i+1; i < j-1; ++h) + for (int h = i+1; h < j-1; ++h) { cum_prob += U_s1h(i,h,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { h1 = h; break; @@ -222,7 +233,7 @@ void rnd_u(int i, int j, int* structure) for (int l = h1+1; l < j; ++l) { cum_prob += U_ihlj_case1(i,h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); @@ -233,7 +244,7 @@ void rnd_u(int i, int j, int* structure) } cum_prob += U_ihlj_case2(i,h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); @@ -244,7 +255,7 @@ void rnd_u(int i, int j, int* structure) } cum_prob += U_ihlj_case3(i,h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); @@ -265,7 +276,7 @@ void rnd_ud(int i, int j, int* structure) for (int l = i+1; l < j ; ++l) { cum_prob += UD_il_case1(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U); @@ -275,7 +286,7 @@ void rnd_ud(int i, int j, int* structure) } cum_prob += UD_il_case2(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UD); @@ -285,7 +296,7 @@ void rnd_ud(int i, int j, int* structure) } cum_prob += UD_il_case3(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UP); @@ -300,26 +311,20 @@ void rnd_up(int i, int j, int* structure) { double rnd = randdouble(); -// printf("%d %d %d %d\n",i, structure[i], j, structure[j]); - -// if (structure[i] > 0){ -// printf("ERROR\n"); -// } -// if (structure[j] > 0) { -// printf("ERROR\n"); -// } + assert(structure[i] == 0); + assert(structure[j] == 0); set_base_pair(i,j,structure); rnd -= Q_ijH(i,j); - if (rnd <= 0) + if (rnd < 0) { set_single_stranded(i+1,j-1,structure); return ; } rnd -= Q_ijS(i,j); - if (rnd <= 0) + if (rnd < 0) { base_pair bp(i+1,j-1,UP); g_stack.push(bp); @@ -327,11 +332,25 @@ void rnd_up(int i, int j, int* structure) } rnd -= Q_ijM(i,j); - if (rnd <= 0) + //printf ("%lf %d %d \n", Q_ijM(i,j),i,j); + if (rnd < 0) { - assert(0); rnd_upm(i,j,structure); + return; } + + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + rnd -= Q_ijhlBI(i,j,h,l); + if (rnd < 0) + { + base_pair bp(h,l,UP); + g_stack.push(bp); + return; + } + } } void rnd_u1(int i, int j, int* structure) @@ -340,7 +359,7 @@ void rnd_u1(int i, int j, int* structure) double cum_prob = 0; cum_prob += U1_ij(i,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp(i,j,U1D); g_stack.push(bp); @@ -351,7 +370,7 @@ void rnd_u1(int i, int j, int* structure) for (int h = i+1; h < j-1; ++h) { cum_prob += U1_ij_s3h(i,h,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { h1 = h; break; @@ -364,7 +383,7 @@ void rnd_u1(int i, int j, int* structure) for (int l = h1+1; l <= j ; ++l) { cum_prob += U1_j_hl_case1(h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp(h1,l,UP); g_stack.push(bp); @@ -372,7 +391,7 @@ void rnd_u1(int i, int j, int* structure) } cum_prob += U1_j_hl_case2(h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U1); @@ -382,7 +401,7 @@ void rnd_u1(int i, int j, int* structure) } cum_prob += U1_j_hl_case3(h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,U1D); @@ -401,7 +420,7 @@ void rnd_u1d(int i, int j, int* structure) for (int l = i+1; i <= j; ++j) { cum_prob += U1D_ij_il_case1(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); set_single_stranded(l+1,j,structure); @@ -410,7 +429,7 @@ void rnd_u1d(int i, int j, int* structure) } cum_prob += U1D_ij_il_case2(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U1); @@ -420,7 +439,7 @@ void rnd_u1d(int i, int j, int* structure) } cum_prob += U1D_ij_il_case3(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i,l,UP); base_pair bp2(l+1,j,U1D); @@ -439,7 +458,7 @@ void rnd_upm(int i, int j, int* structure) for (int l = i+2; l < j; ++l) { cum_prob += UPM_ip1l_case1(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i+1,l,UP); base_pair bp2(l+2,j-1,U1); @@ -449,7 +468,7 @@ void rnd_upm(int i, int j, int* structure) } cum_prob += UPM_ip1l_case2(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i+1,l,UP); base_pair bp2(l+1,j-1,U1D); @@ -461,7 +480,7 @@ void rnd_upm(int i, int j, int* structure) for (int l = i+3; l < j; ++l) { cum_prob += UPM_ip2l_case1(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i+2,l,UP); base_pair bp2(l+2,j-1,U1); @@ -471,7 +490,7 @@ void rnd_upm(int i, int j, int* structure) } cum_prob += UPM_ip1l_case2(i,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(i+2,l,UP); base_pair bp2(l+1,j-1,U1D); @@ -485,7 +504,7 @@ void rnd_upm(int i, int j, int* structure) for (int h = i+3; h < j-1; ++j) { cum_prob += UPM_ijs2h(i,h,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { h1 = h; break; @@ -497,7 +516,7 @@ void rnd_upm(int i, int j, int* structure) for (int l = h1+1; l < j; ++l) { cum_prob += UPM_ijhl_case1(i,h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(h1,l,UP); base_pair bp2(l+2,j-1,U1); @@ -507,7 +526,7 @@ void rnd_upm(int i, int j, int* structure) } cum_prob += UPM_ijhl_case2(i,h1,l,j); - if (rnd <= cum_prob) + if (rnd < cum_prob) { base_pair bp1(h1,l,UP); base_pair bp2(l+1,j-1,U1D); @@ -552,8 +571,10 @@ void set_single_stranded(int i, int j, int* structure) void set_base_pair(int i, int j, int* structure) { - assert(j-i > TURN); - // printf("PAIRING %d %d\n",i,j); + bool cond = j-i > TURN && canPair(RNA[i],RNA[j]); + if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]); + assert(cond); + // printf("PAIRING %d %d\n",i,j); structure[i] = j; structure[j] = i; } From 5e349a2dc0936d916faa4b079c2857133ddff2c8 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Sun, 2 Oct 2011 03:22:54 -0400 Subject: [PATCH 152/187] corrections in ML traceback --- gtfold-mfe/src/stochastic-sampling.cc | 42 +++++++++++++-------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index b89bad7..b91733d 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -60,17 +60,17 @@ double U_ihlj_case3(int i, int h, int l, int j) double UD_il_case1(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/u[i][j]:0; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*Ed3(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0; } double UD_il_case2(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/u[i][j]:0; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/ud[i][j]:0; } double UD_il_case3(int i, int l, int j) { - return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/u[i][j]:0; + return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/ud[i][j]:0; } double Q_ijH(int i, int j) @@ -133,19 +133,19 @@ double UPM_ijhl_case2(int i, int h, int l, int j) // u1d : case 1 double U1D_ij_il_case1(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1d[i][j]:0; } // u1d : case 2 double U1D_ij_il_case2(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(Ed3(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0; } // u1d : case 3 double U1D_ij_il_case3(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0; } // u1 @@ -184,7 +184,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_0(i,j); if (rnd < cum_prob) { - set_single_stranded(i,j, structure); + //set_single_stranded(i,j, structure); return; } @@ -202,7 +202,7 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { base_pair bp(h,j,UP); - set_single_stranded(i,h-1,structure); + //set_single_stranded(i,h-1,structure); g_stack.push(bp); return; } @@ -235,7 +235,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case1(i,h1,l,j); if (rnd < cum_prob) { - set_single_stranded(i,h1-1,structure); + //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U); g_stack.push(bp1); @@ -246,7 +246,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case2(i,h1,l,j); if (rnd < cum_prob) { - set_single_stranded(i,h1-1,structure); + //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UD); g_stack.push(bp1); @@ -257,7 +257,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case3(i,h1,l,j); if (rnd < cum_prob) { - set_single_stranded(i,h1-1,structure); + //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UP); g_stack.push(bp1); @@ -272,7 +272,6 @@ void rnd_ud(int i, int j, int* structure) { double rnd = randdouble(); double cum_prob = 0.0; - for (int l = i+1; l < j ; ++l) { cum_prob += UD_il_case1(i,l,j); @@ -305,12 +304,12 @@ void rnd_ud(int i, int j, int* structure) return; } } + assert(0); } void rnd_up(int i, int j, int* structure) { double rnd = randdouble(); - assert(structure[i] == 0); assert(structure[j] == 0); @@ -319,7 +318,7 @@ void rnd_up(int i, int j, int* structure) rnd -= Q_ijH(i,j); if (rnd < 0) { - set_single_stranded(i+1,j-1,structure); + //set_single_stranded(i+1,j-1,structure); return ; } @@ -332,7 +331,6 @@ void rnd_up(int i, int j, int* structure) } rnd -= Q_ijM(i,j); - //printf ("%lf %d %d \n", Q_ijM(i,j),i,j); if (rnd < 0) { rnd_upm(i,j,structure); @@ -376,7 +374,8 @@ void rnd_u1(int i, int j, int* structure) break; } } - + + assert(h1 != -1); // sample l given h1 rnd = randdouble(); cum_prob = 0; @@ -417,13 +416,13 @@ void rnd_u1d(int i, int j, int* structure) double rnd = randdouble(); double cum_prob = 0; - for (int l = i+1; i <= j; ++j) + for (int l = i+1; l <= j; ++l) { cum_prob += U1D_ij_il_case1(i,l,j); if (rnd < cum_prob) { base_pair bp1(i,l,UP); - set_single_stranded(l+1,j,structure); + //set_single_stranded(l+1,j,structure); g_stack.push(bp1); return; } @@ -474,6 +473,7 @@ void rnd_upm(int i, int j, int* structure) base_pair bp2(l+1,j-1,U1D); g_stack.push(bp2); g_stack.push(bp1); + return ; } } @@ -489,7 +489,7 @@ void rnd_upm(int i, int j, int* structure) return ; } - cum_prob += UPM_ip1l_case2(i,l,j); + cum_prob += UPM_ip2l_case2(i,l,j); if (rnd < cum_prob) { base_pair bp1(i+2,l,UP); @@ -501,7 +501,7 @@ void rnd_upm(int i, int j, int* structure) } int h1 = -1; - for (int h = i+3; h < j-1; ++j) + for (int h = i+3; h < j-1; ++h) { cum_prob += UPM_ijs2h(i,h,j); if (rnd < cum_prob) @@ -572,7 +572,7 @@ void set_single_stranded(int i, int j, int* structure) void set_base_pair(int i, int j, int* structure) { bool cond = j-i > TURN && canPair(RNA[i],RNA[j]); - if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]); + //if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]); assert(cond); // printf("PAIRING %d %d\n",i,j); structure[i] = j; From 8c2c06225b61987c8e4139fe8b336aa40d799b0a Mon Sep 17 00:00:00 2001 From: Manoj Soni Date: Mon, 3 Oct 2011 14:36:44 -0400 Subject: [PATCH 153/187] Wrapper function for Ed3 and Ed5 dangling functions added --- gtfold-mfe/include/partition-func.h | 3 +- gtfold-mfe/src/partition-func.c | 72 +++++++++++++++------------ gtfold-mfe/src/stochastic-sampling.cc | 30 +++++------ 3 files changed, 57 insertions(+), 48 deletions(-) diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index e87fc45..6532bea 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -20,7 +20,8 @@ extern double ** s3; extern double ** u1; extern int part_len; - +double ED3_new(int i, int j, int k); +double ED5_new(int i, int j, int k); double f(int j, int h, int l); void calculate_partition(int len); void free_partition(); diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 9a2e691..ad52a21 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -113,13 +113,21 @@ void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAn void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;} void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;} +double ED3_new(int i, int j, int k){ + //return Ed3(i,j,k); + return Ed5(j,i,k); +} +double ED5_new(int i, int j, int k){ + //return Ed5(i,j,k); + return Ed3(j,i,k); +} double f(int j, int h, int l){ if(j - 1 == l) return 1; else - return exp(-Ed3(h,l,l+1)/RT); + return exp(-ED3_new(h,l,l+1)/RT); } void printMatrix(double** u, int part_len){ @@ -385,8 +393,8 @@ void fill_partition_arrays() int l; for (l = h; l < j; ++l) { - s1[h][j] = up[h][l]*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))* - (exp(-Ed3(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+ + s1[h][j] = up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* + (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+ up[l+1][j]*exp(-(auPenalty(l+1,j)/RT)))); } }*/ @@ -396,12 +404,12 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of += double s1_val = 0.0; for (l = h+1; l < j; ++l)//ERROR { - double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))); - double v2 = (exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j)); + double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); + double v2 = (exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)); double v3 = get_ud(l+1,j); double v4 = (get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))); double val = v1*(v2+v3+v4); - //double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-Ed3(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)))); + //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)))); s1_val += val; } set_s1(h,j,s1_val);//s1[h][j] = s1_val; @@ -414,12 +422,12 @@ void calc_s2(int h, int j) int l; double s2_val = 0.0; for (l = h+1; l < j; ++l)//ERROR - {//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-Ed3(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1))); - double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))); - double v2 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)); + {//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1))); + double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); + double v2 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)); double v3 = get_u1d(l+1,j-1); double val = v1*(v2+v3); - //double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)); + //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)); s2_val += val;//Error: Eb is added } set_s2(h, j, s2_val);//s2[h][j] = s2_val; @@ -432,12 +440,12 @@ void calc_s3(int h, int j) double s3_val = 0.0; for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l { - double v1 = (get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))); + double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); double v2 = (f(j+1,h,l)*exp(-((j-l)*Eb)/RT)); - double v3 = (exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j)); + double v3 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j)); double v4 = get_u1d(l+1,j); double val = v1*(v2+v3+v4); - //double val = get_up(h,l)*(exp(-(Ed5(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(Ed3(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)); + //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)); s3_val += val; } set_s3(h, j, s3_val);//s3[h][j] = s3_val; @@ -482,18 +490,18 @@ void free_partition_arrays() { for(l=i+2; l Date: Tue, 4 Oct 2011 23:12:34 -0400 Subject: [PATCH 154/187] u1d is now of length n+2 instead of length n+1 as suggested by shel --- gtfold-mfe/src/partition-func.c | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index ad52a21..51ceede 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -247,6 +247,11 @@ void init_part_arrays_negatives(){ u1[i][j]=-1; } } + for(i=0; i<=n+1; ++i){ + for(j=0; j<=n+1; ++j){ + u1[i][j]=-1; + } + } } void init_partition_arrays() @@ -288,7 +293,7 @@ void init_partition_arrays() u1[i+1][i] = 0; u1d[i+1][i] = 0; } - for(i=1; i<=n-1; i++){ + for(i=1; i<=n; i++){//for(i=1; i<=n-1; i++){ u1[i+2][i] = 0; } @@ -463,7 +468,7 @@ void create_partition_arrays() s1 = mallocTwoD(len,len); s2 = mallocTwoD(len,len); s3 = mallocTwoD(len,len); - u1 = mallocTwoD(len,len); + u1 = mallocTwoD(len+1,len+1);//u1 = mallocTwoD(len,len); } void free_partition_arrays() @@ -477,7 +482,7 @@ void free_partition_arrays() freeTwoD(s1,len,len); freeTwoD(s2,len,len); freeTwoD(s3,len,len); - freeTwoD(u1,len,len); + freeTwoD(u1,len+1,len+1);//freeTwoD(u1,len,len); } /*void calc_upm(int i, int j){ @@ -600,7 +605,7 @@ void calc_u1d(int i, int j){//printf("Entering calc_u1d: i=%d, j =%d\n",i,j); double p_val = 0; int l; - for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d + for(l=i+1; l<=j; ++l){//for(l=i+1; l<=j && l+2<=part_len; ++l){//ERROR in l,,,//up should be calculated before u1d double v1 = (get_up(i,l)*exp((-1)*(c+auPenalty(i,l))/RT)); double v2 = (f(j+1,i,l)*exp((-1)*(j-l)*b/RT)); double v3 = (exp((-1)*(ED3_new(i,l,l+1)+b)/RT)*get_u1(l+2,j)); From 9d929f2854735c4bb54475666f9d6ceba5e6a149 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Wed, 5 Oct 2011 10:43:04 -0400 Subject: [PATCH 155/187] Fix suboptimal traceback code. --- gtfold-mfe/src/algorithms.c | 506 ++++++++++++++--------------- gtfold-mfe/src/subopt_traceback.cc | 360 ++++++++++---------- gtfold-mfe/src/traceback.c | 3 +- 3 files changed, 436 insertions(+), 433 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index bdf40c4..ab53fa0 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -12,7 +12,7 @@ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . -*/ + */ #include #include #include @@ -33,287 +33,287 @@ along with this program. If not, see . //#define DEBUG 1 void initializeMatrix(int len) { - int i, j; + int i, j; - for (i = 1; i <= len; ++i) - for (j = len; j >= i; --j) - if (canPair(RNA[i],RNA[j]) && j-i > TURN) - PP[i][j] = 1; + for (i = 1; i <= len; ++i) + for (j = len; j >= i; --j) + if (canPair(RNA[i],RNA[j]) && j-i > TURN) + PP[i][j] = 1; } void prefilter(int len, int prefilter1, int prefilter2) { - char** in; - int i, j, k, count; - - in = (char**)malloc(len*sizeof(char*)); - for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char)); - - for (i = 1; i <= len - prefilter2 + 1; ++i) - for (j = len; j >= prefilter2 && j >= i; --j) { - count = 0; - for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) - if (PP[i + k][j - k] == 1) ++count; - if (count >= prefilter1) - for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) - ++in[i + k - 1][j - k - 1]; - } - - for (i = 1; i <= len; ++i) { - for (j = len; j >= i; --j) - if (!in[i - 1][j - 1]) PP[i][j] = 0; - free(in[i - 1]); - } - - free(in); + char** in; + int i, j, k, count; + + in = (char**)malloc(len*sizeof(char*)); + for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char)); + + for (i = 1; i <= len - prefilter2 + 1; ++i) + for (j = len; j >= prefilter2 && j >= i; --j) { + count = 0; + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + if (PP[i + k][j - k] == 1) ++count; + if (count >= prefilter1) + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + ++in[i + k - 1][j - k - 1]; + } + + for (i = 1; i <= len; ++i) { + for (j = len; j >= i; --j) + if (!in[i - 1][j - 1]) PP[i][j] = 0; + free(in[i - 1]); + } + + free(in); } int calcVBI(int i, int j) { - int p=0, q=0; - int VBIij = INFINITY_; - - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==(i+1))?(j-2):(j-1); - - for (q = minq; q <= maxq; q++) { - if (PP[p][q]==0) continue; - if (!canILoop(i,j,p,q)) continue; - VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); - } - } - - return VBIij; + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; } int calcVBI1(int i, int j) { - int p=0, q=0; - int VBIij = INFINITY_; - - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==(i+1))?(j-2):(j-1); - - for (q = minq; q <= maxq; q++) { - if (PP[p][q]==0) continue; - if (!canILoop(i,j,p,q)) continue; - VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij); - } - } - - return VBIij; + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; } int calcVBI2(int i, int j, int len) { - int d, ii, jj; - int energy = INFINITY_; - - for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) - for (ii = i + 1; ii < j - d && ii <= len; ++ii) - { - jj = d + ii; - if (PP[ii][jj]==1) - energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj)); - } - - return energy; + int d, ii, jj; + int energy = INFINITY_; + + for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) + for (ii = i + 1; ii < j - d && ii <= len; ++ii) + { + jj = d + ii; + if (PP[ii][jj]==1) + energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj)); + } + + return energy; } int calculate(int len) { - int b, i, j; + int b, i, j; #ifdef _OPENMP - if (g_nthreads > 0) omp_set_num_threads(g_nthreads); + if (g_nthreads > 0) omp_set_num_threads(g_nthreads); #endif #ifdef _OPENMP #pragma omp parallel #pragma omp master - fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); + fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif - initializeMatrix(len); - if (g_unamode || g_prefilter_mode) { - prefilter(len,g_prefilter1,g_prefilter2); - } - - for (b = TURN+1; b <= len-1; b++) { + initializeMatrix(len); + if (g_unamode || g_prefilter_mode) { + prefilter(len,g_prefilter1,g_prefilter2); + } + + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) #endif - for (i = 1; i <= len - b; i++) { - j = i + b; - - if (PP[i][j] == 1) { - int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin - int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack - - // Internal Loop BEGIN - if (g_unamode) - VBI(i,j) = calcVBI1(i,j); - else - VBI(i,j) = calcVBI(i,j); - // Internal Loop END - - // Multi Loop BEGIN - int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; - int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; - - if (g_unamode || g_mismatch) { // unamode, terminal mismatch - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); - VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec); - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec); - VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + Estackm(i,j) + auPenalty(i,j) + Ea + Eb + 2*Ec); - } else if (g_dangles == 2) { // -d2 - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + d3 + d5 + auPenalty(i,j) + Ea + Eb); - } else if (g_dangles == 0) { // -d0 - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); - } else { // default - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); - VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec); - VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec); - VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + d3 + d5 + auPenalty(i,j) + Ea + Eb + 2*Ec); - } - VM(i,j) = canStack(i,j)?VM(i,j):INFINITY_; - // Multi Loop END - - V(i,j) = MIN4( eh, - es, - VBI(i,j), - VM(i,j)); - } - else { - V(i,j) = INFINITY_; - } - - // Added auxillary storage WMPrime to speedup multiloop calculations - int h; - for (h = i+TURN+1 ; h <= j-TURN-2; h++) { - WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); - } - - // WM begin - int newWM = INFINITY_; - - //ZS: This sum corresponds to when i,j are NOT paired with each other. - //So we need to make sure only terms where i,j aren't pairing are considered. - newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; - - if (g_unamode || g_mismatch) { // unamode - newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle - newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle - if (i1) energy += Ed3(j,i,i-1); - if (j1) energy += Ed3(j,i,i-1); + if (j ii; --jj) { - fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj)); - } - } - fclose(file); - - file = fopen("Eh.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = len; jj > ii; --jj) { - int eh = INFINITY_; - if (PP[ii][jj]) eh = eH(ii,jj); - fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh); - } - } - fclose(file); - - file = fopen("Es.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = len; jj > ii; --jj) { - int es = INFINITY_; - if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj); - fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es); - } - } - fclose(file); - - file = fopen("BP.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = len; jj > ii; --jj) { - fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]); - } - } - fclose(file); - - file = fopen("VM.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = len; jj > ii; --jj) { - fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj)); - } - } - fclose(file); - - file = fopen("WM.txt", "w"); - for (ii = 1; ii <= len; ++ii) { - for (jj = len; jj > ii; --jj) { - fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); - } - } - fclose(file); + FILE* file = fopen("VBI.txt", "w"); + int ii, jj; + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj)); + } + } + fclose(file); + + file = fopen("Eh.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int eh = INFINITY_; + if (PP[ii][jj]) eh = eH(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh); + } + } + fclose(file); + + file = fopen("Es.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int es = INFINITY_; + if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es); + } + } + fclose(file); + + file = fopen("BP.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]); + } + } + fclose(file); + + file = fopen("VM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj)); + } + } + fclose(file); + + file = fopen("WM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); + } + } + fclose(file); #endif - return W[len]; + return W[len]; } diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 2d3d9ed..cbf7e7a 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -1,22 +1,22 @@ /** - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. - You should have received a copy of the GNU General Public License - along with this program. If not, see . - - @author prashant {pgaurav@gatech.edu} +You should have received a copy of the GNU General Public License +along with this program. If not, see . + +@author prashant {pgaurav@gatech.edu} */ @@ -39,194 +39,196 @@ static int length = -1; static int gflag = 0; void process(ss_map_t& subopt_data, int len) { - int count = 0 ; - ps_stack_t gstack; - - // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} - ps_t first(0, len); - first.push(segment(1, len, lW, W[len])); - gstack.push(first); // initialize the partial structure stacka - - while (1) { - if (gstack.empty()) break; // exit - ps_t ps = gstack.top(); - gstack.pop(); - - if (ps.empty()) { - count++; - subopt_data.insert(std::make_pair(ps.str,ps.ae_)); - continue; - } - else { - segment smt = ps.top(); - ps.pop(); - - gflag = 0; - if (smt.j_ - smt.i_ > TURN) { - (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); - } - - // discarded current segment, using remaining ones - if (!gflag) { - ps_t ps1(ps); - gstack.push(ps1); - } - } - } - + int count = 0; + ps_stack_t gstack; + + + // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} + ps_t first(0, len); + first.push(segment(1, len, lW, W[len])); + gstack.push(first); // initialize the partial structure stacka + + while (1) { + if (gstack.empty()) break; // exit + ps_t ps = gstack.top(); + gstack.pop(); + + if (ps.empty()) { + count++; + subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + continue; + } + else { + segment smt = ps.top(); + ps.pop(); + + gflag = 0; + if (smt.j_ - smt.i_ > TURN) { + (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); + } + + // discarded current segment, using remaining ones + if (!gflag) { + ps_t ps1(ps); + gstack.push(ps1); + } + } + } + #ifdef DEBUG - printf("# SS = %d\n", count); + printf("# SS = %d\n", count); #endif } ss_map_t subopt_traceback(int len, int _delta) { - trace_func[0] = traceW; - trace_func[1] = traceV; - /* trace_func[2] = traceVBI;*/ - trace_func[3] = traceVM; - trace_func[4] = traceWM; - trace_func[5] = traceWMPrime; + trace_func[0] = traceW; + trace_func[1] = traceV; + trace_func[2] = traceVBI; + trace_func[3] = traceVM; + trace_func[4] = traceWM; + trace_func[5] = traceWMPrime; - mfe = W[len]; - delta = _delta; - length = len; + mfe = W[len]; + delta = _delta; + length = len; - ss_map_t subopt_data; - process(subopt_data, len); + ss_map_t subopt_data; + process(subopt_data, len); - return subopt_data; + return subopt_data; } void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { - // Hairpin Loop - if (eH(i,j) + ps.total() <= mfe + delta) { - ps_t ps1(ps); - ps1.accumulate(eH(i,j)); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { - ps_t ps1(ps); - ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); - ps1.accumulate(eS(i,j)); - ps1.update(i, j , '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Internal Loop - if (VBI(i,j) + ps.total() <= mfe + delta) { - traceVBI(i,j,ps,gstack); - } - - // Multiloop - if ( VM(i,j) + ps.total() <= mfe + delta) { - ps_t ps1(ps); - ps1.push(segment(i, j, lVM, VM(i,j))); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } + // Hairpin Loop + if (eH(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.accumulate(eH(i,j)); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Stack + if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); + ps1.accumulate(eS(i,j)); + ps1.update(i, j , '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Internal Loop + if (VBI(i,j) + ps.total() <= mfe + delta) { + traceVBI(i,j,ps,gstack); + } + + // Multiloop + if ( VM(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i, j, lVM, VM(i,j))); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } } void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { - int p,q; - - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==(i+1))?(j-2):(j-1); - for (q = minq; q <= maxq; q++) { - if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) { - ps_t ps1(ps); - ps1.push(segment(p, q, lV, V(p, q))); - ps1.update(i, j , '(', ')'); - ps1.accumulate(eL(i, j, p, q)); - push_to_gstack(gstack, ps1); - } - } - } + int p,q; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { + if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(p, q, lV, V(p, q))); + ps1.update(i, j , '(', ')'); + ps1.accumulate(eL(i, j, p, q)); + push_to_gstack(gstack, ps1); + } + } + } } -void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack) { - for (int i = 1; i < j-TURN; ++i) { - int wim1 = MIN(0, W[i-1]); - int d3 = (i>1)?Ed3(j,i,i-1):0; - int d5 = (ji)?Ed3(j,l,l-1):0; + int d5 = (j Date: Thu, 6 Oct 2011 19:59:35 -0400 Subject: [PATCH 156/187] 1. Merge Pseudoknot Detection Tests. 2. Fix a segmentation fault issue that occurred due to change in subopt code fix. --- gtfold-mfe/src/algorithms.c | 2 +- gtfold-mfe/src/subopt_traceback.cc | 2 +- gtfold-mfe/tests/config/test-list.conf | 3 +- gtfold-mfe/tests/config/test-params.conf | 13 ++- .../seq1.constraint | 4 + .../pseudoknot_detection_sequences/seq1.ct | 20 ++++ .../seq1.expectedresult | 1 + .../pseudoknot_detection_sequences/seq1.seq | 1 + .../seq2.constraint | 2 + .../seq2.expectedresult | 1 + .../pseudoknot_detection_sequences/seq2.seq | 1 + .../seq3.constraint | 3 + .../seq3.expectedresult | 1 + .../pseudoknot_detection_sequences/seq3.seq | 1 + .../seq4.constraint | 4 + .../seq4.expectedresult | 1 + .../pseudoknot_detection_sequences/seq4.seq | 1 + .../seq5.constraint | 1 + .../seq5.expectedresult | 1 + .../pseudoknot_detection_sequences/seq5.seq | 1 + .../seq6.constraint | 5 + .../seq6.expectedresult | 1 + .../pseudoknot_detection_sequences/seq6.seq | 1 + .../seq7.constraint | 4 + .../seq7.expectedresult | 1 + .../pseudoknot_detection_sequences/seq7.seq | 1 + .../seq8.constraint | 4 + .../seq8.expectedresult | 1 + .../pseudoknot_detection_sequences/seq8.seq | 1 + .../tests/scripts/PseudoKnotDetection.pm | 49 +++++++++ .../tests/scripts/Scoregtwithunafold.pm | 2 +- gtfold-mfe/tests/scripts/start_test.pm | 102 ++++++++++++------ gtfold-mfe/tests/scripts/test_utils.pl | 4 +- 33 files changed, 197 insertions(+), 43 deletions(-) create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult create mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq create mode 100755 gtfold-mfe/tests/scripts/PseudoKnotDetection.pm diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index ab53fa0..1f6da10 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -257,7 +257,7 @@ int calculate(int len) { Wj = MIN(Wj,Wij); } - W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj; + W[j] = (j!=0 && canSS(j))?MIN(Wj, W[j-1]):Wj; } #ifdef DEBUG diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index cbf7e7a..b27b059 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -228,7 +228,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { } } -void push_to_gstack(ps_stack_t& gstack , ps_t& v) { +void push_to_gstack(ps_stack_t& gstack, const ps_t& v) { gflag = 1; gstack.push(v); } diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf index b339d8d..827ab10 100644 --- a/gtfold-mfe/tests/config/test-list.conf +++ b/gtfold-mfe/tests/config/test-list.conf @@ -1 +1,2 @@ -Scoregtwithunafold +#Scoregtwithunafold +PseudoKnotDetection diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf index 2922a50..d1fdec2 100644 --- a/gtfold-mfe/tests/config/test-params.conf +++ b/gtfold-mfe/tests/config/test-params.conf @@ -2,21 +2,26 @@ G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ -G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ -G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/ G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf -#Sequence Inclusion Filters +# Sequence Inclusion Filters #G_INCLUDE_SEQUENCES=rad #G_INCLUDE_SEQUENCES=d.16.e.B.g* #G_INCLUDE_SEQUENCES=d.16.e.B.m* #G_INCLUDE_SEQUENCES=d.16.e.B.h* -G_INCLUDE_SEQUENCES=d.16.e.G.va* +#G_INCLUDE_SEQUENCES=d.16.e.G.va* #G_EXCLUDE_SEQUENCES=d.16.e.A.* #G_EXCLUDE_SEQUENCES=d.16.e.B.ma* #G_INCLUDE_SEQUENCES=acc1 #G_INCLUDE_SEQUENCES=a.*j #G_INCLUDE_SEQUENCES=a..tb* +# Local Sequence Directories + +# Directory containing sequences for testing pseudoknot detection logic +L_PSEUDOKNOTDETECTION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/pseudoknot_detection_sequences/ diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint new file mode 100644 index 0000000..2a01386 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct new file mode 100644 index 0000000..da642b1 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct @@ -0,0 +1,20 @@ +19 dG = 10.1 +1 C 0 2 0 1 +2 C 1 3 0 2 +3 C 2 4 0 3 +4 C 3 5 0 4 +5 A 4 6 0 5 +6 A 5 7 0 6 +7 G 6 8 0 7 +8 A 7 9 0 8 +9 A 8 10 0 9 +10 G 9 11 0 10 +11 C 10 12 0 11 +12 A 11 13 0 12 +13 A 12 14 0 13 +14 A 13 15 0 14 +15 G 14 16 0 15 +16 A 15 17 0 16 +17 A 16 18 0 17 +18 G 17 19 0 18 +19 G 18 0 0 19 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint new file mode 100644 index 0000000..2a8e728 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint @@ -0,0 +1,2 @@ +F 1 19 2 +F 15 21 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq new file mode 100644 index 0000000..23023c5 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq @@ -0,0 +1 @@ +CCAAAAAAAAAAAACAAGGAG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint new file mode 100644 index 0000000..bcbe409 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint @@ -0,0 +1,3 @@ +F 1 19 2 +F 3 10 2 +F 15 23 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq new file mode 100644 index 0000000..6b590de --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGAAAACAAGGAAAG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint new file mode 100644 index 0000000..cece32a --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 18 1 +F 4 7 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint new file mode 100644 index 0000000..7029d7d --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint @@ -0,0 +1 @@ +F 1 8 8 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq new file mode 100644 index 0000000..0984ecd --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq @@ -0,0 +1 @@ +CCCCCGGGGGGAAAGGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint new file mode 100644 index 0000000..adb4fdb --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint @@ -0,0 +1,5 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 +F 24 25 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq new file mode 100644 index 0000000..9a1d7d8 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGGCCCACGAAAA diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint new file mode 100644 index 0000000..2ce893a --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint @@ -0,0 +1,4 @@ +F 0 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint new file mode 100644 index 0000000..65ea20f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 24 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm b/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm new file mode 100755 index 0000000..1bdfc38 --- /dev/null +++ b/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm @@ -0,0 +1,49 @@ +#!/usr/bin/perl +package PseudoKnotDetection; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + # For testing pseudoknot detection logic + # we may only test the sequences specified in local_sequences + while (($key, $value) = each(%local_sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$dirname/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1"; + my $x = system("$gtcmd") >> 8; + + my $expected_result_file = "$dirname/$seqname.expectedresult"; + my $expected_result = `head -n 1 $expected_result_file`; + + if ($expected_result =~ $x) { + $logger->error("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result"); + } + else { + $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm index 41ffe28..7cdfb82 100755 --- a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm +++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm @@ -8,7 +8,7 @@ sub test() { my(%Config) = %{$_[1]}; my(%Sequences) = %{$_[2]}; - my $logger = $_[3]; + my $logger = $_[4]; my $gtdir = $Config{"G_GTFOLD_DIR"}; my $unadir = $Config{"G_UNAFOLD_DIR"}; diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm index 16e53c3..83fb8ee 100755 --- a/gtfold-mfe/tests/scripts/start_test.pm +++ b/gtfold-mfe/tests/scripts/start_test.pm @@ -10,9 +10,11 @@ use Log::Log4perl qw(:easy); require 'test_utils.pl'; my $configdir="../config"; + Log::Log4perl::init( "$configdir/root-logger.conf" ); my $logger = Log::Log4perl->get_logger; + $logger->info("Starting Tests..."); # Read Parameter File @@ -37,30 +39,10 @@ my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}}; my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"}; my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"}; -foreach (@seqdir_arr) { - - opendir(DIR, $_) || die $!; - while (my $seqfile = readdir(DIR)) { - - my $seqname; - my $path; - my $suffix; - ($seqname,$path,$suffix) = fileparse($seqfile); - - if (-d $seqfile) { - next; - } - - $seqfile = "$_$seqname"; - my $seq_include = (not defined($seq_include_regex)) || ($seqname =~ /$seq_include_regex/); - - my $seq_exclude = (not defined($seq_exclude_regex)) || ($seqname !~ /$seq_exclude_regex/); - if ( $seq_include && $seq_exclude ) { - $Sequences{$seqname} = $seqfile; - $logger->info("Selected Sequence ... $seqname"); - } - } -} +%Sequences = find_sequences_from_dir( + seq_include_regex => $seq_include_regex, + seq_exclude_regex => $seq_exclude_regex, + seq_dirs => @seqdir_arr); my $test_include_regex = $Config{"G_INCLUDE_TESTS"}; my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"}; @@ -78,17 +60,71 @@ open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file $testname =~ s/\s*$//; # Remove spaces at the end of the line if ( ($testname !~ /^#/) && ($testname ne "") ) { # Ignore lines starting with # and blank lines - my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/); + my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/); + my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/); + + if ( $test_include && $test_exclude ) { + my $uppertestname = uc($testname); + my $local_sequence_dirname = "L_".$uppertestname."_SEQUENCE_DIR"; + my $local_sequence_include_regex = $Config{"L_".$uppertestname."_SEQUENCE_INCLUDE"}; + my $local_sequence_exclude_regex = $Config{"L_".$uppertestname."_SEQUENCE_EXCLUDE"}; + my @local_sequence_dir; + my %local_sequences; + + if (defined($Config{$local_sequence_dirname})) { + @local_sequence_dir = @{$Config{$local_sequence_dirname}}; + %local_sequences = find_sequences_from_dir( + seq_include_regex => $local_sequence_include_regex, + seq_exclude_regex => $local_sequence_exclude_regex, + seq_dirs => @local_sequence_dir); + } + + my $module = $testname; + load($module); + $module->test(\%Config, \%Sequences, \%local_sequences, $logger); + } + } + } - my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/); - if ( $test_include && $test_exclude ) { - my $module = $testname; - load($module); - $module->test(\%Config, \%Sequences, $logger); - } - - } +sub find_sequences_from_dir +{ +my %args = @_; + +my %seq_hash; +my $include_regex = $args{seq_include_regex}; +my $exclude_regex = $args{seq_exclude_regex}; +my @seqdirs = $args{seq_dirs}; + +if (scalar(@seqdirs) eq 0) { + return %seq_hash; +} + +foreach (@seqdirs) { + + opendir(DIR, $_) || die $!; + while (my $seqfile = readdir(DIR)) { + + my $seqname; + my $path; + my $suffix; + ($seqname,$path,$suffix) = fileparse($seqfile, (".seq", ".constraint")); + + if ((-d $seqfile) || $suffix ne '.seq') { + next; + } + + $seqfile = "$_$seqname$suffix"; + my $seq_include = (not defined($include_regex)) || ($seqname =~ /$include_regex/); + my $seq_exclude = (not defined($exclude_regex)) || ($seqname !~ /$exclude_regex/); + + if ( $seq_include && $seq_exclude ) { + $seq_hash{$seqname} = $seqfile; + $logger->info("Selected Sequence ... $seqname"); + } } +} + return %seq_hash; +} diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl index 2191bdf..2a62542 100755 --- a/gtfold-mfe/tests/scripts/test_utils.pl +++ b/gtfold-mfe/tests/scripts/test_utils.pl @@ -22,7 +22,7 @@ () if ( ($line !~ /^#/) && ($line ne "") ) { # Ignore lines starting with # and blank lines ($Name, $Value) = split (/=/, $line); # Split each line into name value pairs - if ($Name =~ /G_INCLUDE_SEQUENCES|G_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) { + if ($Name =~ /.*_INCLUDE_SEQUENCES|.*_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) { $orig_value= %Config->{$Name}; $Value =~ s/[.]/\\./g; $Value =~ s/[*]/.\*/g; @@ -31,7 +31,7 @@ () } } - if ($Name eq "G_SEQUENCE_DIR") { + if ($Name =~ /.*_SEQUENCE_DIR/) { my @seqdir_arr = %Config->{$Name}; push (@{%Config->{$Name}}, $Value); next; From 85b7ac7ba83b8e5e4abcbd73e87d884dcc042606 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Thu, 6 Oct 2011 20:53:18 -0400 Subject: [PATCH 157/187] Fix subopt error along with constraints error. --- gtfold-mfe/src/algorithms.c | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 1f6da10..0bbdceb 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -226,7 +226,8 @@ int calculate(int len) { } } - for (j = 0; j <= len; j++) { + W[0] = 0; + for (j = 1; j <= len; j++) { int i, Wj, Widjd, Wijd, Widj, Wij, Wim1; Wj = INFINITY_; for (i = 1; i < j-TURN; i++) { @@ -257,7 +258,7 @@ int calculate(int len) { Wj = MIN(Wj,Wij); } - W[j] = (j!=0 && canSS(j))?MIN(Wj, W[j-1]):Wj; + W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj; } #ifdef DEBUG From 17c8e511357f8a870a7def09c3ef619a7af084fe Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 7 Oct 2011 14:24:07 -0400 Subject: [PATCH 158/187] Merge the set of sequences that can be used by tests. Filtered out the ones which contain ambiguous bases. --- gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq | 2 ++ .../tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq | 2 ++ .../tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq | 2 ++ .../tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq | 2 ++ .../tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq | 2 ++ gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq | 2 ++ .../tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq | 2 ++ .../tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq | 2 ++ .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq | 2 ++ .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq | 2 ++ .../tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq | 2 ++ gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq | 2 ++ 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gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq create mode 100644 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gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq create mode 100644 gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq new file mode 100644 index 0000000..b8c95c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.16.a.H.volcanii +AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCUAGUUGCACGAGUUCAUACUCGUGGCGAAAAGCUCAGUAACACGUGGCCAAACUACCCUACAGAGAACGAUAACCUCGGGAAACUGAGGCUAAUAGUUCAUACGGGAGUCAUGCUGGAAUGCCGACUCCCCGAAACGCUCAGGCGCUGUAGGAUGUGGCUGCGGCCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCCAAGUGCGAGGGCAUAUAGUCCUCGCUUUUCUCGACCGUAAGGCGGUCGAGGAAUAAGAGCUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGAAGGUUCAUCGGGAAAUCCGCCAGCUCAACUGGCGGGCGUCCGGUGAAAACCACGUGGCUUGGGACCGGAAGGCUCGAGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGACACAGGCUACGAGCCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCUCCGACUACAGUGAUGACGAUCAGGUUGAUGACCUUAUCACGACGCUGUAGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUUCUAAUUGCCAGCAGCAGUUUCGACUGGCUGGGUACAUUAGAAGGACUGCCGCUGCUAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGAGCUGGGCUACACGCGGGCUACAAUGGUCGAGACAAUGGGUUGCUAUCUCGAAAGAGAACGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAAUAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAGCACCCGAGUGAGGUCCGGAUGAGGCCACCACACGGUGGUCGAAUCUGGGCUUCGCAAGGGGGCUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq new file mode 100644 index 0000000..e3a500d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq @@ -0,0 +1,2 @@ +>d.16.a.Halobacterium.sp +AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUUGUGCGGGUUUAGACCCGCAGCGGAAAGCUCAGUAACACGUGGCCAAGCUACCCUGUGGACGGGAAUACUCUCGGGAAACUGAGGCUAAUCCCCGAUAACGCUUUGCUCCUGGAAGGGGCAAAGCCGGAAACGCUCCGGCGCCACAGGAUGCGGCUGCGGUCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGUACGAAAGUGCGAUAAGGGGACUCCGAGUGUGAAGGCAUAGAGCCUUCACUUUUGUACACCGUAAGGUGGUGCACGAAUAAGGACUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCUGAACAAGUCCGUUGGGAAAUCUGUCCGCUUAACGGGCAGGCGUCCAGCGGAAACUGUUCAGCUUGGGACCGGAAGACCUGAGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUGGCGAAAGCGCCUCAGGAGAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGCUACGAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGGACCGCCUGGGAAGUACGUCUGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCCCCGACAGUAGUAAUGACGGUCAGGUUGAUGACCUUACCCGAGGCUACUGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUCCUAAUUGCCAGCAGUACCCUUUGGGUAGCUGGGUACAUUAGGUGGACUGCCGCUGCCAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGGGCUGGGCAACACGCGGGCUACAAUGGUCGAGACAAUGGGAAGCCACUCCGAGAGGAGGCGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAUCACCCGAGUGGGGUUCGGAUGAGGCCGGCAUGCGCUGGUCAAAUCUGGGCUCCGCAAGGGGGAUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq new file mode 100644 index 0000000..c32cdc8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq @@ -0,0 +1,2 @@ +>d.16.a.P.abyssi +CGUACUCCCUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq new file mode 100644 index 0000000..14395d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq @@ -0,0 +1,2 @@ +>d.16.a.P.horikoshii +AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq new file mode 100644 index 0000000..0afb8fa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq @@ -0,0 +1,2 @@ +>d.16.a.S.solfataricus.2 +AAAUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUCGUACGCUCCCGGGCAAGGGAGCGUGGCGGACGGCUGAGUAACACGUGGCUAACCUACCCUGAGGAGGGAGAUAACCCCGGGAAACUGGGGAUAAUCUCCCAUAGGCGAGGAGUCCUGGAACGGUUCCUCGCUGAAAGGCUCAUGGGCUAUUCCCCGCUCAUGAGCGCCUCAGGAUGGGGCUGCGGCCCAUCAGGUAGUUGGGGGGGUAAGGGCCCCCCAAGCCUAUAACGGGUAGGGGCCGUGAGAGCGGGAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGGAAGCGUGAGGGCGCCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUCUACAAAGGCGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACUCUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGACAAGUCACUCCUUAAAGACCCCGGCUCAACCGGGGGAAUGGGGGUGAUACUGUCGGGCUAGGGGGCGGGAGAGGCCAGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGAGGACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGCUUAGAGCCCAUGUGGUGCCGCAGGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCUUACUAGGGGAGACCGCAGGAUGACGGCCAGGCUAACGACCUUGCCUGACUCGCGGAGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGUUGUGAAAUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCACCACUAGUUGGUAUCCUGGUCUCCGGGCCGGGACCACACUAGUGGGACUGCCGGCGUAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAGCAUGCCCCGAAACCCCUGGGCCGCACGCGGGUUACAAUGGCAGGGACAGCGGGAUUCCGACCCCGAAAGGGGAAGGUAAUCCCUUAAACCCUGCCGCAGUUGGGAUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCGCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGCCUUUGGGUGGGGGGUCGAGCUUCUCUCCUGCAAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq new file mode 100644 index 0000000..8d706e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq @@ -0,0 +1,2 @@ +>d.16.b.A.globiformis +UUUCAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAUCCGGUGCUUGCACCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUCUGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACUCCUCAUCGCAUGGUGGGGGGUGGAAAGCUUUUUGUGGUUUUGGAUGGACUCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGUAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUUUGUCGCGUCUGCCGUGAAAGUCCGGGGCUCAACUCCGGAUCUGCGGUGGGUACGGGCAGACUAGAGUGAUGUAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGAUGGCGAAGGCAGGUCUCUGGGCAUUAACUGACGCUGAGGAGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGUUGGGCACUAGGUGUGGGGGACAUUCCACGUUUUCCGCGCCGUAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGGCUUGACAUGGACCGGACCGCCGCAGAAAUGUGGUUUCUCCUUUUGGGGCCGGUUCACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUCCAUGUUGCCAGCGCGUAAUGGCGGGGACUCAUGGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCCUUAUGUCUUGGGCUUCACGCAUGCUACAAUGGCCGGUACAAAGGGUUGCGAUACUGUGAGGUGGAGCUAAUCCCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGUCACGAAAGUUGGUAACACCCGAAGCCGGUGGCCUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGACUGGCGAUUGGGACUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq new file mode 100644 index 0000000..dca4e6e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.16.b.A.tumefaciens +CUCAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGCCCCGCAAGGGGAGUGGCAGACGGGUGAGUAACGCGUGGGAAUCUACCGUGCCCUGCGGAAUAGCUCCGGGAAACUGGAAUUAAUACCGCAUACGCCCUACGGGGGAAAGAUUUAUCGGGGUAUGAUGAGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUCACCGGAGAAGAUAAUGACGGUAUCCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCGGAUAUUUAAGUCAGGGGUGAAAUCCCAGAGCUCAACUCUGGAACUGCCUUUGAUACUGGGUAUCUUGAGUAUGGAAGAGGUAAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACGCCAGUGGCGAAGGCGGCUUACUGGUCCAUUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGCAGUAUACUGUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCUCUUGACAUUCGGGGUUUGGGCAGUGGAGACAUUGUCCUUCAGUUAGGCUGGCCCCAGAACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUUUAGUUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGAGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUGACAGUGGGCAGCGAGACAGCGAUGUCGAGCUAAUCUCCAAAAGCCAUCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUCAGCAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGUAGUGCGCUAACCGCAAGGAGGCAGCUAACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq new file mode 100644 index 0000000..040091c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Anabaena.sp +GAAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGGUCUCUUCGGAGAUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUAGCUUCAGGUCGGGGACAACCACUGGAAACGGUGGCUAAUACCGGAUGUGCCGAAAGGUGAAAGAUUUAUUGCCUGAAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGUGGUAAGAGCGCACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAGGAAGGCUCUUGGGUUGUAAACCUCUUUUCUCAGGGAAUAAAAAAAUGAAGGUACCUGAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCCGCAGGUGGCACUGUAAGUCUGCUGUUAAAGAGCAAGGCUCAACCUUGUAAAGGCAGUGGAAACUACAGAGCUAGAGUACGUUCGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAGAUCAGGAAGAACACCGGUGGCGAAAGCGCUCUGCUAGGCCGUAACUGACACUGAGGGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGUGGCUUGUAUCGACCCGAGCCGUGCCGGAGCCAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCACGCAAGUGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGACUUGACAUGUCGCGAAUCUUCUUGAAAGGGAAGAGUGCCUUAGGGAGCGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAGCAUUAAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCUUGGGCUACACACGUACUACAAUGCUACGGACAGAGGGCAGCAAGCUAGCGAUAGCAAGCAAAUCCCGUAAACCGUAGCUCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGGAGGAAUCGCUAGUAAUUGCAGGUCAGCAUACUGCAGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGCAACGCCCGAAGUCAUUACUCCAACUUUUAGGAGAGGAGGAUGCCUAAGGCAGUGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq new file mode 100644 index 0000000..b4e37d1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq @@ -0,0 +1,2 @@ +>d.16.b.B.bronchiseptica2 +UGAACUGAAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGGAUGCUUUACACAUGCAAGUCGGACGGCAGCACGGGCUUCGGCCUGGUGGCGAGUGGCGAACGGGUGAGUAAUGUAUCGGAACGUGCCCAGUAGCGGGGGAUAACUACGCGAAAGCGUGGCUAAUACCGCAUACGCCCUACGGGGGAAAGCGGGGGACCUUCGGGCCUCGCACUAUUGGAGCGGCCGAUAUCGGAUUAGCUAGUUGGUGGGGUAACGGCCUACCAAGGCGACGAUCCGUAGCUGGUUUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUCCCGCGUGUGCGAUGAAGGCCUUCGGGUUGUAAAGCACUUUUGGCAGGAAAGAAACGGCACGGGCUAAUAUCCUGUGCAACUGACGGUACCUGCAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUCGGAAAGAAAGAUGUGAAAUCCCAGGGCUUAACCUUGGAACUGCAUUUUUAACUACCGGGCUAGAGUGUGUCAGAGGGAGGUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAGCCUCCUGGGAUAACACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUAGCUGUUGGGGCCUUCGGGCCUUGGUAGCGCAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCUUGACAUGUCUGGAAUCCCGAAGAGAUUUGGGAGUGCUCGCAAGAGAACCGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCAUUAGUUGCUACGAAAGGGCACUCUAAUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGGGUAGGGCUUCACACGUCAUACAAUGGUCGGGACAGAGGGUCGCCAACCCGCGAGGGGGAGCCAAUCCCAGAAACCCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGUCGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUUUACCAGAAGUAGUUAGCCUAACCGCAAGGGGGGCGAUUACCACGGUAGGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq new file mode 100644 index 0000000..818a7c0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq @@ -0,0 +1,2 @@ +>d.16.b.B.burgdorferi +AUAACGAAGAGUUUGAUCCUGGCUUAGAACUAACGCUGGCAGUGCGUCUUAAGCAUGCAAGUCAAACGGGAUGUAGCAAUACAUUCAGUGGCGAACGGGUGAGUAACGCGUGGAUGAUCUACCUAUGAGAUGGGGAUAACUAUUAGAAAUAGUAGCUAAUACCGAAUAAGGUCAGUUAAUUUGUUAAUUGAUGAAAGGAAGCCUUUAAAGCUCUCGCUUGUAGAUGAGUCUGCGUCUUAUUAGCUAGUUGGUAGGGUAAAUGCCUACCAAGGCAAUGAUAAGUAACCGGCCUGAGAGGGUGAACGGUCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUCUUCCGCAAUGGGCGGAAGCCUGACGGAGCGACACUGCGUGAAUGAAGAAGGUCGAAAGAUUGUAAAAUUCUUUUAUAAAUGAGGAAUAAGCUUUGUAGGAAAUGACAAAGUGAUGACGUUAAUUUAUGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUGUUCGGGAUUAUUGGGCGUAAAGGGUGAGUAGGCGGAUAUAUAAGUCUAUGCAUAAAAUACCACAGCUCAACUGUGGACCUAUGUUGGAAACUAUAUGUCUAGAGUCUGAUAGAGGAAGUUAGAAUUUCUGGUGUAAGGGUGGAAUCUGUUGAUAUCAGAAAGAAUACCGGAGGCGAAGGCGAACUUCUGGGUCAAGACUGACGCUGAGUCACGAAAGCGUAGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCUACGCUGUAAACGAUGCACACUUGGUGUUAACUAAAAGUUAGUACCGAAGCUAACGUGUUAAGUGUGCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAGGGCUUGACAUAUAUAGGAUAUAGUUAGAGAUAAUUAUUCCCCGUUUGGGGUCUAUAUACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCUGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUAUCUGUUACCAGCAUGUAAUGGUGGGGACUCAGAUAAGACUGCCGGUGAUAAGUCGGAGGAAGGUGAGGAUGACGUCAAAUCAUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGCCUGUACAAAGCGAAGCGAAACAGUGAUGUGAAGCAAAACGCAUAAAGCAGGUCUCAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAUAUCAGAAUGAUACGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGAGGAUACCCGAAGCUAUUAUUCUAACCCGUAAGGGAGGAAGGUAUUUAAGGUAUGUUUAGUGAGGGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAAGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq new file mode 100644 index 0000000..4c06124 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq @@ -0,0 +1,2 @@ +>d.16.b.B.japonicum +CCAACUUGAGAGUUUGAUCCUGGCUCAGAGCGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGCGUAGCAAUACGUCAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCUUUUGGUUCGGAACAACACAGGGAAACUUGUGCUAAUACCGGAUAAGCCCUUACGGGGAAAGAUUUAUCGCCGAAAGAUCGGCCCGCGUCUGAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUGUGCGGGAAGAUAAUGACGGUACCGCAAGAAUAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGGGUGCGUAGGCGGGUCUUUAAGUCAGGGGUGAAAUCCUGGAGCUCAACUCCAGAACUGCCUUUGAUACUGAAGAUCUUGAGUUCGGGAGAGGUGAGUGGAACUGCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGCAAGAACACCAGUGGCGAAGGCGGCUCACUGGCCCGAUACUGACGCUGAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGCCAGCCGUUAGUGGGUUUACUCACUAGUGGCGCAGCUAACGCUUUAAGCAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUACCAGCCCUUGACAUGUCCAGGACCGGUCGCAGAGAUGUGACCUUCUCUUCGGAGCCUGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGUCCUUAGUUGCUACCAUUUAGUUGAGCACUCUAAGGAGACUGCCGGUGAUAAGCCGCGAGGAAGGUGGGGAUGGCGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAUGCUAAGGGGCGACCCUUCGCAAAUCUCAAAAAGCCGUCUCAGUUCGGAUUGGGCUCUGCAACUCGAGCCCAUGAAGUUGGAAUCGCUAGUAAUCGUGGAUCAGCACGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGCUUUACCUGAAGACGGUGCGCUAACCAGCAAUGGAGGCAGCCGGCCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq new file mode 100644 index 0000000..9433d8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq @@ -0,0 +1,2 @@ +>d.16.b.B.subtilis +UUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGGACAGGUGGGAGCUUGCUCCCGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUACCGUUCGAAUAGGGCGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq new file mode 100644 index 0000000..f65748e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.C.pneumoniae +UUUUCUGAGAAUUUGAUCUUAGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAGUACAUAGAUAAUCUGCCCUCAACUUGGGGAUAACGGUUGGAAACGAUCGCUAAUACCGAAUGUAGUGUAAUUAGGCAUCUAAUAUAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGAAGAGUUUAUGCGAUAUCAGCUUGUUGGUGGGGUAAAAGCCCACCAAGGCGAUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCCUUAGGGUUGUAAAGCACUUUCGCCUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUUUUGGGGCUCAACCCCAAGUCAGCAUUUAAAACUAUCUUUCUAGAGGAUAGAUGGGGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGUGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGACUUGACAUGUAUUUGACAACUGUAGAAAUACAGCUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGUCCAGGGCGACACACGUGCUACAAUGGUUAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUAAAAGCUAGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCUAUUUAUAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq new file mode 100644 index 0000000..4218316 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq @@ -0,0 +1,2 @@ +>d.16.b.C.psittaci +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAAUACAUAGAUAAUCUGUCCUCAACUUGGGAAUAACGGUUGGAAACGACCGCUAAUACCGAAUGUGGUAUGUUUAGGCAUCUAAAACAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGGAGAGUCUAUGGGAUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCUUUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUCUUGGGGCUCAACCCCAAGCCAGCAUCUAAUACUAUCUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUACACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUAGUCUCAACCCUAUCCGUGUCGUAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGCUUGACAUGUAUUUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAACACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCUACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAUAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCUAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUGCCUUAAGUCGUUGACUCAACCUGCAAAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq new file mode 100644 index 0000000..5084a44 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq @@ -0,0 +1,2 @@ +>d.16.b.C.testosteroni +CGAACUAUAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGCAUGCUUUACACAUGCAAGUCGAACGGUAACAGGUCUUCGGAUGCUGACGAGUGGCGAACGGGUGAGUAAUACAUCGGAACGUGCCUAGUAGUGGGGGAUAACUACUCGAAAGAGUAGCUAAUACCGCAUGAGAUCUACGGAUGAAAGCAGGGGACCUUCGGGCCUUGUGCUACUAGAGCGGCUGAUGGCAGAUUAGGUAGUUGGUGGGGUAAAGGCUUACCAAGCCUGCGAUCUGUAGCUGGUCUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUGCCGCGUGCAGGAUGAAGGCCCUCGGGUUGUAAACUGCUUUUGUACGGAACGAAAAGCCUGGGGCUAAUAUCCCCGGGUCAUGACGGUACCGUAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUUUGUAAGACAGUGGUGAAAUCCCCGGGCUCAACCUGGGAACUGCCAUUGUGACUGCAAGGCUAGAGUGCGGCAGAGGGGGAUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAAUCCCCUGGGCCUGCACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUGGUUGUUGGGUCUUAACUGACUCAGUAACGAAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCUUACCCACCUUUGACAUGGCAGGAACUUACCAGAGAUGGUUUGGUGCUCGAAAGAGAACCUGCACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGCCAUUAGUUGCUACAUUCAGUUGAGCACUCUAAUGGGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUAGGUGGGGCUACACACGUCAUACAAUGGCUGGUACAAAGGGUUGCCAACCCGCGAGGGGGAGCUAAUCCCAUAAAGCCAGUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGUCACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCGGGUCUCGCCAGAAGUAGGUAGCCUAACCGUAAGGAGGGCGCUUACCACGGCGGGGUUCGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq new file mode 100644 index 0000000..4ae3dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq @@ -0,0 +1,2 @@ +>d.16.b.C.trachomatis.L2 +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAGCAAUUGUUUCGGCAAUUGUUUAGUGGCGGAAGGGUUAGUAAUGCAUAGAUAAUUUGUCCUUAACUUGGGAAUAACGGUUGGAAACGGCCGCUAAUACCGAAUGUGGCGAUAUUUGGGCAUCCGAGUAACGUUAAAGAAGGGGAUCUUAGGACCUUUCGGUUAAGGGAGAGUCUAUGUGAUAUCAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUAUGACGUCUAGGCGGAUUGAGAGAUUGGCCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGGAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAAGGCGGUUAAUACCCGCUGGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGUAAGUUAGUUGUCAAAGAUCGGGGCUCAACCCCGAGUCGGCAUCUAAUACUAUUUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUUCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGGUUUGACAUGUAUAUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAUAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCGACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCCGCAAGGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUAGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq new file mode 100644 index 0000000..6f67dd9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.16.b.E.coli +AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq new file mode 100644 index 0000000..7592528 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Frankia.sp +UUGAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGGGAGCUUCGGCUCUCAGCGGCGAACGGGUGAGUAACACGUGGGCAACCUGCCCCGAGCUCUGGAAUAACCUCGGGAAACCGGGGCUAAUGCCGGAUAUGACAUUGCCGGGCAUCUGGUGGUGUGGAAAGAUUUAUCGGCUCGGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGGAAGCCUGACGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCCUGUUGCGUCGGCUGUGAAAACCCGGGGCUCAACUCCGGGCCUGCAGUCGAUACGGGCAGGCUAGAGUCCGGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCCGGAACUGACGCUAAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGCGCUAGGUGUGGGGGACCUUCCACGGCCUCCGUGCCGCAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCAGGGAAAUCUCGUAGAGAUACGGGGUCCGUAAGGGUCCUGCACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUCCUAUGUUGCCAGCGAGUCGUGUCGGGGACUCAUAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUACGUCCUGGGCUGCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGUGAGGUGGAGCGAAUCCCAAAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCUUGUGGGGGGAGCCGUCGAAGGUGGGACCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq new file mode 100644 index 0000000..dada154 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq @@ -0,0 +1,2 @@ +>d.16.b.H.influenzae +AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGGUAGCAGGAGAAAGCUUGCUUUCUUGCUGACGAGUGGCGGACGGGUGAGUAAUGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGGGAACCCUGACGCAGCCAUGCCGCGUGAAUGAAGAAGGCCUUCGGGUUGUAAAGUUCUUUCGGUAUUGAGGAAGGUUGAUGUGUUAAUAGUACAUCAAAUUGACGUUAAAUACAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUAACUGGGCGUAAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCUGGGCUUAACCUAGGAAUUGCAUUUCAGACUGGGUAACUAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGAAGGCGAAGGCAGCCCCUUGGGAAUGUACUGACGCUCAUGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGCUGUCGAUUUGGGGAUUGGGCUUAGAGCUUGGUGCCCGUAGCUAACGUGAUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCUAAGAAGAGCUCAGAGAUGAGCUUGUGCCUUCGGGAACUUAGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGACUUGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGAAUCAGAAUGUCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGUACCAGAAGUAGAUAGCUUAACCUUUUGGAGGGCGUUUACCACGGUAUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq new file mode 100644 index 0000000..042147f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq @@ -0,0 +1,2 @@ +>d.16.b.L.interrogans +AACACGGAGAGUUUGAUCCUGGCUCAGAACUAACGCUGGCGGCGCGUCUUAAACAUGCAAGUCAAGCGGAGUAGCAAUACUCAGCGGCGAACGGGUGAGUAACACGUGGGUAAUCUUCCUCUGAGUCUGGGAUAACUUUCCGAAAGGGAAGCUAAUACUGGAUGGUCCCGAGAGAUCACAAGAUUUUUCGGGUAAAGAUUUAUUGCUCGGAGAUGAGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUCGGUAGCCGGCCUGAGAGGGUGUUCGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCUCAAUGGGGGGAACCUGAAGCAGCGACGCCGCGUGAACGAUGAAGGUCUUCGGAUUGUAAAGUUCAGUAAGCAGGGAAAAAUAAGCAGCAAUGUGAUGAUGGUACCUGCCUAAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAUGGUGCAAGCGUUGUUCGGAAUCAUUGGGCGUAAAGGGUGCGUAGGCGGACAUGUAAGUCAGGUGUGAAAACUGCGGGCUCAACUCGCAGCCUGCACUUGAAACUAUGUGUCUGGAGUUUGGGAGAGGCAAGUGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAGUGGCGAAGGCGACUUGCUGGCCUAAAACUGACGCUGAGGCACGAAAGCGUGGGUAGUGAACGGGAUUAGAUACCCCGGUAAUCCACGCCCUAAACGUUGUCUACCAGUUGUUGGGGGUUUUAACCCUCAGUAACGAACCUAACGGAUUAAGUAGACCGCCUGGGGACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGUCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUCACCUAGGCUUGACAUGGAGUGGAAUCAUGUAGAGAUACAUGAGCCUUCGGGCCGCUUCACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCACCUUAUGUUGCCAUCAUUCAGUUGGGCACUCGUAAGGAACUGCCGGUGACAAACCGGAGGAAGGCGGGGAUGACGUCAAAUCCUCAUGGCCUUUAUGUCUAGGGCAACACACGUGCUACAAUGGCCGGUACAAAGGGUAGCCAACUCGCGAGGGGGAGCUAAUCUCAAAAAUCCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGACCUUGUACACACCGCCCGUCACACCACCUGAGUGGGGAGCACCCGAAGUGGUCUUUGCCAACCGCAAGGAAGCAGACUACUAAGGUGAAACUCGUGAAGGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq new file mode 100644 index 0000000..1c5e7c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq @@ -0,0 +1,2 @@ +>d.16.b.M.gallisepticum +UUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAUGUAGCAAUACAUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUGCCUUAUAGUGGGGGAUAACUAGUCGAAAGAUUAGCUAAUACCGCAUAACAAGUUAACUAUCGCAUGAGAAUAACUUUAAAGAAGCAACUGCUUCGCUAUAAGAUGAGGGUGCGGCAUAUCAGCUAGUUGGUGAGGGUAAUGGCCCACCAAGGCGAUGACGUGUAGUUAUGCUGAGAGGUAGAAUAACCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGGACGAAAGUCUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUAGAUUGUAAAGUUCUUUUAUUUGGGAAGAACAGUUAGUAGAGUGGAAAGCUAUUAAUUUGACUGUACCAUUUGAAUAAGUAACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAACAAGCGCAGGCGGAUUAGAAAGUCUGGUGUUAAAAGCAAUUGCUUAACGAUUGUAUGCAUUGGAAACUUCUAGUCUAGAGUUUGGUAGAGAGUCCUGGAACUCCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGAGGCGAAGGCGAGGACUUGGGCCAAUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACUGUAAACGAUGGAUGUUAAGUGUCGGAGCGAAUACUUCGGUGCUGCAGUUAACACAUUAAACAUCCUGCCUGAGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCUUGGGCGAAGCUAUAGAAAUAUAGUGGAGGUCAACCCAAUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACUUUGUCUAACGAGACUGCCAACGUAAGUUGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUUGCAAAUCCGUAAGGUGGAGCUAAUCUGUAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGCCCUCAUGAAGUCGGAAUCACUAGUAAUCGCGAAUCAGCCAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAGAGCUGGUAAUAUCUAAAACCGUGUUGCUAACCGCAAGGAAGCGCAUGUCUAGGGUAGGGCCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUUACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq new file mode 100644 index 0000000..b13dc11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.16.b.M.genitalium +CAAUUUUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAAGUAGCAAUACUUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUACCUUAUAAUGGGGGAUAACUAGUUGAAAAACUAGCUAAUACCGCAUAAGAACUUUAGUUCGCAUGAAUUAAAGUUGAAAGGACCUGCAAGGGUUCGUUAUUUGAUGAGGGUGCGCCAUAUCAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCAAUGACGUGUAGCUAUGCUGAGAAGUAGAAUAGCCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGAGCGAAAGCUUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUGAUUGUAAAGUUCUUUUAUUUGGGAAGAAUGACUCUAGCAGGCAAUGGCUGGAGUUUGACUGUACCACUUUGAAUAAGUGACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGCGGAUUGAAAAGUCUGGUGUUAAAGGCAGCUGCUUAACAGUUGUAUGCAUUGGAAACUAUCAGUCUAGAGUGUGGUAGGGAGUUUUGGAAUUUCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGAAGGAACACCAGUGGCGAAGGCGAAAACUUAGGCCAUUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACCGUAAACGAUAGAUACUAGCUGUCGGAGCGAUCCCUUCGGUAGUGAAGUUAACACAUUAAGUAUCUCGCCUGGGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCCUUGGCAAAGUUAUGGAAACAUAAUGGAGGUUAACCGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACAUUGUUUAACGAGACUGCUAAUGUAAAUUGGAGGAAGGAAGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUAGCCAACUUGUAAAAGUGAGCAAAUCUGAAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGUCCUCAUGAAGCUGGAAUCACUAGUAAUCGCGAAUCAGCUAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAAAGCUGGUAAUAUUUAAAAACGUGUUGCUAACCUUUAUUGGAAGCGCAUGUCAAGGAUAGCACCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq new file mode 100644 index 0000000..340893a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.hyopneumoniae +CGCAAUCAUGAGAGUUUGAUCCUGGCUCAGGAUAAACGCUAGCUGUGUGCUUAAUACAUGCAUGUUGAACGGAAUAUUUUAGUUCGCUAAAAUAUUUAGUAGCAAAUGGGUGAGUAACACGUACCUAACCUACCUUUUGGACUGGGAUAACCAUUGGAAACAGUGGCUAAUACCAGAUAUGAUAAAAAUUUGCAUGAAUUUUUAUUCAAAGGAGCCUUCAAGCUUCACCAAGAAAUGGGGGUGCGCAACAUUAGUUAGUUGGUAGGGUAAAAGCCUACCAAGACGAUGAUGUUUAGCGGGGCCAAGAGGUUGUACCGCCACACUGGGAUUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUAUUCCACAAUAAGCGAAAGCUUGAUGGAGCGACACAGCGUGCAGGAUGAAGUCUUUCGGGAUGUAAACUGCUGUUGUAAGGGAAGAAAAAACUAGAUAGGAAAUGCUCUAGUCUUGACGGUACCUUAUUAGAAAGCGACGGCAAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGUCCGUAGGUUUUUUGUUAAGUUUAAAGUUAAAUGCUAAAGCUCAACUUUAGUCCGCUUUAGAUACUGGCAAAAUAGAAUUAUGAAGAGGUUAGCGGAAUUCCUAGUGGAGUGGUGGAAUACGUAGAUAUUAGGAAGAACACCAAUAGGCGAAGGCAGCUAACUGGUCAUAUAUUGACACUAAGGGACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAUCAUUAGUUGGUGGCAAAAGUCACUAACACAGCUAACGCGUUAAAUGAUCCGCCUGAGUAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGGAACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUUGAAGAUACGCGUAGAACCUUACCCACUCUUGACAUUCUCGCAAAACUAUAGAGAUAUAGCCGAGGCUAACGAGAUCACAGAUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUAGGUUAAGUCCUGCAACGAGCGCAACCCUUUUCUUUAGUUGCUAACAUUUAGUUGAGAACCCUAAAGAUACUGCCGGCGCAAGCCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCUCUUACGAGUGGGGCAACACACGUGCUACAAUGGCUACUACAAAGAGCAGCAAAACAGUGAUGUCAAGCUAAUCUCAAAAAAGUAGUCUCAGUUCGGAUUGAAGUCUGCAACUCGACUUCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCUAUACUGCGGUGAAUACGUUCUCGGGUUUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUAAUGCCCAAAGUCGGUGAGUUAACUUCGGAGACCAUUGCCUAAGGCAGGACCGAUGACUGGGGUGAAGUCGUAACAAGGUAUCCCUACGAGAACGUGGGGAUGGAACACCUCCUUUCUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq new file mode 100644 index 0000000..86728a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.leprae +UUGUUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGUCUCUAAAAAAUCUUUUUUAGAGAUACUCGAGUGGCGAACGGGUGAGUAACACGUGGGUAAUCUGCCCUGCACUUCAGGGAUAAGCUUGGGAAACUGGGUCUAAUACCGGAUAGGACUUCAAGGCGCAUGUCUUGUGGUGGAAAGCUUUUUGCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGACGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGUCCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCACCAUCGACGAAGGUCUGGGUUUUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCAGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGUACUAGGUGUGGGUUUCCUUCCUUGGGAUCCGUGCCGUAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUGCACAGGAUGCGUCUAGAGAUAGGCACUCCCUUGUGGCCUGUGUGCAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGUAAUGGUGGGGACUCGUGAGAGACUGCCGCGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGCAAGGUUAAGCGAAUCCUUUUAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCAGUGGCCUAACCCUCGGGAGGGAGCUGUCCAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq new file mode 100644 index 0000000..539e3c1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq @@ -0,0 +1,2 @@ +>d.16.b.P.pacificensis +AGAGUUUGAUCAUGGCUCAGAUUGAUCGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGAACGAUGAUAGCUUGCUAUCAGGCGUCGAGCGGCGGACGGGUGAGUAAUACUUAGGAAUCUACCUAGUAGUGGGGGAUAGCUCGGGGAAACUCGAAUUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCAUUAGACCUUGCGCUAUUAGAUGAGCCUAAGUCGGAUUAGCUAGAUGGUGGGGUAAAGGCCUACCAUGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACCGGGACUGAGACACGGCCCGGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGCCUUUUGGUUGUAAAGCACUUUAAGCAGUGAAGAAGACUCUUCGGUUAAUACCCGGGGACGAUGACAUUAGCUGCAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGAGCGUAGGUGGCUUGAUAAGUCAGAUGUGAAAUCCCCGGGCUUAACCUGGGAACUGCAUCUGAAACUGUUAGGCUAGAGUAGGUGAGAGGGAAGUAGAAUUUCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGAUGGCGAAGGCAGCUUCCUGGCAUCAUACUGACACUGAGGCUCGAAAGCGUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCUACUAGUCGUUGGGUCCCUUGAGGACUUAGUGAUGCAGCUAACGCAAUAAGUAGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCCGGUCUUGACAUACACAGAAUCUUGUAGAGAUACGAGAGUGCCUUCGGGAAUUGUGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUUAGUUACCAGCGGGUUAAGCCGGGAACUCUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACCACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGUAGGUACAGAGGGCAGCUACACAGCGAUGUGAUGCGAAUCUCAAAAAGCCUAUCGUAGUCCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGUAGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGAUUGCACCAGAAGUGGUUAGCCUAACUUAGUGAGGGCGAUCACCACGGUGUGGUCGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCCGUAGGGGAAACCUGCGGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq new file mode 100644 index 0000000..a0ca78a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.b.P.vulgaris +UAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGUAACAGGAGAAAGCUUGCUUUCUUGCUGACGAGCGGCGGACGGGUGAGUAAUGUAUGGGGAUCUGCCCGAUAGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUGACGUCUACGGACCAAAGCAGGGGCUCUUCGGACCUUGCGCUAUCGGAUGAACCCAUAUGGGAUUAGCUAGUAGGUGAGGUAAUGGCUCACCUAGGCAACGAUCUCUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUAGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGUGAUAAAGUUAAUACCUUUAUCAAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUCAAUUAAGUCAGAUGUGAAAGCCCCGAGCUUAACUUGGGAAUUGCAUCUGAAACUGGUUGGCUAGAGUCUUGUAGAGGGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGUCGAUUUAGAGGUUGUGGUCUUGAACUGUGGCUUCUGGAGCUAACGCGUUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCAGCGAAUCCUUUAGAGAUAGAGGAGUGCCUUCGGGAACGCUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGCGUAAUGGCGGGAACUCAAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGAACUCAUAAAGUCUGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUCAGAAUGCUACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq new file mode 100644 index 0000000..37dd472 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq @@ -0,0 +1,2 @@ +>d.16.b.R.erythropolis +UCAACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGUAAGGCCUUCGGGGUACACGAGCGGCGAACGGGUGAGUAACACGUGGGUGAUCUGCCCUGCACUUCGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACCUCCUAUCGCAUGGUGGGUGGUGGAAAGAUUUAUCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGACCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGCAAGUGACGGUACCUGCAGAAGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGUUCGUAGGCGGUUUGUCGCGUCGUUUGUGAAAACCAGCAGCUCAACUGCUGGCUUGCAGGCGAUACGGGCAGACUUGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAACGAAAGCGUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCGCUAGGUGUGGGUUCCUUCCACGGAAUCCGUGCCGUAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUAUACCGGAAAGCUGCAGAGAUGUGGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAUCUUAUGUUGCCAGCACGUUAUGGUGGGGACUCGUAAGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCAGUACAGAGGGCUGCGAGACCGUGAGGUGGAGCGAAUCCCUUAAAGCUGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCGGUGGCUUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq new file mode 100644 index 0000000..4cea7ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq @@ -0,0 +1,2 @@ +>d.16.b.R.felis.URRWXCal2 +GACAGAAUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGGACGGACUAAUUGGGGCUUGCUCCAAUUAGUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUGCCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACAGAGGAAAGAUUUAUCGCUGAUGGAUGAGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAAGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUCGCGGAUCGCAGAGAUGCUUUCCUUCAGCUCGGCUGGACCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCAUUCUUAUUUGCCAGCGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAGACGGCGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq new file mode 100644 index 0000000..4768ec6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq @@ -0,0 +1,2 @@ +>d.16.b.R.prowazekii +AUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGAACGGAUUAACUAGAGCUCGCUUUAGUUAAUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUACCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACGGAGGAAAGAUUUAUCGCUGAUGGAUGGGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAAUGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAGGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUUACGGAUUGCAGAGAUGCUUUCCUUCAGUUCGGCUGGGCCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUCUUAUUUGCCAGUGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAUACGGUGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq new file mode 100644 index 0000000..639b9c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq @@ -0,0 +1,2 @@ +>d.16.b.S.acidiscabies +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUCACUCCUGCCUGCAUGGGCGGGGGUCGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGGAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUGUGUUGCCAGCGUGCCCUUCGGGGUGACGGGGACUCACAGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAAGAGCUGCGAAACCGUGAGGUGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq new file mode 100644 index 0000000..1181b57 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.aureus +UUUUAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGAACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUGCAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGUAAGUAACUGUGCACAUCUUGACGGUACCUAAUCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCGCGUAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGAAAACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGCAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAUGUGCGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAAAUCUUGACAUCCUUUGACAACUCUAGAGAUAGAGCCUUCCCCUUCGGGGGACAAAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAAGCUUAGUUGCCAUCAUUAAGUUGGGCACUCUAAGUUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACAUCAAAUCAUCAUGCCCCUUAUGAUUUGGGCUACACACGUGCUACAAUGGACAAUACAAAGGGCAGCGAAACCGCGAGGUCAAGCAAAUCCCAUAAAGUUGUUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGUAGAUCAGCAUGCUACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGCCGGUGGAGUAACCUUUUAGGAGCCAGCCGUCGAAGGUGGGACAAAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq new file mode 100644 index 0000000..2548398 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.bottropensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUCGCCCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGGUGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq new file mode 100644 index 0000000..bc38f32 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq @@ -0,0 +1,2 @@ +>d.16.b.S.diastatochromogenes +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACCACUAGGGGCAUCUCUUGGUGGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq new file mode 100644 index 0000000..8d346c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.eurythermus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCUCCUUCGGGAGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCUCCAAGGCAUCUUGGAGGUUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq new file mode 100644 index 0000000..89dcb68 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.griseus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAACACUCUGUCCCGCAUGGGACGGGGUUAAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCUAGCUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUAUACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCGCGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq new file mode 100644 index 0000000..ea52e53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.neyagawaensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACGCGCUCGGGCAUCCGAUGUGCGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACGCCGGAAACACCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq new file mode 100644 index 0000000..a046f62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.nodosus +UUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCGGGGAGGCAUCUCCCUGGUUGGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGCCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGCGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCCAAGGUGGGACUGGCGAUUGGGACGAAAUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq new file mode 100644 index 0000000..f530e47 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq @@ -0,0 +1,2 @@ +>d.16.b.S.sampsonii +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCGCUUUCGGGCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUGACUGUCCAUCGCAUGGUGGAUGGUGUAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGUCUGGAGACAGGCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq new file mode 100644 index 0000000..1155f53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq @@ -0,0 +1,2 @@ +>d.16.b.S.scabiei +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCGUAAGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq new file mode 100644 index 0000000..8cd1523 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq @@ -0,0 +1,2 @@ +>d.16.b.S.tendae +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACUGACCCUCGCAGGCAUCUGCGAGGUUCGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGCAAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq new file mode 100644 index 0000000..d849fb4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Streptomyces.sp +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAAUACCUUCCCUCGCAUGGGGGUGGGUUCAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACAUCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCUUACGGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq new file mode 100644 index 0000000..0e4a9bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Synechococcus.sp +CAAAAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGGCUCUUCGGAGCUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUGCCUACAGGACGGGGACAACAGUUGGAAACGACUGCUAAUACCCGAUGUGCCGAGAGGUGAAACAUUUAUGGCCUGUAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCGACGGAGCAACGCCGCGUGGGGGAGGAAGGUUUUUGGACUGUAAACCCCUUUUCUCAGGGAAGAAGAAAGUGACGGUACCUGAGGAAUAAGCCUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCCUGCAGGCGGUUAAUCAAGUCUGUUGUCAAAGCGUGGGGCUCAACCUCAUACAGGCAAUGGAAACUGAUUGACUAGAGUAUGGUAGGGGUAGCGGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAAGAACACCAGCGGCGAAAGCGCGCUACUGGGCCAUAACUGACGCUCAUGGACGAAAGCUAGGGGAGCGAAAGGGAUUAGAUACCCCUGUAGUCCUAGCCGUAAACGAUGAACACUAGGUGUUGCGUGAAUCGACCCGCGCAGUGCCGUAGCCAACGCGUUAAGUGUUCCGCCUGGGGAGUACGCACGCAAGUUGGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUCCCCCGAAUCUCUUGGAAACGAGAGAGUGCCUUCGGGAGCGGGGAGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCACGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAGAGAAACUGCCGGUGACAAACCGGAGGAAGGUGUGGACGACGUCAAGUCAUCAUGCCCCUUACAUCCUGGGCUACACACGUACUACAAUGCUCCGGACAGCGAGACGCGAAGCCGCGAGGUGAAGCAAAUCUCCCAAACCGGGGCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUCAGCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUUGGCCAUGCCCGAAGUCGUUACCCUAACCGUUCGCGGAGGGGGGCGCCGAAGGUAGGGCUGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq new file mode 100644 index 0000000..2d0e8e9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq @@ -0,0 +1,2 @@ +>d.16.b.T.maritima +UAUAUGGAGGGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAACACAUGCAAGUCGAGCGGGGGAAACUCCCUUCGGGGAGGAGUACCCAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUCCGGAGGGGGAUAACCAGGGGAAACCCUGGCUAAUACCCCAUACGCUCCAUCAACGCAAGUUGGUGGAGGAAAGGGGCGUUUGCCCCGCCGGAGGAGGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGACGGGUAGCCGGCCUGAGAGGGUGGUCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGGAAACCCUGAUCCAGCGACGCCGCGUGCGGGACGAAGCCCUUCGGGGUGUAAACCGCUGUGGCGGGGGAAGAAUAAGGUAGGGAGGAAAUGCCCUACCGAUGACGGUACCCCGCUAGAAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUACCCGGAUUUACUGGGCGUAAAGGGGGCGUAGGCGGCCUGGUGUGUCGGAUGUGAAAUCCCACGGCUCAACCGUGGGGCUGCAUCCGAAACUACCAGGCUUGGGGGCGGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGCAGGAACGCCGGUGGGGAAGCCGGUCUCCUGGGCCGACCCCGACGCUGAGGCCCGAAAGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCCCACUAGGUGUGGGGGGGUAAUCCCUCCGUGCUGAAGCUAACGCGUUAAGUGGGCCGCCUGGGGAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCGUGUGGUUUAAUUGGAUGCUAAGCCAAGAACCUUACCAGGGCUUGACAUGCCGGUGGUACCUCCCCGAAAGGGGUAGGGACCCAGUCCUUCGGGACUGGGAGCCGGCACAGGUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGCCCCUAGUUGCCAGCGGUUCGGCCGGGCACUCUAGGGGGACUGCCGGCGACGAGCCGGAGGAAGGAGGGGAUGACGUCAGGUACUCGUGCCCCUUAUGCCCUGGGCGACACACGCGCUACAAUGGGCGGUACAAUGGGUUGCGACCCCGCGAGGGGGAGCCAAUCCCCAAAGCCGCCCUCAGUUCGGAUCGCAGGCUGCAACCCGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCACCCGAGUCGGGGGCUCCCGAAGACACCUACCCCAACCCGAAAGGGAGGGGGGGUGUCGAGGGAGAACCUGGCGAGGGGGGCGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq new file mode 100644 index 0000000..23d8958 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq @@ -0,0 +1,2 @@ +>d.16.b.T.pallidum.A +AUGAUGGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGUGCGUUUUAAGCAUGCAAGUCGAACGGCAAGGAAGCGAAUUUUCGUUUCUCUAGAGUGGCGGACUGGUGAGUAACGCGUGGGUAAUCUGCCUUUGAGAUGGGGAUAGCCUCUAGAAAUAGGGGGUAAUACCGAAUACGCUCUUUUGGACGUAGUCUUUGAGAGGAAAGGGGCUGCGGCCUCGCUCAGAGAUGAGCCUGCGACCCAUUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGUCGAUGGGUAUCCGACCUGAGAGGGUGACCGGACACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUAUUCCGCAAUGGGCGAAAGCCUGACGGAGCGACACCGCGUGGAUGAGGAAGGUCGAAAGAUUGUAAAGUUCUUUUGCCGACGAAGAAUGAGGACGGGAGGGAAUGCCCGUUUGAUGACGGUAGUCGUGCGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCAUGCAGGCGGACUGGUAAGCCUGGUGUGAAAUCCCCGAGCUCAACUUGGGAACUGCACUGGGUACUGCUGGUCUAGAAUCACGGAGGGGAAACCGGAAUUCCAAGUGUAGGGGUGGAAUCUGUAGAUAUUUGGAAGAACACCGGUGGCGAAGGCGGGUUUCUGGCCGAUGAUUGACGCUGAGGUGCGAAGGUGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACACAGUAAACGAUGUACACUAGGUGUUGGGGCAUGAGUCUCGGCGCCGACGCGAACGCAUUAAGUGUACCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGUUUGACAUCAAGAGGAGCGCCGUAGAAAUGCGGUGGCGUAGCGAUACGCCUCUUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUACUGCCAGUUGCCAGCAAGUGGUGUUGGGGACUCUGGCGGAACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGUCCGGGGCUACACACGUGCUACAAUGGUUGCUACAGAGCGAUGCGAGGUUGUGAAGUGGAGCAAACCGCAAAAAGGCAAUCGUAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGCACAUCAGCAUGGUGCGGUGAAUGUGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUCCGAGUUGGAGAUACCCGAAGUCACUAGCCUAACCCGCAAGGGAGGGCGGUGCCGAAGGUAUGUUUGGUAAGGAGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq new file mode 100644 index 0000000..575befd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq @@ -0,0 +1,2 @@ +>d.16.c.C.caldarium +UAUAAUGGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGUACGAGAAUUUUAUUCUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCUCUAGGAGGGGGAUAACAGUUGGAAACGAUUGCUAAAACCCCAUAUGCCAUUAUUGGUGAAAAAGAUUUAUCUGCCUGGAGAUGAGCUCGCGGCUGAUUAGCUAGUUGGUAGGGUAAUGGCUUACCAAGGCAACGAUCAGUAGCUGGUCUUAGAGGAUGAUCAGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCACAAUGGGCGAAAGCCUGAUGGAGCAAUACCGUGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUUUCAGGAAAGAAACUUUGACGGUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAUCAAGUCUGCUGUUAAAGCUUGAGGCUUAACCUCAAAAAAGCAGUGGAAACUGAUAGACUAGAGAAUGGUAGGGGCAGAGAGAAUUCUCAGUGUAGCGGUGAAAUGCGUAGAUAUUGAGAAGAAUACCGAUAGCGAAGGCGCUCUGCUGGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUGUGAGUAAAAUUGUGCAGUAUCGAAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGUUACUAAUUUCCUUGAAAGAGGAAAGUGCCUUUGGGAAAGUAAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUACCAUCAUUAAGUUGGGGACUCUAAAGAGACUGCCGGUGAUAAACCGGAGGAAGGUAAGGAUGAGGUCAAGUCAUCAUGCCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGUUAGGACAAUAAGUCGCAAAUUCGUGAGAACUAGCUAAUCUUAUAAACCUAAUCUCAGUACGGAUUGUAGGCUGCAACUCGCCUACAUGAAGACGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCCAUGUCCGAAAUCAUUACUCUAACCUUAAUGGAGGAGGAUGCUUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUUACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq new file mode 100644 index 0000000..b5a551f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq @@ -0,0 +1,2 @@ +>d.16.c.C.fragile +UUGAAAUGGAGAGGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGAUAUGCUUAACACAUGCAAGUCGAACGAAUAUUAAGUUUUCUUAAAUUUGUAGAAAUUUAAUAUUAGUGGCGAACGGGUGAGUAACGCGUAAGAAUCUGCUUUUGGGUAAAGAAUAACAAUUGGAAACGAUUGCUAAUACUUUAUAGGCUGAGGAGUUAAAGGUUUUAUUUCCGCCCAGAAAUGAGCUUGCGUCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAAUGAUCAGUAGUUGGUCUGAGAGGAUGAUCAACCACACUGGGACUGAGAUACGGCCCAGACCUUUACGGAGGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUAUCGCGUGAAGGAUGACGGCCUGUGGGUUGUAAACUUCUUUUCUUAAGAAAGAAUUCUGACGGUACUUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGAAAUUAUUGGGCGUAAAGAGUUUGUAGGUGGUUUUUUAAGUCUACUGUUAAAUAUCAGAGCUUAACUUUGAACAAGCAGUAUGAAACUAAUUAACUUGAGUUUGGUAGAGGCAGAGGGAACUCUCGAUGUAGUGGUGAAAUACGUAGAUAUCGGGGGGAACACCAGUAGCGAAAGCGCUCUGCUGGGCCAUAACUGACACUGAGAAACGAAAGCUAGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCUAGCUGUAAACGAUGGAUACUAAGUAUUGGGCUUUUUGAAGUUCAGUGUUGAAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAAUUGACAUACUCGUUGGUUUUUUAGAAAUAAAAAACUGUUAAAGAGAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGUUAUCUAGAGAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAAGUCCUGGGCGACACACGUGCUACAAUGGUAUAGACAAAGGGAAGCAAAUCUGCGAAGAGUAGCAAAUCUCAAAAACUAUAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCCAUACAGCGGUGAAUAUGUUCUCGGGCCUUGUACACACCGCCCAUCACGCUCGAGAAAUUGGAAAUACCCAAAGUCAUCAUUCUAACCAUAUUUUUUGGAAGAUAAUGCCAAAGGUAGAGCUAGUGACUCAAGCGAAGUUGUAACAAGGUAACCGUACUGGAAGGUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq new file mode 100644 index 0000000..665ca3f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq @@ -0,0 +1,2 @@ +>d.16.c.C.reinhardtii +AUCCAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGAGCAAAGCAAUUUGUGUAGUGGCGAACGGGUGCGUAACGCGUAAGAACCUACCUAUCGGAGGGGGAUAACAUUGGGAAACUGUUGCUAAUACCCCAUACAGCUGAGGAGUGAAAGGUGAAAAACCGCCGAUAGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGGGGGUAACGGCCUCCCAAGGCCACGAGCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUUCGCAAUGGGCGCAAGCGACGGAGCAAUGCCGCGUGCAGGAAGAAGGCCUGUGGGUCGUAAACUGCUUUUCUCAGAGAAGAAGUUCUGACGGUAUCUGAGGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUGUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUCGUAAAGUCUAAUGUCAAAUACCAGGGCUCAACCUUGGACCGGCAUUGGAGUACUCACGAGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCAUGUGGAGCGGUGAAAUGCGUAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGCUCUGCUGGGCCGAAACUGACACUGAGAGACGAAAGCUGGGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCCCAGCCGUAAACUAUGGAGACUAAGUGCUGCCGCAAGCAGUGCUGUAGCUAACGCGUUAAGUCUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGACCGCACAAGCGGUGGAUUAUGUGGAUUAAUUCGAUACAACGCGAAGAACCUUACCAGGGUUUGACAUGUCAAGAACCUCUCAGAAAUGGGAGGGUGCCCUAACGGACUUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCUGUGAAGUGUAUAGUUAAGUCUCAUAACGAGCGCAACCCUCGUCUUUAGUUGCCAUUUGGUUCUCUAAAGAGACUGCCAGUGUAAGCUGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACAUCCUGGGCUUCACACGUAAUACAAUGGUUGGGACAAUCAGAAGCGACUCGUGAGAGCUAGCGGCUCUGUUAAACCCAACCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCAGUCAGCUAUAUGGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUCUGCUCCAAGUCGUUACCCUAACCUUCGGGAGGGGGGCGCCUAAAGCAGGGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGGGCUACUGGAAGGUGGCCCUGGCUCACCUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq new file mode 100644 index 0000000..c5ee178 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.c.C.vulgaris +UGCCUGCAGAGAGUUYGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGCAUGCAAUUUGGCUUGCCAGAUUGCGAUGAGUGGCGGACGGGUGAGUAACACGUAAGAACCUACCUUUUGGAGAGGGAUAACCAUUGGAAACGAUGGCUAAUACCUCGUAUUGCUGAGAAGUGAAAGAUGAAAAUCGCCAAUAGAUGGGCUUGCGGCUGAUUAGCUUGUUGGUGAGGUAAUGGCUUACCAAGGCAAUGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGACAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGAAGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAGAAGAAGCAUUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUAAAAAGUCUCCUGUCAAAGAUCAGGGCUUAACCCUGGGCCGGCAGGAGAAACUCUUAGGCUAGAGUUUGGUAGGGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACACCAAAGGCGAAAGCACUCUGCUGGGCCAUAACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAAGGGAUUAGAUACCCCUGUAGUCCUCGCCGUAAACGAUGGAUACUAGAUGUUGGGUAGGUUAAAUCACUCAGUAUCGUAGCUAACGCGUGAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGCCACUUUUUCCCUGAAAGGGGAAGUUCCAGAGUGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUUGAAUUGCCAGUAAUGGGAAAUUCAAAAGACUGCCGGUGACAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGAGAUGCAAACCCGCGAGGGCUAGCCAACCUCAAAAACCCGGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCUUUUAGGAGGGGGACGCCUAAGGCAGAGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGWGGYUGGAUCACCUCCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq new file mode 100644 index 0000000..3b7fc1b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq @@ -0,0 +1,2 @@ +>d.16.c.Cryptomonas.sp +AAAUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGUACGAAAGUUUUUAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUAGGAGGAGGGGGAUAACAGCUGGAAACGGCUGCUAAUACUCCAUAUGCUGAAGAGUGAAAGGGAAACCACCUAAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUAGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUCUCAAGGAAGAAGUUCUGACGGUACUUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGAUGCAAGCGUUAUCCGGAAUUACUGGGCAUAAAGCGUCUGUAGGUUGUUUAGUAAGUCUGCUGUUAAAGACUAGGGCUUAACCCUAGAAAAGCAGUGGAAACUGCUAGACUUGAGUGUGGUAGAGGUAGAGGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAAGAACACCAAUGGCGAAAGCACUUUACUGGGCCAUAACUGACACUGAGAGACGACAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUACGUAUUAACCCGUACAGUAUCGUAGCUAAGGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCACAAAUUUUCUUGAAAAAGAAAAGUGCCUUCGGGAAUGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCAUCAUUAAGUUGGGCACUUUAAAAAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGACGACGUCAAGUCAGCAUGCCCCUUACACUCUGGGCUACACACGUACUACAAUGGUCGAGACAAAAAGUCGCAAACUUGUGAAAGUAAGCUAAUCUUAUAAACUCGAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUAGUCAUACCCAAAGUCGUUACCUUAACCAUUCGGAGGGGGGCGCCUAAGGUAGGGUUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq new file mode 100644 index 0000000..6c04b9e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq @@ -0,0 +1,2 @@ +>d.16.c.E.gracilis +UGGAAAUGACGAGUUUGAUCCUUGCUCAGGGUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUUGAACGAAAUUACUAGCAAUAGUAAUUUAGUGGCGGACGGGUGAGUAAUAUGUAAGAAUCUGCGCUUGGGCGAGGAAUAACAGAUGGAAACGUUUGCUAAUGCCUCAUAAUUUACUAGAUCUAUGUGAGUAGCUAGUUAAAGAGAAUUUCGCCUAGGCAUGAGCUUGCAUCUGAUUAGCUUGUUGGUGAGGUAAAGGCUUACCAAGGCGACGAUCAGUAGCUGAUUUGAGAGGAUGAUCAGCCACACUGGGAUUGAGAACGGAACAGACUUCUACGGAAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAAGGAAGACGGCCUUUGGGUUGAAAACCUCUUUUCUCAAAGAAGAAGAAAUGACGGUAUUUGAGGAAUAAGCAUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAUGCGAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGUUUGUAGGCGGUCAAGUGUGUUUAAUGUUAAAAGUCAAAGCUUAACUUUGGAAGGGCAUUAAAAACUGCUAGACUUGAGUAUGGUAGGGGUGAAGGGAAUUUCCAGUGUAGCGGUGAAAUGCGUAGAGAUUGGAAAGAACACCAAUGGCGAAGGCACUUUUCUAGGCCAAUACUGACGCUGAGAAACGAAAGCUGAGGGAGCAAACAGGAUUAGAUACCCUGUAGUCUUGGCCGUAAACUAUGGAUACUAAGUGGUGCUGAAAGUGCACUGCUGUAGUUAACACGUUAAGUAUCCCGCCUGGGGAGUACGCUUGCACAAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACACGAAGAACCUUACCAGGAUUUGACAGGAUCUAGGAAGUUUGAAAGAACGCAGUACCUUCGGGUAUCUAGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUUAAUUAACGCUUGUCAUUUAGAAAUACUGCUGGUUAUUACCGGAGGAAGGUGAGGACGACGUCAAGUCAUCAUGCCCCUUAUAUCCUGGGCUACACACGUGCUACAAUGGUUAAGACAAUAAGUUGCAAUUUUGUGAAAAUGAGCUAAUCUUAAAACUUAGCCUAAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUCGGCUGUGCCCGAAGUUAUUAUCUUGCCUGAAAAGAGGGAAAUACCUAAGGCCUGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGUGGCUGGAACAACUCC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq new file mode 100644 index 0000000..13a55b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq @@ -0,0 +1,2 @@ +>d.16.c.H.africana +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGAACGAGAAAUAGAACAACUAUUUCUAGUAGCGAACGGGUGCGUAAUUACAUAAGAACUUAUCCUUUUAAGAAGGAAAUAACAAAUAACAAAUGGAAACAUUUGCUAAUGUCCUAUAAGCUGAAAAGUAAAAGGAUUAAAUCCACUAAAGGUAAGGCUUAUGUCUAGUUAGUUGGUAAGGUAACAGCUUAACAAGACAAUGAUCAGUAAUUGGUCUGAGAGGAUGAUCAAUCACACUGGAACUGAGAUAAGGUCCAGACUCCUACGGGUGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGGGCAAUGUUGCGUGAAGGCAGAAGGCCGAUAGGUUGUAAACUUCUUUUGUGAGAAAAUAAGGAAAAUGACAGUAUCUCAAGAAUAAGCAUCGGCUAACUUUGUGCCAGCAGCCGCGGUGAUACAGAGGAUGCGAGCAUUAUCCGGAAUUAUUGGGCGUAAAGUGUUUUAAGGUGGCUUUAUAAGUCUAUCGUUAAAUCUCAGAGCUUAACUCUGAUUAGGCGAUUGACUAUUAAGCUAGAGCUUUGAAUAAAGCAAGGGGAAUUUCUAAUGAAGCGGUUAAAUGCGUUGAGAUUGGAAAGAACACCAAGGGCGAAAGCACUCUGCUGGGCCAAAAUUGACACUGAUAAACGAAAGCUAGGGUAGCGAGAGGGAUUAGACACCCCAAUAGUCCUAGCUGUAAACAAUGGAUACUUAGCAUUACUAUAUGAAAAGAUAGCUAAGCUUAAAGCUAACGCAAUAAGUAUCCCGCCUGGGAAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGGCGGGGGUUCACGCAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGAUUGUAUGUCGUAAUCUUUCUGAAAAAGUAAGAUACGUAUUUAUUUAAUAAAUAAAUACGUAGACACAGGUGGUGCAUGGCUGUCGUCAGCCCGUGCUGUCAAGCGUAGGGUUAACUCCCAUAACGGGCGCAACUCCCAUGUUUAGUUACCAAUUUAUGGUACUCUAAACAAACAGCUAAUGAUAAAUACUAAAUUAGAGGAAGGUGGGGAAGACGUCAAGUCAUCAUGCCCUUUAUACUCUGGGCUACACGCGUGCUACAAUGGCUGGGACAAAAUGUUGCAAUUCUGUAAAGAUAUAGCAAAACAUAAAACCCAGUCUCAGUUCGGAUUCGGGCUGCAACUCGCCCGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCAAUACAGCGGUGAAUAAGUCACCGGACCUUGUACACACCGCCCGUCACACUCAGGAAAUUGGUCAUGCCCUAACUCAUUUUAAUAUAAUGAUAAAGGUGAGGCUGGUAACUAGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq new file mode 100644 index 0000000..7f1d3dd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq @@ -0,0 +1,2 @@ +>d.16.c.H.akashiwo +UUUUAGGAUAUAAUUGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAGAGGUUUUUAAAGAUUUUUCUUAAAAAACUGAAAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUGCCUUUAGGAAAGGGACAACAUUUGGAAACGAAUGCUAAUACCUUAUAUGCCUAUUAUAACUUGUAUAAUUAAUAGGUGAAAAGUUUUCUGCCUAGAGAGGAGCUCGCGGCUGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCAGUAACUGAUUUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAAGCCUGACAGAGCAAUACCGCGUGAGGGAUGACAGUCCUAUGGAUUGUAAACCUCUUUUUUCAGGGAGGAAGUUCUGACGUUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGUGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAAUGUGUCUGUUGUUAAAUCUUAAGGCUCAACCUUAAACCAGCAAUGGAAACUAUUAUGACUUGAGUGUGGUAGAGGUAGAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAUAUUGGAAAGACCACCAAUGGCGAAGGCACUCUACUGGGCCAUUACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGGAUACUAGAUGUCGCAUGUAUCGACCCAUGCGGUAUUAUAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUAGUACGAAGUUUUUUGAAAAAAAAACCACCUUCGGGAACGUACAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCUUUCGAGGAUAUUUAGAAAGACUGCCGAUUAUAAAUCGGAGGAAGGUAAGGACGACGUCAAGUCAUCAUGCCCCUUACACUCUGGGCUACACACGUGCUACAUUGGGUAGAACAAUAAGUUGCUAAGUUGCGAAACCAAGCGAAUCUUCAAAUCUACUCUAAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUAAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUCACACCCAAAGUCGUUAUUCUAACCGUUUGGAGGAAGGCGCCUAAGGUAGGAUUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUAUAAAGGUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq new file mode 100644 index 0000000..516122e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq @@ -0,0 +1,2 @@ +>d.16.c.M.polymorpha +UCUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGGGAAGGAUCCUAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGGACAACAGCUGGAAACGGUUGCUAAUACCCCAUAGGCUGAGGAGCAAAAGGAGGAAUCCGCCUAAGGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCUUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAACGUGACGGAGCAAUGCCGCGUGGAGGUAGAAGGCUCACGGGUCGUAAACUCCUUUUCUCAGAGAAGAUGCAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAAUGGCGAAAGCACUCUUCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAAGCGCUGUGCUAUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCGUGAAUCUUUUUGAAAGAAAAGAGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCUUGUUUAGUUGCCAUCAUUAAGUUUGGAACCCUAAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGACCUCGCGAGAGAAAGCUAACCUCAAAAACCCGGCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACUCUAACCGUAAGGAGGGGGGUGCCGAACAGGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq new file mode 100644 index 0000000..09f3dac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq @@ -0,0 +1,2 @@ +>d.16.c.P.falciparum +UUAUAUUGCGAGUUUGAUCCUAGCUCAGAAUUAACGCUAGAAAUAUACAUUACACAUGCAAAUUAAUGAUAAUAUCAUAGUGUAUAGGUGAGGAUAUAUAAAUUUUUAAUUUUAAAUAGAUUAUAAAUUUUAUUAAAUAAUAAUCUAUAAGCGCAAAAAUAUAUGUACUAUAUUAAAAAUUAAUAUUAUUUAAAAUAAAAUUUAUAUUUGAUUAACUAGUUGGUAAUUUAAAAGACUACCAAGGUUAUUAUCAAAAAUUGGUUUGAAAGAAUGUACAAUCACAUUAGGAUUGAAAUAAAGCCUAAAUUUUUAUAAAAAAUCAGCAGUGAGGAAUAUUUUACAAUAAGUGUAAGCUUGAUAAAGUAAUAUUUCUUUUAGGAAGACAGUAUUAUUAAAAUAUUGUAAACUUUUUAUUUUAUUUUUAAAUAUUGAUAAAAAUAAAAAAUAGUAUUUGCUAUUUCUGUGCCAGCAGCAGCGGUAAUACAGAAAAUGCAAGCGUUAUUCAUUUUAUUAGGCGUAAAGCGUUUUAAGGUUUUAUAUUAAUUUUAUGUUUAAAUAUUUAAAUUAAAUUUAAAAUAAAUUAAUAAAUAAUAAUAUAAUAGAGUAUUAUAAAAGUAUUAAGAAUUUUUUGAGAAGUAGUGAAAUACAAUGAUACAAAAAAGAAUAUCAAAGGCGGAAGCAUAAUACUAUAUAAUUACUGACACUUAAAAACGAAAGCUAAGGUAGCAAAUAGGAUUAGAUACCCUAGUAGUCUUAGCUGUAAACUAUGAAUAUUUUAUAUUUAUAUUUUAUAAAUAUAAUAACUAACGUGAUAAAUAUUCCGCCUGAGUAGUAUAUUCGCAAGAAUGAAAUUCAAAGGAAUUGACGGGAGCUUAUACAAGUGGUGGAACAUGUGGCUUAAUUCGAUGCAACACGAUAAACCUUACCAAAAUUUAACAAUAUUUUUAAUAUUAAGAAAUUAAUAUUUUAAUAAAAUAUAUAGGUAGUGCAUGGCUGUCGUCAGUUCGUGCUGUGAAGUGUUAAUUUUAGUAUUAUAACGAACGUAACCUUUUAUAAAAAAAAUUUUUAUAAUAAAUAAUAAUAAAGAUUACGUCAAGUCAUUAUGCUCCUUAUAUUUUGGGCUGCUCACGUGUUACAUAAAAUAUUACAAUAUUUUAUUAUAUGUUAAAUAUAAUAAUUAAAAUAUAUUUAUAGUUCAGAUUAUAAAUUGAAACUCAUUUAUAUAAAGAUGGAAUCACUAGUAAUCGCUAAUCAGAAUUAUAGCGGUGAAUAAGUUCUUAAGCUUUGUACACACCGCCCGUCACAUCUAAAAAGUAUCAUAUUAUAUAAAAAUUAUUGUUAAAUAAUAAUAUAUAAUUAUAUAAUUUAGAUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUAAUAAAAUAAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq new file mode 100644 index 0000000..6a92f4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq @@ -0,0 +1,2 @@ +>d.16.c.P.littoralis +AAACUAUCGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUUACACAUGCAAGUCGUACGAAAGUGUUAAAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUUUACCUUUAGGAGGGGAAUAACAGUUGGAAAUGACUGCUAAUGCCGCAUAUCGUAAUUAUGAGACAUAUCAUAACUAUGAAAGAAGAAAUUCGCCUAAAGAAAAGCUUGCGUCUGAUUAGCUAGUUGGUAAGGGUAAAGGCUACAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGACCAGUCACACUGGACUGAGACACGGUCCAGACUACUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAACUGAACAGAGCAAUACCGCGUGAGGGAAGAAAGCCCACAGGGUUGUAAACCUCUUUUGUCAAGGAAGAAGAUUCUGACGUUACUUGACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGGACGGGGGAUGCAAGUGUUAUCCGGAAUUACUGGGCGUAAAGCGUUUGUAGGUGGUUUAGUAAGUCUAUUGUUAAAGCUUGAAGCUUAACUUCAAAAGUGUAAUAGAAACUACUAGACUUGAGGAUAGUAGGGGUAAAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAGAUUGGAAGGACCACCGAUGGCGAAGGCACUUUACUGGGCUAUUUCUGACACUAAGAGACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGAAUACUAGAUGUUGCGUGUAUCGAUCCAUGCAGUAUCGUAGCUAACGCGUUAAGUAUUCCGCCUGGGAACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGCAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUUAUGUAAAUCUAUUUGAAAGAACAGAGUGCCCUCGGGAAUACAUAAACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUCUAGUUGCUUUACAAAAGGAAUCUUGAAGACUGCCGGUUAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUACCCUGGGCUACACACGUGCUACAUUGGAUAAGACAAAAAGUUGCGAAUUUGUGAAAAUAAGCUAAUCUUUAAACUUAUUCCUAAGUUCGGAUUGAAGGCUGCAACUCGCCUUCAUGAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUCCGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUAUACCCGAAGUCGUUUUCUUAACCUUUUUGGAGAGAGGCGCCUAAGGUAAGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACGGGAACGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq new file mode 100644 index 0000000..42ff17e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq @@ -0,0 +1,2 @@ +>d.16.c.P.minor +AUUUUUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGAACUAGCUCUAGCGCAAGUUAGAGUGGGUGGCGGACGGGUGAGGAACACGUAAGAACCUACCCUUUGGAGGAGGAUAACUGUUGGAAACGGCAGCUAAUACUCCAUAUGCUGAGGAGUAAAAGGUCGAAAGGCCGCCAAGGGAUGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAAUGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAAGGAUGAAGGCCUGUGGGUUGUAAACUUCUUUUCUCAGAGACGAAUAAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUCCAAGUCUUUUGUCAAAUCCCAGAGCUUAACUUUGGAUCGGCACGAGAAACUCGAGAGCUUGAGUAUGGUAGGGGCAGAGGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCAUUACUGACACUGAGAGACGAAAGCUAAGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCUUAGCCGUAAACGAUGGAAACUAAGUGCUUGGGCCGCGAGUAAUCGCUGCUUGAGUCCUGUAGCUAACGCGUUAAGUUUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCACUCUUUCGGGAGGUCAUGGUGAAAGCCAGUUUAGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCUUGUUGCAACUUUGUUGUUAUCGAGAGAGACUGCCGGUGAUAAGUCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCAACACACGUGCUACAAUGGCCAGGACAAAGAGAUGCAACCUCGCAAGAGCAAGCCAACCUCAAAAACCUGGUCUCAGUUCGGAUUAGUCUCUGCAACCCGAGACUAUGAAGCCGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCGUUUGGAGGGGGAUGCCUAAGGCAGAGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq new file mode 100644 index 0000000..69f34fd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.c.P.palmata +ACACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGGUUUUACCUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUGGGAGGGGAAUAACAGUUGGAAACGAUUGCUAAUGCCCCAUAAGCUGAAAAGUAAAAUGAUUUUUCGCCCAGGGAUGAGCUCGCGCCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUUCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGAGCAAUACCGCGUGAGGGAAGAAUGCCCGUGCGUUGUAAACCUCUUUUCUUAGGGAAGAAGCUCUGACGGUACCUAAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGUGUAGUAGGUGGCUUAUAAAGUCCGCUGUUAAAUCUUAGGGCUCAACCCUAAGCCAGCAGUAGAAACUUCUAGGCUAGAGUAUGGUAGGGGCAGAGGGAAUUCCCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAAGAACACCAGAGGCGAAAGCGCUCUGCUAGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGAUGUUGCGCGUAUCGAUCCGUGCAGUAUCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGAGCUUGACAUGUCACGAAUUUUUUCGAGAGAAAAAAGUGCCUUAGGGAACGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGCCAUCAUUUAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUAAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCUCUGGGCUACACACGUGCUACAAUGGUCGCGACAAAGAGUUGCCAGUCUGCAAAGACGCGCUAAUCUCAUAAACGUGGCCUCAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUACACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGAAGCUGGCCACGCCCAAAGUCGUUACCCUAACCUUUUGGAGGGGGGCGCCUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq new file mode 100644 index 0000000..6ae32f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq @@ -0,0 +1,2 @@ +>d.16.c.P.wickerhamii +UGUGAAAACGAAGAGUUUGAUCCUGGCUCAGGAUAAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGUACGAAGGUAUUUAUCUUUCGAGCUAAAUAUACUGAGUAGCGGACGGGUGAGUAACACGUAAGAAUCUACCUUUUGGAGAGGGAUAACUACUGGAAACGGUAGCUAAUACCUUAUAUUGCUGAGAAGUGAAAAAUGUAAAUUGCCAGAAGAUGAGCUUGCGCCUGAUUAGCUAGUUGGUGUGGUAACUGCAUACCAAGGCAAUGAUCAGUAGCUGUUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGACGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAAAAGAUUAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUCUGUCAAAAAUUAGGGCUUAACCCUAUACAGGCAGAAUAAACUUUUAAGCUAGAGUUUGGUAGAGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAAAGGCGAAGGCACUCUGCUGGGCCAAUACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUCGCUGUAAACGAUGGAUACUAGGUGUUGGGUGUAUCAAAAACAUUCAGUAUCGUAGCUAACGCAUUAAGUUUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGAACCCGCACAAUUGGUGGGGUACGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAUUUGACAUGUCAUUUGUUUCUUCAACUUAAUACUUUAAUUUGUUUUAAGUAGAAACAUAAAAAAAUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUGAAUUGCUUGGGGCAUUAUAUGCCUUUUUACAGAGGAAAUUCAAAAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAUAUCCUGGGCGACACACGUGCUACAAUGGACGUAACAAAGAGAAGCUACUUCGCGAGAACAAGCUAAUCUCAAAAAUACGUUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCAAUAGUAAUCGCAGGUCAGCCACACUGCGGUGAAUACGUUUCCGGGUUUUGCACACACCGCCCGUCACACCACGGAAAUUGGCUACGCCCUAAAUCAUUACCCUAACCAUUCUGUGGAGGGGGAUGCCUAAGGCGGGGCUGGUAACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq new file mode 100644 index 0000000..8de7320 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq @@ -0,0 +1,2 @@ +>d.16.c.S.oleracea +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGGACGGGAAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAGCUGGAAACGGCUGCUAAUACCCCGUAGGCUGAGAAGCAAAAGGAGGAAUCCGCCCGAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGCAGAAGGCCCACGGGUCGUGAACUUCUUUUCCCGGAGAAGAAGCAAUGACGGUAUCCGGGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGCUGUGCGUAUCGACCCGUGCAGUGUUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCAACGUUGAGUUUGGAACCCUGAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGAUCCCGCGAGGGUGAGCUAACCCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACCUUAACCGCAAGGAGGGGGAUGCCGAAGGCAGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq new file mode 100644 index 0000000..b37e535 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.c.T.gondii +AAAUUAUUACGAGUUUGAUCCUGGCUCCGGAAGAACGCAAGAGAUGUGCUUAACACAUGCUAAUUGAAUGGUAUUAAUAUAUCAUAGUGUAAUAGUGAGUAAUGUAUGAGAAUUUAUUUUUAGAAUAUAAUAAAAAUUUAAUAAUUUAUAAUAAACGCAAUAGUGUUUUAAAAGAUAAUUAUUGUCUAAAAAAAAGCUCAUAUCUAAUUAGCUAGUUGGUGAAGUAAUAGUUUUACCAAGGCGAAGAUUAGUAGCUGCCUUGAGAGGGGAAACAGCCACAUAGAGAUUGAAAUACAGCUCUAACUCCUAAGGGGGGCAGCAGUGGGGAAUUUUCUGCCAAUAAGCGCAAGCUUGACAGAGCGUCAUCACAUGAAGGAGGAAGGCCUAUAAAGGUUGUAAACUUCUUUUGCUUAAAAAAAUAAUACUGACGUUUAAGUUUAAAAAGUAUCGGCUAACUCCGUGCCAGCAGCCGCGGUCAUACGGGGGAUACAAGCGUUUUCCAAAAUUACUGGGCGUAAAGUGUAUGUAGGUGGAUUGGUAUGUUCUUCCUUAAAUACUAUUUGAUAAAUUUAGAAAAAGGAAGAAAACUAUUAAUCUUGAGUUCGAUAAGGGUAAGAGGAAUUUUUUGAGGAGUAGUGAAAUGCGAAGAUACAAAAAAGAAGAUCAACAGCGAAAGCAUCUUACUGGGUCGAUACUGACACUGAGAUACGAAAGUUAAGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCUUAACUGUAAACAAUGGAUACUCGGUACUGGAGACAUUAAAUAUAUAAAUUCAGUACCCUAGCUAACGCGUUAAGUAUUCCGCCUGAGUAGUACGCUCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCUCGUACAAGCGGUGGAGCACGUAAUUUAAUUCGAUGUAACGCGAUAAACCUUACCAGAACUAGACUAAAUUUAUUUUAAAUUAUUAAUAUUAAUUAAUAAAAAAUUUACAGGAGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCUACGAGCGCUACCCUUAUUUAAAGUUUUUUAUAUCUUUAAAAACAGACUAUAUAAAUUUUUGUACUAAAUUAGUAGGAAGGAGAGGAAAACGUCAAGUCUUUAUGCCCUUUAUGUUCUGGGCUACAUACGUGCUACAAUAGAUGGUACAAUAAUUUUUAAAAAUAAAUACAAUAUCAAUUUAUUUUUAAUUUAUUUGUGAAAAUAAAUGUAAUAAUUGAAAACCAUUUUUAGUUCGGAACAUAAACUGCAAUUUGUUUAUGUAAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCAUUACGGCGGUGAAUAAGUCUUCGAGCCUUGUACACACCGCCCGUCACGCCACGGAAAUUGAUUAUUUUUUAAAACUUUUGAUAAAAGGAUAAAUAAUAAUAAAUAACUGGGGUGAAGUCGUAACAAGGUAGCUGUACUGGAAGGUGCUGCUGGAUAAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq new file mode 100644 index 0000000..9bffa4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.c.Z.mays +CUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGGGAAGUGGUGUUUCCAGUGGCGAACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAACUGGAAACGGUUGCUAAUACCCCGUAGGCUGAGGAGCAAAAGGAGAAAUCCGCCCAAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGCAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGUGGAAGGCCUACGGGUCGUCAACUUCUUUUCUCGGAGAAGAAACAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUCAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCAUUGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAGACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGUGCUGUGCGACUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAGGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCCUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCUCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCACUAUGAGUUUGGAACCCUGAACAGACCGCCGGUGUUAAGCCGGAGGAAGGAGAGGAUGAGGCCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGGCGGGACAAAGGGUCGCGAUCUCGCGAGGGUGAGCUAACUCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCAGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGCGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUAGGAGCUGGCCAGGUUUGAAGUCAUUACCCUUAACCGUAAGGAGGGGGAUGCCUAAGGCUAGGCUUGCGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq new file mode 100644 index 0000000..32b6e40 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.albicans +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCCCGACUGUUUGGAAGGGAUGUAUUUAUUAGAUAAAAAAUCAAUGCCUUCGGGCUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGCUUGGCUGGCCGGUCCAUCUUUUUGAUGCGUACUGGACCCAGCCGAGCCUUUCCUUCUGGGUAGCCAUUUAUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUAUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGUAUCAGUAUUCAGUUGUCAGAGGUGAAAUUCUUGGAUUUACUGAAGACUAACUACUGCGAAAGCAUUUACCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGUUGUUGUUCUUUUAUUGACGCAAUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGCUGCUAGCAUUUGCUGGUAUAGUCACUUCUUAGAGGGACUAUCGACUUCAAGUCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUAUAAGCCUUGGCCGAGAGGUCUGGGAAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUGUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGCCUCCGGAUUGGUUUAGGAAAGGGGGCAACCUCAUUCUGGAACCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq new file mode 100644 index 0000000..69158d5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq @@ -0,0 +1,2 @@ +>d.16.e.C.citrina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGCGUCGAAGUGAGCUCGUUGCUUGUACUGAGAUGCCCUUCCAUCCUACUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGUUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUUAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGCCUUUAGGCUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq new file mode 100644 index 0000000..b680862 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq @@ -0,0 +1,2 @@ +>d.16.e.C.crispus +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUACUACUUGGAUACCCGUAGUAAUUCUAGAGCUAAUACAAGCCUUAAAGCGACAUUUAUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGAGUGACGGAUCGUGGGUGCGAGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGAUACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAACGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCAGUCCAGGGCGUCCUCGCGGACGGAUCUGGAGUUGGCCGCCUUUGUGGAUGGGGGCCUAGUGGAGCUUCACUGCUUCAUUGUGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACGGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGGAGGACUGUAUUUUGGCCUACCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCAGUACCGUUUUUUGGUACUGAGGCUUGCCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAACUUUCCCUCUUGAACGAGGAACACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGAUGGAUGGAUUGUGUUUCACAAACUAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq new file mode 100644 index 0000000..275fcb0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq @@ -0,0 +1,2 @@ +>d.16.e.C.lunata +CACCAGGUUGAUUCUGCCUGACGUGGACACUUGCCUUGAAGAGUAAGCCAUGCAAGCUUGUGAAUAAAUCCUGAAACAGUGAACGGCUCAGUAGAACACAUUUCAUCUACCCAAGUUAAAAAUAACCAUGGGAAACUAUGGCUAAAUAUAAUUUGGAUGAGAGUGUGACCUAUCAGCUAGUAGGUACGGUAAGAGCGUACCUAGGCUAUGACGGGUAACGGGGAAUCAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUACCUAUGUAAUAUAAUUAUAUAGGGAUGAGGUAUGAUUUCAAAUCAUGCACGACAUACUGGAGGGCAAGGCUGGUGCCAGCAGCUGCGGUAAUUCCAGCUCCAGUAGUGUCUAUGUAAAUUGUUGCGGUUAAAACGUGCGUAGUCUGAUUUGCGAGAUCUAAAGUAAAGAUGCUUUUAUCUAAAAGUAGAAUAUUUUAGAGAUCAAAAAUCUUGAGACAGAGGAGAGGUAACGAAAUUCGAUGGCGAGAGGUGAAAAUUGAUGACCCAUCGAGGAGAAACAGAGGCGAAAGCGGUUACCAGAAGCUGUUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGACACCGUCGUAGUUCCUUGCAGUAAACGAUGCCCACACUGAUGUGCUUAACGCAUGUCAGACGCAAAAGUUAAAGUGAGGCUCCGGGGAUAGUACGGUCGCAAGAUUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCAGUACAGAUUACUAUCGUAUGAAGGAAUACCUGAUGAUGUAAUACGUGGUGCAUGGCCGUUCUUAACACGUGAAGUGAUUCCUCGUGUCAAAUCAGCUAACGCGUGAGAGGCGAGUCUUAUUUUAUAAAUAAGAGACGGCAUAGGCAACUAUGAGGAAGCAACGCCCAAUAACAGGUCCGUGAUGCCCGUAGAUGUUCUGGGCUCCACGCGCACUACAAUUAUAAAUACUAUUUUGUAAUUUAUAAUCAGUAGGGAUUGUUUGUUGUAAAACUUACAUGAACGUGGAAUUCCUAGUAUAUAGAUGUAAGCAACGUCUAUUGAAUAUUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUUAUUAGGGGGAAGCUGAUAUAUUAUAUCAGAAGACUUCUGGUAACUAGAUUGGAUGUAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAGUAG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq new file mode 100644 index 0000000..0bf8af5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.neoformans +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGAAUUCAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUAUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUGAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGGGUUUCGGCCCUCUAUGGUGAAUCAUAAUAACUUCUCGAAUCGCAUGGCCUUGUGCCGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAUCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGCCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGAACUUCAGGUCUGGCGAGGCGGUCCUCCUCACGGAGUGCACUGUCUUGCUGGACCUUACCUCCUGGUGGUCCUGUAUGCUCUUUACUGGGUGUGCAGGGGAACCAGGAAUUUUACCUUGAAAAAAUUAGAGUGUUCAAAGCAGGCAAUCGCCCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGAUCGCCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUUGGUAUUCCGUUGCUAGAGGUGAAAUUCUUAGAUUGACGGAAGACCAACAACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAGGUUAGGGGAUCAAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACGAUGCCGACUAGGGAUCGGCCCACGUCAAUCUCUGACUGGGUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAAAUAGUCAGGCCGGCUUUGGCUGGUCGUUUGACUUCUUAGAGGGACUGUCGGCGUCUAGUCGACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACUGAGCCAGCGAGUCUUACCGCCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAAACUCAGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUACCUAGUAAGCGUGAGUCACCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGAUCUCCGGAUUGGCGUUGGGGAGCCGGCAACGGCACCCCUUGGCUGAGAAGCUGAUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAGUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq new file mode 100644 index 0000000..6c217f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.C.officinalis +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUGAGGAAUAAUUAAGACGAAACUGCGAAUGGCUCGGUAAAACAGCAAUAAUUUCUUCGGUGAUUUUUACUACUCGGAUAAUCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAUGCUUGGGUUUACUCAGGCAGUGCCGUUUAGAUAACAACACCAACAUAUGGUGAUUCAUAAUCGUCUUUCGGAUCGCUGGCGAAAGCCGGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGCAACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCAGACUCUGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCAUAAAGUCUUCUAAUUGGAAUGAGAACAAGCUAAACAGCUUAUCGAGAAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACUUUGGCAAUUCCGGAUGUGUGCGCGUCGUGCGCGCACUUUGCAGGGGUUGCUUUUGUGGGCAUGCGUGGGAUGAUGCGACUUUAUUGUCGAACGUCCCUACGCAACCACCUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCAAUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUCUUAUUUUGUUGGUUUGUUAGGGCUGAGUAAUGAUUAAGAGGGACAGUUGGGGGCAUUUGUAUUCAGGCGCUAGAGGUGAAAUUCUUAGAUUGCUGGAAGACAAACUGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGAGGAAUAUCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUACUACCAUUUUGGUAGUACGUUUUCCCCUUCUUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGUGGAUCAGCGGGUCAGGUUGCACGAAAGUGUUUCCUAAUCUUUAAAUCCGCUCGUGAUGGGGAUUGACGGUUGCAAUUUUCCGUCAUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGAUUGCGAUGGAAAGAGCGUCUCGCUCGUUCUGUCGUGAGAACUCAGUCGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq new file mode 100644 index 0000000..bb1658f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.e.C.paradoxa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUAUUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAACAAAUCCCGACUUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAACACCGGGCAACCGGAUCCCUUGGUGAUUCAUAAUAACUUCUCGAAUCGCAUGGCUUUACGCCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGCGCCUGAGAGAUGGCGACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCGCAACUCGCGGAGGUAGUGACAAUAAAUAACAAUACGGGGCUUUUCAAGUCUCGUAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCCAUUGGAGGGAAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGGAUUUCGGGGCGGGGCAGUCGGUCUGCCUAAUAGGUGUGUACUGGCUGUACCCGUCCUUCCUUCCGGGGAUGGGUGCUGCUCUUAACUGAGUGGCAUUCAGACACGGAUCUUUUACUUUGAGUAAAUUGGAGUGUUUAAAGCAGGCCUACGCUCUGAACAUUAUUAGCAUGGAAUAAUAAAAUAGGACCCUGGUUCUAUUUUGUUGGUUUCUAGGAUUGGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCAUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGAUGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACUUACGAUCAGCAGGUGUUAAUUUAACGACCCUGUUGGCAGUAUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACACGAACUUCUAGUUCGUGGUCAACUUCUUAGAGGGACUAUUUGUGUCUAAUGAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACGAAUUCAACGAGUUUUUCCUUGACCGAUAGGUCUGGGUAAUCUUUGAAACUUCGUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUCGGUCCGGUGAAAUCUUCGGAUCGUGGCCAUGUACCUGGUCUCCAGGAACAAGGUCGCGAGAAGUUGAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq new file mode 100644 index 0000000..2b1cbde --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq @@ -0,0 +1,2 @@ +>d.16.e.C.rubrum +CACCCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAAUACGUGCCAUACGGCGAGGUUUUACCUCGUGGUACUAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACACUUAUUUUUCUGAUUGCACAUUUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACACGGUAAACAUCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACGUUGGCGGGCGCCUCGAGUCGGCCUCACGGUCGAUCUUGUUGGCGGCCGCCUUUGUGGAGGGGGGCUUAGGUCGGUGCUUUAUUGUCACUCCUUUGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUCCUGUUUUGUUGGUUUGUGAGUAUCAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACCAUAAACUAUGAGGACUGGGGAUCGGGCGUGGCUAUUUGGUACGCUCGGCACCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACUUGGGCGUGCUAGCUAGGCGCUGUUACCAUUUCCGGUAGCGAGGCGGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAAAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGAUGGGGAUAGAGGCUUGCAACUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGUCUGCAUGUCCUGUGUUUCACUUGUGUGCAGGUUGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq new file mode 100644 index 0000000..658da2a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq @@ -0,0 +1,2 @@ +>d.16.e.D.melanogaster +AUUCUGGUUGAUCCUGCCAGUAGUUAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACACACGAAUUAAAAGUGAAACCGCAAAAGGCUCAUUAUAUCAGUUAUGGUUCCUUAGAUCGUUAACAGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCAAUUAAAACAUGAACCUUAUGGGACGUGUGCUUUUAUUAGGCUAAAACCAAGCGAUCGCAAGAUCGUUAUAUUGGUUGAACUCUAGAUAACAUGCAGAUCGUAUGGUCUUGUACCGACGACAGAUCUUUCAAAUGUCUGCCCUAUCAACUUUUGAUGGUAGUAUCUAGGACUACCAUGGUUGCAACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUCCCAGCUCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCAUAUCCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACAAGGACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAACGUUCGUAGUUGAACUUGUGCUUCAUACGGGUAGUACAACUUACAAUUGUGGUUAGUACUAUACCUUUAUGUAUGUAAGCGUAUUACCGGUGGAGUUCUUAUAUGUGAUUAAAUACUUGUAUUUUUUCAUAUGUUCCUCCUAUUUAAAAACCUGCAUUAGUGCUCUUAAACGAGUGUUAUUGUGGGCCGGUACUAUUACUUUGAACAAAUUAGAGUGCUUAAAGCAGGCUUCAAAUGCCUGAAUAUUCUGUGCAUGGGAUAAUGAAAUAAGACCUCUGUUCUGCUUUCAUUGGUUUUCAGAUCAAGAGGUAAUGAUUAAUAGAAGCAGUUUGGGGGCAUUAGUAUUACGACGCGAGAGGUGAAAUUCUUGGACCGUCGUAAGACUAACUUAAGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUACCGCCCUAGUUCUAACCAUAAACGAUGCCAGCUAGCAAUUGGGUGUAGCUACUUUUAUGGCUCUCUCAGUCGCUUCCGGGAAACCAAAGCUUUUUGGGCUCCGGGGGAAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCGAACAUAAGUGUGUAAGACAGAUUGAUAGCUCUUUCUCGAAUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCAAAUAUAUUAAAUAGAUAUCUUCAGGAUUAUGGUGCUGAAGCUUAUGUAGCCUUCAUUCAUGUUGGCAGUAAAAUGCUUAUUGUGUUUGAAUGUGUUUAUGUAAGUGGAGCCGUACCUGUUGGUUUGUCCCAUUAUAAGGACACUAGCUUCUUAAAUGGACAAAUUGCGUCUAGCAAUAAUGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACAAUGAAAGUAUCAACGUGUAUUUCCUAGACCGAGAGGUCCGGGUAAACCGCUGAACCACUUUCAUGCUUGGGAUUGUGAACUGAAACUGUUCACGAUGAACUUGGAAUUCCCAGUAAGUGUGAGUCAUUAACUCGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUUAUUUAGUGAGGUCUCCGGACGUGAUCACUGUGACGCCUUGCGUGUUACGGUUGUUUCGCAAAAGUUGACCGAACUUGAUUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq new file mode 100644 index 0000000..dcf55c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq @@ -0,0 +1,2 @@ +>d.16.e.E.aediculatus +AAUCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAGGAUUAAGCCAUGCAUGUCUAAGUAUAAAGGAUUUAUAAUGAAACUGCAAAUGGCUCAUUCAAACAGUUAUAGUUUAUUUGAUAUUCAAGCUAAUAUUCUUAUUAGUUAAAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUUACGGGGAACUUUACGGGACCCCAGCGUUUAUUAGAUUUAAACCAAUAUUCCGCAAGGUCUACUGAGAUGAUUCAUGAUAACUGAUCGAAUUGCUGGAACUCUAGCAAUAAAUCAUGUAGGUUUCUGCUUCCCAUCAGCUUGAUGGUAGUGUAUUGGACAACCAUGGCAUUCACGGGCUAUCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAUAAACGGCUACCACUUCUACGGAAGGCAGCAGGCGCGAAAAUUAUCCAAUCCUGAUUCAGGGAGGUAGUGAAAGAAAUAAUGAACUAGGAUUUAUCCUGGGAUCACAAUGGGCUUGAUUUGCAAACACUUAGCGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGAGUAUAUAAACGUUCCUGCAGUUAUUCGAUGCUCGUAGUUGGAUUUCUGAGGUUGAGACGGGAGGGUGGCUAUGGCCAUCGCCCGACUCUUUCCUCAUCCACCUGUUUGCGAAGUCCGGGAUUGAUUUCUCGGCUUCGGGCGCAGUAUCUUACCAUUUCAAUAUUCGUAGUCUUCAUCGAUUAUGUUGUUUCUUUGAGCAAAUUAUAGUGUUUCAGGCAGGCGUGCGCCGGAAUACAUUAGCAUGGUAUAAACGAAUUGGACCGUGUGCCCGUAACUGGGCUUCUCCUUAUUGUUGGUUUGAAGGACACGGAGAUGGUUAAUAGGGACAGCGUUUAUUUCACAAGGAGGCAUUAGUAUUUAAUUUCCAGAGGUGAAAUUCUUUGAAAUAUUAAAGACUAACUUAUGCGAAAGCAUCGUUUGCCAAUGAUGUUUUCAUUAAUCAUUGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACGUUGCCGACUAGGGAUCGGAGGGCGUGCACAAUCCGCCUUCGGCACCUUACGAGAAAUCAAAGUCUUUUGGGUUCUGUGGGUAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAUCUUACCAGGUCCAGACAUAGCGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAUUUUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUCGUCUGGUUAAUUCCGUUAAACGAACGAGACCUCAGCCUGCUAAAUAGUUGCUCGCCUUUUCUAUAAGACUUGACAACUUCUUAGAGGGACUUUGUGUGCAACCACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUACGUACAACGAGGUAUAUGUACUUGUACAUCAAUGCUGCUCCGAAAUAGACGAGCUUAAUCUUAUAAAUACGUAUCGUGCUGCGGAUAGAUCGUUGAAAUUAUGAAUCUUGAAGGUGGAAUUCCUAGUAAGCGCACGUCACUAACGUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCAAUUUCGAGUGAUCUGGUGAACCUCUUUGGACUGUCGAGCAAUCGCGAAAUUAGAGUGAACCUGACUACUUAGCAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAAUCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq new file mode 100644 index 0000000..2b84de0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.bieneusi +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCAGUGAAGCCUUACGGUGGAACGGCGAACGGCUCAGUAAUGUUGCGGUAAUUUGGUCUCUGUGUGUAAACUAACCACGGUAACCUGUGGCUAAAAGCGGAGAAUAAGGCGCAACCCUAUCAGCUUGUUGGUAGUGUAAAGGACUACCAAGGCCAUGACGGGUAACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGUCCACUCCUUACGGGGGAGACAGUCAUGAGACGUGAGUAUAAGACCUGAGUGUAAAGACCUUAGGGUGAAGCAAUUGGAGGGCAAGCUUUGGUGCCAGCAGCCGCGGUAACUCCAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCGUGAAUGCAAUUAAAUGUCGUUGUUCAAUAGCGAUGAGUUUGCUAAUGUUUGCGGAACGGAUAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUCUCAAGACCCAGUUUGGACUAACGGAGGCGAAGGCGACACUCUUAGACGUAUCUUAGGAUCAAGGACGAAGGCAGGAGUAUCGAAAGUGAUUAGACACCGCUGUAGUUCCUGCAGUAAACUAUGCCGACAGCCUGUGUGUGAGAAUACGUGGGCGGGAGAAAUCUUAGUGUUCGGGCUCUGGGGAUAGUACGCUCGCAAGGGUGAAACUUAAAGCGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUAACUCAACGCGGGAAAACUUACCAGGGUCAAGUCAUUCGUUGAUSGAAUACGUGAGAAUGGCAGGAGUGGUGCAUGGCCGUUGGAAAUUGAUGGGGCGACCUUUAGCUUAAAUGCUUAAACCAGUGAGACCUCCUUGACAGGUGUUCUGUAACACAGGAGGGUGGAGGCUAUAACAGGUCCGUGAUGCCCUUAGAUAUCCUGGGCAGCAAGCGCAAUACAAUAUCUCUUCAGUAGACAAAGUGAUUUGAGAUGAGUAGGAUCUACGUUUGUAAAUACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCCUCAUCAAGGCAUGGUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUUCAGAUGGUCAUAGGGAUGAAGAGCUUCGGCUCUGAAUAUCUAUGGCUAGAUAAAGUACAAGUCGUAACAAGGUUUCAGUUGGAGAACCAGCUGAAGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq new file mode 100644 index 0000000..74a3bfa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.cuniculi +CACCAGGUUGAUUCUGCCUGACGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGCUUGUGAACUCUUUGUGGGGGAUUAGCGGACGGCUCAGUGAUAGCACGAUGAUUUGUUUGCGGGAUGAGCAGUAGCUGCGGGAAACUGCAGAUAGUGGUCUGCCCCUGUGGGGUUGGCAAGUAAGUUGUGGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGCAGACGGGAUACGGGGGAUCAGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAUGUGUGUGCGAGUGCAAAGGGGUCGCAUGUGAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGGAUGCUGCAGUUAAAAUGUCCGUAGUCUGUUGUGUAUGUCUUUGUGUGUGAUGUUUGUGGUUGUGUGUGGAUGUAGUGAUGUGUGUGGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUGCGAAGACCCUGACUGGACGAGCGGAAGCGAAGGCUGUGCUCUUGGACUAAUGUUGCGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACAGUGUGUGUUGUCCAUGAGAAAUCUUGAGUAUGCGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGCUCUGAAGGAUGCCUGUGAGUGCAUGGCAUGAGGCAUGCGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGAGCUUUGUCUUAAGUUGCGUAAGAUGUGAGACCCUUUGACGGUGUUCUACGGAGCAAGGAGGGGAUGGAAAAGAACAGGUCCGUUAUGCCCUGAGAUGAGGCGGGCUGCACGCGCAUACGAUAGAUGGCGCUUCUGCCUGCUGUGAGGGAUGAAGCUGUGUAAGGGGCUUCUGAACGUGGAAUUCCUAGUAAUAGCGGCUGACGAAGCUGCUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCACUGGACGAAGAUCGGAAGGUCUGAGUCCUGAGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq new file mode 100644 index 0000000..f6afe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq @@ -0,0 +1,2 @@ +>d.16.e.E.hellem +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGUUUAUGAAGCCUUUAUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGAUUGGGUGCCUGGAUGUAACUGUGGGAAACUGCAGGUAAGUUCUGGGUGUGGUAGUUUUUAGCUACUGCGUACCGAGUAAGUUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUAUUGGGGAGGCGGUUAUGAGAAGUAAGAUGUUUAGCAAGUAUAAAUUUGUUGUGAUUUACUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAGUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAUGUCCGUAGUUGUUUGUAUGUCUUUUGUGUGAUGUUUAUAGUUUUUAGUGGAUGUAGUUUGGUUGUAGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGAAGAGAAGCGAAGGCUGUGUUCUUGGACUUUUGUGGUGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUGUUUUAGUGUUGUCCGAGAGAAAUCUUAAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGUGAGUGUGAGAGUGUUUUUACAUGAUGCUUACGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGGGCUUUGGAUUAAGUUACGUAAGAUGUGAGACCCUUUUUGACUGUGCUCUAUGGGGCAAGGAAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGCCUAUGUGGGCUACUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAGAAUGAUUGAACAAGUUAUUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAGUGGACGAAGAUUGAGAGGUCUGAGUCUUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq new file mode 100644 index 0000000..ad17f45 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq @@ -0,0 +1,2 @@ +>d.16.e.E.histolytica +UAUCUGGUUGAUCCUGCCAGUAUUAUAUGCUGAUGUUAAAGAUUAAGCCAUGCAUGUGUAAGUAUAAAGACCAAGUAGGAUGAAACUGCGGACGGCUCAUUAUAACAGUAAUAGUUUCUUUGGUUAGUAAAAUACAAGGAUAGCUUUGUGAAUGAUAAAGAUAAUACUUGAGACGAUCCAGUUUGUAUUAGUACAAAAUGGCCAAUUCAUUCAAUGAAUUGAGAAAUGACAUUCUAAGUGAGUUAGGAUGCCACGACAAUUGUAGAACACACAGUGUUUAACAAGUAACCAAUGAGAAUUUCUGAUCUAUCAAUCAGUUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAUAACGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCSCGUAAAUUACCCACUUUCGAAUUGAAGAGGUAGUGACGACACAUAACUCUAGAGUUGAGUAAAAUCAAUUCUUGAAGGAAUGAGUAGGAGGUAAAUUCUCCUACGAAAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGAAUUAAAAUGUGGUUUUAUACAUUUUGAAGACUUUAUGUAAGUAAAGUUUCUAGAAAUGUUAAAUUAAAAUCAAAGAAGGAAACAAUUCAAGUAAUUGAGUUGUUAUUACUUUGAAUAAAAUAAGGUGUUUAAAGCAAAACAUUAUGUUAAUGAAUAUUCAAGCAUGGGACAAUGCUGAGGGGAUGUCAAUAAGACAUUUCGAGAGAAGGAUUAAAAGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGGAUUGGAUGAAAUUCAGAUGUACAAAGAUAGAGAAGCAUUGUUUCUAGAUCUGAGUAUAUCAAUAUUACCUUGUUCAGAACUUAAAGAGAAAUCUUGAGUUUAUGGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACCGAACAGUAGAAGGAAUGACAGAUUAAGAGUUCUUUCAUGAUUUAUUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAACCUAUUAAUUAGUUUUCUGCCUAUAAGACAGAAAUGUUCGCAAGAACAGGUGCGUAAGUACCACUUCUUAAAGGGACACAUUUCAAUUGUCCUAUUUUAAUUGUAGUUAUCUAAUUUCGGUUAGACCUCUUUUAACGUGGGAAAAAGAAAAAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAGACAUCUUGGGCCGCACSCSCGCUACAAUGGAGUUACUAGAGAGUAUUUUAUCAUUUACACCUUAUUUAUUAGGCUUUGUCUAAUAAUUAAGGAUAGUAAGUGGUGUACCGAGAUUGAAAUAGUUAAGGAAAACUCAAAAGAACGUACAUGACAGGGAUAAAUGAUUGGAAUUAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUUAACUCGAGAUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUAAAGAGGUGAAAUUCUAGGAUUCUGUCUUAUAGAUAGAAAAAUGGAUUUAAAUCUCCUUAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq new file mode 100644 index 0000000..ca7e6aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq @@ -0,0 +1,2 @@ +>d.16.e.E.mobilis +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUGCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCUCCAAUGUCCGCUGAUGCGUGUGCAGCGGAGCCCUCUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUAUUGUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAGCCAAUCCCGAUUGGCCCCGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGACAUCCUCGUGGUGUUUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq new file mode 100644 index 0000000..69b8094 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.schubergi +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCUAUGGAACAAGGACGAACAGCUCAGUAAAACUGCGAUGAUUCAGUCUGUCUGUCAAGAUAACCACGCGAAAGUGUGGCUAAGAGGGGACAGAACAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGGUGACGGUUGACGGGGAAUGAGGGUUCUAUACCGGAGAGGGAGCCUGAGAGAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUGUUUGGAGGAGGCAGUUAUGAGACGUGAGAAAGAGUGCUUGUAAAGAGAAGCAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCGUGGAGACGGAAAGAGAGGCGGAGCCUCUUUGAGAUGCUCUGGAGAAGCCAACAGGGGGCACAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAAGCGGUGCUCUUGUGGGUGUUCGGUGAUCAAGGACGAAGGCUGGAGGAUCGAAAGUGAUUAGAUACCGCUGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCGGUGGCAACACGGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAGCUUACCAGGGCCAAGUGCUGUGGAGAAAGGAGCAGUACAGAAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGGCCUUAAAUGGCUGAAUGAGUGAGAUCUUUGGACAUGUUCCCACGGAACAGGAAGGGGAGGCUAUAACAGAUCAGAGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCACGUAGACGUAGAGAACAACACGUGCUGAGGUGGACUGUGCUCUGCAAGGGGCACACGAAAGAGGAAUUCCUAGUAAGCGCCCAUCACCAGUGGGCGUUGAAUCAGUCCCUGUAGCUUGUACACACCGUCCGUCACUAUCUCAGAUGUUUUUCGGGAUGAAGAGUCCAGGCUCUGAAUAACGGAAAGUAGAUAAGAUGUAAGUCGUAGCAAGGUUGCGGUCGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq new file mode 100644 index 0000000..a4c4989 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Encephalitozoon.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUGUUCUCUGGGACUAAGCCAUGCAUGUUGAUGAACCUUGUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGGUUGGCGGGAGAGCUGUAACUGCGGGAAACUGCAGGUAGGGGGCUAGGAGUGUUUUUGACACGAGCCAAGUAAGCUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAGUUUUUUUCGAGUGUAAAGGAGUCGAGAUUGAUUGGAGGGCAAGUCGCGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAAGUCCGUAGUCUUUUGUAUGUCUUUGUUUGGGGGAUUAUGUCCUGAUGUGGAUGUAAGAGGUUUGGCAGAGGACGAGGGGCACCGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGGACAGAAGCGAAGGCUGUGCUCUUGGACUUAUGUGACGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUAUAUAGUGUUGUGCAUGAGAAAUCUUGAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGCGGGCAGGAGAACGAGGACGGGAUGCGUGCGGCGGUGGUGCAUGGCCGUUUGAAAUGGAUGGCGUGAGCUUUGGAUUAAGUUGCGUAAGAUGUGAGACCCUUUGACAGUGCUCUUUGGGGCAAGGGAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGGCGAGGGAGCCUGCUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAUAACGAUUGAACAAGUUGUUUUGAAUGGGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCCAAGAUGACGCAGUGGACGAAGAUUGGAAGGUCUGAGUCCUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq new file mode 100644 index 0000000..1b84530 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq @@ -0,0 +1,2 @@ +>d.16.e.F.x.ananassa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAAUCCCGACUUCUGAGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACGCGGGCUCUGCUCGCAUUGAUGAUUCAUGAUAACUCGACGGAUCGCACAGCCUUUGUGCUGGCGACGCAUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGACCGGUCCGCCUUAUGGUGUGCACCGGUCGGCUCGUCCCUUCUACCGGCGAUACGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUCUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUACUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUCGGGAGGUCUCCUCGGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGCGAACCAAGUUUGAGGCAAUAACAGGUCUGUCAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACCACGGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUUGUUCGGAUCGCGGCGACGGGGGGCCGGUUCGCUGCCCGCGACGUCGCGAGAAGUUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq new file mode 100644 index 0000000..4d70b84 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.G.intestinalis +CAUCCGGUCGAUCCUGCCGGAGCGCGACGCUCUCCCCAAGGACGAAGCCAUGCAUGCCCGCUCACCCGGGACGCGGCGGACGGCUCAGGACAACGGUUGCACCCCCCGCGGCGGUCCCUGCUAGCCGGACACCGCUGGCAACCCGGCGCCAAGACGUGCGCGCAAGGGCGGGCGCCCGCGGGCGAGCAGCGUGACGCAGCGACGGCCCGCCCGGGCUUCCGGGGCAUCACCCGGUCGGCGCGGUCGCGGCGCGCCGAGGGCCCGACGCCUGGCGGAGAAUCAGGGUUCGACUCCGGAGAGCGGGCCUGCGAGACGGCCCGCACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCCCAAUGCGCGGCGCGCGAGGCAGCGACGGGGAGCGCGCGAGCGAGGCGGGCCCACAGCCCCCGCCGCGGAGCCGAGGGCAAGGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCGGCGAGCGUCGCGCGGCGCUGCUGCAGUUGAAACGCCCGUAGUUGGCCCCCCGCCGCCACGAGGAAACGGGAGCGCUCCAGGCAGGCCCGUUGGACCCGCCGCGUGGGACCGCGCAGCGGGCCGGCGCGCCGCGGCAGCCCCGAGGAGAGCGGGCGGGGGCACCGGUACCGGCCGGGGACGGGUGAAACAGGAUGAUCCCGCCGAGACCGCCGGCCGCGCAGGCGCCUGCCAAGACCGCCUCUGUCAAUCAAGGGCGAAGGCCGGGGGCUAGAAGGCGAUCAGACACCACCGUAUUCCCGGCCGUAAACGGUGCCGCCCCGCGGCCGGCGCGCGCGUCCCGCCGGCCGCCCAGGGAAACCGGGAGGCUCCGGGCUCUGGGGGGAGUAUGGCCGCAAGGCUGAAACUUGAAGGCAUUGACGGAGGGGUACCACCAGACGUGGAGUCUGCGGCUCAAUCUGACUCAACGCGCGCACCUCACCAGGCCCGGACGCGCGGAGGACCGACAGCCGGGCGCGCUUUCGCGAUCGCGCGGGCGGUGGUGCAUGGCCGCUCCCAGCCCGUGGCGCGAGCCGUCUGCUCCAUUGCGACAACGAGCGAGACCCCGGCCGCGGGCGCCGCGGGACGGCCCGCGCGAGCGGGAGGACGGCGGGGCGAUAGCAGGUCUGUGAUGCCCUCAGACGCCCUGGGCCGCACGCGCGCUACACUGGCGGGGCCAGCCGGCGCGCGCGAGGACGCGCGGAGCCCCCGCCGUGGCCGGGACCGCGGGCUGGAACGCCCCCGCGCACCAGGAAUGUCUUGUAGGCGCCCGCCCCCACCGCGCGCCGGACGCGUCCCUGCCCCUUGUACACACCGCCCGUCGCUCCUACCGACUGGGCGCGGCGGCGAGCGCCCCGGACGCGCGAAGGGCCGCGAGCCCCCGCGCCUGGAGGAAGGAGAAGUCGUAACAAGGUAUUCCGUAGGUGAACCUGCGGAUGGAUCCCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq new file mode 100644 index 0000000..6e4347c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq @@ -0,0 +1,2 @@ +>d.16.e.G.max +UACUUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACACAGGCUCUGCCUGUUGCUUUGAUGAUUCAUGAUAACUCGUCGGAUCGCACGGCCUUUGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAUGGAUCCAUUGAAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGAUCGGUCCGCCUCCGGUGUGCACCGGUCGGCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGUCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACACCACAGGAUUCUGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAAAUAGCUAUGUGGAGGUAACCCUCCACGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACAGGUCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUGCGGCGACGUGAGCGGUUCGCUGCCCGCGACGUUGUGAGAAGUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq new file mode 100644 index 0000000..2188860 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq @@ -0,0 +1,2 @@ +>d.16.e.G.steinii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCGUCUUGUUGAUUGUGCAGAGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCAGAGGCGCGCUUUAUCCGCCUUUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGCUUAGCGGACACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACCGCGGAGUUCUCGUAAUUCUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq new file mode 100644 index 0000000..78438aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Gracilariopsis.sp +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUAUAGGACUAAGCCAUGCAAGUGCAAGUAUGAGUGUAUUAUACAACGAAACUGCGAAUGGCUCUGUAAAACAGCUAUAAUUUCUUCGGUGCUAAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCUACACAGCGACGCAAGUCGUGGUACAAAUUAGAUACACAAGCCAGCUUUUUUGGUGAUUCUAGAUUUUUUUUCUGAUCGCACAUUGUUGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAAUGGCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGAUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAUUUUGGCGUGUGAUUUGGGUCGUUCUCGCGGACGCGCUCAGGUUGUGCGCCUUUGUGGAGAGGGGGUGUGGUGGUGCUUGAGUGCGCUGCCAUGCUGCCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCCGGUUCUAUUUUGUUGGUUUGUUUGAAUCAGGUAAUGAUUAACAGGGACGGUUGGGGGCAUUCGUAUUCCGGCGCUAGAGGUGAAAUUCUUGGAUUGUCGGAAGACGAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGACAAGACUGAUUUAUGGCUUGUUCGGCAUCCUUCGAGAAAUCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCAAUUGAGUUUGGUAGCGAGGCGGUGCCUUCCUAGACGGACUGUGGGCGUCUAGCCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAACGGCCCAACGAGUGGAGGAUGUGCGAGAGCAUUUCCGAAUCUCCAAAUCCGUUCGUGAUGGGGAUCGACGGUUGCAAUUUUCCGUCGUCAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUGGAUGCGCUGUUUUUAUGCAGACAUUUUGGCCUGAACCUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq new file mode 100644 index 0000000..9c2f96f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq @@ -0,0 +1,2 @@ +>d.16.e.H.anguillarum +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAGGCGAAGCAUUUUGUGGAGCGGCGGAAGGCUCAGUAACGGGCGUCUAUUUGAUCUUCUGAGACGGACAACCUCUGUAACCGGAGGCCAAUACGUCAGAGGCACGGUUACCCUGUGUGGUGGUGUGCCGAAAGCAUUGCGCGGAAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUGUGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGGAAACGAUGAGGAGGUAAAGAAUGCUCUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGCGUGAAAGGCCUUCUUUCAAGGGGGGCACAGCGCGGGGAAAGCAGAGGAUAAGGAGCGUUUUGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGGAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCGUGCGCGCGACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUUGUACACGAUAGGUCGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUCCGGCAGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGCGUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAAUCGCGGAGAGACAAUGGUGAUCGAGAGGGAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq new file mode 100644 index 0000000..4d623b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq @@ -0,0 +1,2 @@ +>d.16.e.H.plana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCUAAGACGACGCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACGAUUUCUUUUCUGAUUGCACUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAGUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAAUUUGGCGGGCGACUUAAGUCGUCUUUACCGACGAUCUUAGGUUGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUAACCGCUUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGGAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCCCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUAGUCGGUGUUUUCACAGAUCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq new file mode 100644 index 0000000..734e464 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq @@ -0,0 +1,2 @@ +>d.16.e.H.rubra +CAACCUGGUUGAUCCUGCCAGUGGUAUAGUCUUGUCUCAAGGACUAAGCCAUGCAAGUGCCAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGGGGGUAAUACUACCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCGAAAGCGAGUCUCUCGCGGUACAAAUUGGAGACACAAGCCAAUAUUUUGGUGAUUCACAAUUUUUUUUCUGAUUGCACUUUUUAGUGCGACACCCCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAYUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACUAAUUCAGUGAGGUAGUGACAAAGAGUAUCAAUAGGGGGGCCAUCGGCUCUUCUAGUUGGAAUGAGUACAGAGUAAACAAUUUAACGAGGACCAAUAGGAGGGCAAGCCAAGUGCCAGCAGCCGCGGUAAUACUUACUCCUAGGGUGUUUGUUCACAGUGCUGCAGUUAAAAAGUUCGUAGUCGGACCUAUGAGCUGGGCGGUGGUGUGGGCGCAAGCCUGUGGUGCCGCCCGGCUCUUUUGGGGAAAUGGCCGGAGUAGGGUUUUAAGCGGCUUUGCUCCGGGCGUCCCCCGUUUACUGUGAAAAAAUGAGAGUGUUCAAAGCAGGCGAUGAGCCGUGAAUACCAUAGCAUGGAAUAAUAGAAUAGGGCCGCUGAUGCCUAUUUUGUUGGUUUCGAGGUGUCGGGCAAUGAUUAAGAGGGACGGUUGGGGUCAUUUGUAUUAAGUCGUCAGAGGUGAAAUUCUUAGAUUGACGUAAGACAAACAGCUGCGAAAGCGUCUGACAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUAAGAACUGGGGAUCGGAAGAGUAUUUAAAUAGGGCUCAUCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAGUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGAGCGUGGUAGCUAGGGGACUUGUGCAUUUAUGCACGGGCUUUUUCUCCUUCCUACACGGACUGCUGGCGAAUAGUCAGCGGAAGCCUCAGGCAAUAACAGGUCUGUGAUGCCCUUUGAUGUUCUGGGCCGCACGCGCGCUGCACUGAGCGGACCAGCGGGCGAGGAUAGCCGAAAGGUUUUCCGGACCCUUAAAUUCGCUCGUGCUGGGGAUGGAGGCUUGCAAUUGUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGAGUCAUCAGCUCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGAGGAGGUGAGAAGUUGGGAGGUGUUGGUUCGGGCCCGCAAGGUGUCUGGGCUAGCGCUAAACUCGUUCAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq new file mode 100644 index 0000000..c04feb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq @@ -0,0 +1,2 @@ +>d.16.e.H.sapiens +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq new file mode 100644 index 0000000..f212fda --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq @@ -0,0 +1,2 @@ +>d.16.e.I.hoferi +CAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUAAUACCUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGAAAAAACCCGACUUCUGGAAGGGUUGUAUUUAUUAGAUACAGAACCACUGCAGGGCAACCUGGUUACUUGGUGAUUCAUAAUAACUUCGCGAAUCGAAUGGCUUGUGCCGUCGAUGAUUCAUUCAAAUCUCUGCCCUAUCAACUUUCGGUGGUAAGGUAUUGGCUUACCAUGGUUCCAACGGGUAACGGAGAAUUAGGGUUCGAUUCCCGAGAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAAAAAUAACAAUACAGGAUCUUUAAAGGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGAAAUUGCUUACUGGUCGGCCGCAAGGUCUGUACUGGUACGGCAGUUUCUUCUUCUCGAAGGCAGUGGGUGCUCUUAAUUGAGUGUCUACUGAGUUCGGGACUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCUUGAAUAUUGCAGCAUGGAAUAAUGGAAUAGGAUCCCGAUCUUAUUUUGUUGGUUUCUAAGAUCGAGAUAAUGAUUAAUAGGGACGGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGGAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCGUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUAGUGGACGUUUAAUAAUGACACCAUUAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCCCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCCGGACAUAGGAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGCCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACAUGAUUUUCGAAUCAUGGGCAACUUCUUAGGGGGACUAUUGGUGUAUAAUCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAGGUCAACGAGUAUCAUCCUUCACCGGAAGGUGCGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUUAGUGAGGUCCUCGGACUGGUACAGCGCGUGGCAACACAUACUGCGCCGGGAAGUUGAACAAACUUGAUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCUAGU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq new file mode 100644 index 0000000..aea2f0f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Ichthyosporidium.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCUAAAGUUAAGCCAUGGAUGUCUAAGCAAAGCGUAAGUCGAGCGGCACAGGCUCAGUAACGGGCGAAUAUUUAAUCUCCUCGAGUGGAUAUCCUCUGUAACCGGAGGGCAAAACACAGGACGUGCAGUUGUAUAAGGAUUGUUCGUUUAACAUUAGUGGGGGAGAGUAAGACGCCAGUCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAUACGGAUACGGGGAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAACAGCAGGCGCGAAAAUUACCGCAGCCUGCAUUCAGGUCGGUAGUAAGGAGACGUGUAAACGAUGUGCAGGUAAAGAAUGCACUGUAUACAGGAGGACAAGACUGGUGCCAGCACCCGCUGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGAACCGGGUUGAAUUGCGUGACAGUCAGACUCUCAAGGUGUGAUGAGCGCUGUGAUUCUGGGGAAUAAGGAGUGUUUAGGGGCCAGGGUAUUAAACGGCAAGCGGUGAAAUGUGUUGACCCGUUUAUGGAGCGACAGAGGCGAAAGGCUGGCCAGGGGCAAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACAAUGCCGAUGUUGUGGUGCCGUAACGGACGCAAAAGAGAAAUCUAGUAGGGCCCUGGGGAGAGUACACGCGCAACAGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACACCUUACCGGGCCCACGGCCACACGAGUGUGACACACGAUAGCCGAGGAGUGGUGCAUGGCCCGUUAACGACAAGUGAGUGAUCUUUGGGUUAAGUCCGUAAAUUAGUGAGACCCCAGCAAAGGACAGGUGCGCAAAGCACAGGAAGGAUGGGUCAAGGACAGGUCAGUGAUGCCCUUAGAUGGUCCGGGCUGCACGCGCACUACAGUGGUCGCCGAAAUUUAGAUAUAGAGCUAAAGGCGAUCGAGAGGGAAUGAGCUUUGGAAGAGGCUCAGGAACGUGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAUACGGUGCUCGGCGCGAGCAAGGUGAAAUCACUGAGCGAGCGCAAGGUACCGGAUCUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq new file mode 100644 index 0000000..0970601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq @@ -0,0 +1,2 @@ +>d.16.e.J.debaisieuxi +CACCAGGUUGAUUCUGCCUGACGUAUGUGCUUGUCUUAAAGAUUUAGCCAUGCAAGUUAGUGAAACUUUUUAAGUGAAACGACAGACAGCUCAGUAAUACAGUAAUGAUUAACUUGCCUAAUAUAGGAUAACCUUGGUAACCUAAGGCUAACACUUUUUUCAAAUUAAAAUGUAGGUGAAACUAUUUUUAAUUUUUUUUUGGGGCAAUUAAGUUUCUGACCUAUCAGCUAGAUGUUAGGGUAAAGGCUUAACAUGGCUACAACGGGUAACGGAGAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAUUAGCUACCACGUCUAAGGAUGGCAGCAGGCGCGAAAAUUACCCAAUUCCUUAAUGGGAGAGGUAGUGAAAAGACAUGAUUUUCAUUUCGAUUGAGUCGGUACAUUAAAUAAGUACUGAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAAUGUCCGUAGUUGAUUUAAUUAAACUGUGAGUAAAUUAUAGAGCUCAAAACUAUAAGUAAGCAUGGUAUUAUAAGAUAAUAGGAACAGAUGAUGGCAAUAGUAUUCAAUAGUUAGAGGUGAAAAUUUAAGACCUAUUGAGGACUACCAGAAGCGAAAGCGAUUGUCAAGGAUGUCUCCAUUAAUAAGGGACUUAAGCUAGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCUAGCUGUAAACGAUGCCUACUAGGUGAUGUUUAAAUGGCUAUGCCUUAGGAGAAAUCAAAGUCUACGGGCUCUGGGGAUAGUAUACUGGCAACGGUGAAACUUAAAUGAAAUUGACGGAAGAAUACCACGAGGAGUGGAUUAUGCGGCUUAAUUUGACUCAACGCGGGACAACUUACCAGAGCCGAACCUGUAUGAGAAUUUAUAAUGUAAAUGAUAAUAGGGAAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACUUGUCAGGUUAAUUCCGAUAACGCGUGAGGUUUAUUAAAUAAUUGUUUAUUUGACGGAUGAUAAGAAAUCAUAGGAAGUUAAGCUAUAACAGGUCGGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGUACUACAAUGAUAUAUUUAAUAUUAAUAUUGAGAAAUAUAACUCUAAUAUAUAUCGAAGCUGGGAUAAGCUAUUGUAAAUUAGUUUUGAACUUGGAAUUCCUAGUAAUCAUAAGUCAUUAUGUUAUGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUAAGAUGGAUGUAUAGGUGAAAUGGCUAGACGUAAAUGGAAAGCAGUUAACCUGUGCAACUAAUAGGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq new file mode 100644 index 0000000..b74a2ea --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq @@ -0,0 +1,2 @@ +>d.16.e.L.acerinae +CACCAGGUUGAUUCUGCCUGGUGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCAAAGCUAGAAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGGACAUUUGAUCUUCUCGUGUGGACAUCCUCUGUAAGCGGAGGGAAAAACACAGGACGCGCGGACGCAGCCCGUGGGUGUAACGGCGGUGGAGAAGAGUAAGACGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUGAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGCAGCCUGCCUCAGGGCGGUAGUAAGGAGACGUGAAUGCGAAGUGCUAGCAAAGAAAGCACUGACAACAGGAGGACAAGACUGGUGCCAGCACCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGGGUUCGUAGUCUGAGCGGAACGAGGGGUGUGACGGGUCCCAGCUCAAGGGGGACAUAGCACCGCGAUGCCGCGGAACAAGGAGCGUCUAGGGGCCAGGGUAUUAAGCGACGAGGGGUGAAAUCUGGUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAGUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCCGCAAGGCGACGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGUCCCGACGAUCGGAGGAGUGUGUUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGUGAAGUAGUGAGACCCCUGCCGCAAGGGACAGGUGCCGAACGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUCAGAUGGGCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAAGGAAGGAAAGAGAUAAAGGCGAUCGAGAGGGAACGAGCUUUGGAAGAGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAGGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq new file mode 100644 index 0000000..1e52f3a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.musculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUGAGCUCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUGCGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq new file mode 100644 index 0000000..93e0dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.racemosus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUAAAUUUAUAUUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGAUCUACGUGACAUAUUCUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAACCCAAACUUACGAAUGGGUGCACUUAUUAGAUAAAGCCAACGCUGGGUAAAACCAGUUUCCCUUGGUGAUUCAUAAUAAUUUAGCGGAUCGCAUGGCCUUGUGCUAGCGACAGUCCACUCGAUUUUCUGCCCUAUCAUGGUUGAGAUUGUAAGAUAGAGGCUUACAAUGCCUACAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCUUUAAGGUCUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAACGUCCGUAGUCAAAUUUUAGCCUUUAGAUGAGGUGGCCUGGUCUUCAUUGAUCAAGCUCGCUUUUAUCGAGGCUUUUUUUCUGGUUAUGCUAUGAAUAGCUUCGGUUGUUUAUAGUCUCUAGCCAGAUGAUUACCAUGAGCAAAUCAGAGUGUUUAAAGCAGGCUUUCAAGCUUGAAUGUGUUAGCAUGGAAUAAUGAAAUAUGACUUUAGUCCCUAUUUCGUUGGUUCAGGAACUUAAGUAAUGAUGAAUAGAAACGGUUGGGGACAUUUGUAUUUGGUCGCUAGAGGUGAAAUUCUUGGAUUGACCGAAGACAAACUACUGCGAAAGCAUUUGAUCCAGGACGUUUUCAUUGAUCAAGGUCUAAAGUUAAGGGAUCGAAGACGAUUAGAUACCGUCGUAGUCUUAACCACAAACUAUGCCGACUAGAGAUUGGGCUUGUUUAUUAUGACUAGCUCAGCAUCUUAGCGAAAGUAAAGUUUUUGGGUUCUGGGGGGAGUAUGGGACGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAAAGCUCUUUCUAGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAUUCUGCUAAAUAGGCAGGUCAACUUUUUAGUUGAUUAAUAGAUUUAUCUAUCUGGCUUCUUAGAGAGACUAUCGGCUUCAAGCCGAAGGAAGUUUUAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAAAUCAGCGAGUUUAUAACCUUAGCCGGAAGGUUUGGGUAAACUUUUGAAAUUUCAUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUAUAGUGAGCAUAUGGGAUCAGUAGAAUUAGGUUGGCAACAACCUUUCUCUGCAGAGAACUAUGGCAAACUAGGCUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq new file mode 100644 index 0000000..100309a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq @@ -0,0 +1,2 @@ +>d.16.e.Microsporidium.sp.DP119 +CACCAGGUUGAUUCUGCCUGGUGUAGAUGCUAGUUUCUAAGAUUUAGCCAUGCAUGUUUUGUGAAUUCUUACGAAGGAACGGCGAACGGCUCAGUAAUAUUGCGUUAAUCUGGUCUAAAUAUAAAAAUAACUACGGUAACCUGUAGCUAAUAAUUUAGAAUGAGACGCAAAUUUAUCAGUUUGUUGGUAGUGUAAUGGACUACCAAGACUAUGACGAAUAACGGGAAAUUAGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGUCCACUCUUUUAUGAGGAGACAGUUAUGAAACGUGAAUAUAAGUUUGAAUUUUAAAAUAAUUUAUUUUAUGCAAUUGGAGGGCAAGUUUUGGUGCCAGCAGCCGCGGUAAUACCAACUCCAAGAGUGUCUAUGAARGUUGCUGCAGUUAAAGCGUCCGUAGUUUUUUUAUUGCAAUUUAAAAACUAUGAUUAAAUUAGUUAAGUUUCCAAUACAUUGUGAAACGGAUAGGGAAAAUUGUAUAGCUAGGUGAAGAAUGAAAUCUCAAGACCCUAACUCGACAAACAGAGGCGAAGGCGAUUUUCUUAUACGUAUUCUUAAAUAAAGGACGAUAGUUAGAGGAUCGAAGGUGAUUAGAGACCGCUGUAGUUCUAACUGUAAACUUUGCCGACAUUUCAUAUUGUUUUGAUAAGAAAGGGAGAAAUCUUAGUUUUCGGGCUCUGGGGAUAGUACACUCGCAAGGGAGAAACUUAAAGCGAAAUUGACGGAAGAACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUGACUCAACGCGGGAAAACUUACCAGAGUCAAAUAUAUUUAUGAUUUUUUUAAAUGAAAUAUAUAAAAGUGGUGCAUGGCCGUUGCAAAUUGAUGGGUUGACUUUUAACUUAAUUGUUGAAACCAGUGAGAUCAUUUAUGACUGGUAUUUUAAAUACAGGAAGGAAAUGGCAAUAACAGGUCCGCACGCCCUUAGACAUUCUGGGCUGCAAGCGCAAUACAAUAUCUUGUUAUUUAUAUUUAUUUAUACAAUUAUAUGUAGGAUUAAUUCUUGUAAAUGAAUUAUGAAUCAGGAAUUCCUAGUAAUAAUAUUUCAUUAAGAUAUUAUGAAUUUGUCCCUGUUCUUUGUACACACCGUCCGUCACUAUUUCAGAUGGUUAUAAAGAUGAAGAGCUAAGGUUCUGAAUAUUUAUAACUAGAUAAAGUACAAGUCGUAGCAAGGUUGCAGUCGGUGAACCAUCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq new file mode 100644 index 0000000..6ff328d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq @@ -0,0 +1,2 @@ +>d.16.e.O.colligata +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUGUCUGAGAUUAAGCCAUGCAUGUGAGUGAAUGUAGUAAGCAGGAACUGCGGACGGCUCAGUAAGACUACGAUGAAAUGAUCUGCGAAGAAGAAGUAACGGCGGGAAACUGAAGAAGAGAGUUUUUGAGAAUACUUGAAGGGAUGCGGAGAAGUGAUUUUUGAAGUGAUGUUGAGUAUUUGAGCGGAGUGUGUUGUAGACCUAUCAGCUGGUAGCUAGGGUAAUGGCCUAGGUAGGCGACGACGGGAGACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUGUGGGGAGGCGGUUAUGAGACGUAUGAUAUUGUUAUGAAGCGGACGAUGAAAGAGUCAGUGGAUAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCGAUGGUGUCUAUGGUGAAUGCUGCGGUUAAAAAGUCUGUAGUCAAGUGAGGAUGUGUAUGAGUAUGAAGGUGAGUGAACUAGAGUUGAAUAAGCUUGUAUGUAUGAGGAGAGCAACGGAGGGGGUGCACUGGAUAGCUGGGCGAGAGGUGAAAUGUGAAGACCCUGGCUGGACGAACGGAGGCGAAGGCUGUGUGCCAUGACGAAUGUGAUGAUCAAGGACGAAGGCCAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUGGCAGUAAACGAUGCUGACGGGAUGACAUGUAUGUGUGUUAUGCAAGAGAAAUUGAGUAUGUGAGCUCUGGGGAUAGUAUGUUCGCAAGGGUGAAACUUAAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCUGAAGAUGUGUGGAGAACUGAGAGGGGAGCACAUUGGCGGUGGUGCAUGGCCGUUUGAAACGGAUGGCGUGAGCUGAGGAUUAAUUUCCGGAAGGCGUGAGACCCACAAGACAGGUUGUUUGGAUGACAGGAGGGAGUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGUCCUGGGCGGCACGCGCACUACGAUACGUGUAUGAGAUGUGUGAGGGAUGAAUGUGUGGAAUGGCAUUCUGAACGUGGAAUUCCUAGUAAUGGUGGCUCAACAAGCCGACGUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGCACAUGGGACGAACACCGAGGGGUGUGAGUCUUCUGUGGUAGAUGAGAUAUAAGUCGUAACAUGGCUGCGGUUGGAGAACCAGCUGCAGGAUCAUCA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq new file mode 100644 index 0000000..7ec9865 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.cuniculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq new file mode 100644 index 0000000..d6a7e62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.1 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGUGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUCGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUCUCCGAUUGGCUGCGACUUCUUAGAGGGACUUUGUGGGCCAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGCGAGGCCCCGAGCCUUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq new file mode 100644 index 0000000..024562d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.2 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAACUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUCUUACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCACAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCUGAUGUCCGCAUGUUUGCGUGUGCAGAGCGCCCUCCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUACUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCAUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUUCCGAUUGGCUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACACAUACAACGAGUACAUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGUGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCAUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCUUACCGAUUUUGAGUGAUCCGGUGAACCUUUUGGACUGCGCGGAGUCUCGUGCUCUGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq new file mode 100644 index 0000000..f69e872 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.longa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCUUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAAGGGGUGCCAAUGUCCGCUGUUGCGUGUUCAGCGGCGCCCCUUCAUCCUUCUGUUAACGUCUCGGGUAUUCAUUUACUCGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCUAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGUCCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGUGGUCCUCGUGGCCGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq new file mode 100644 index 0000000..4acb186 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq @@ -0,0 +1,2 @@ +>d.16.e.O.operophterae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGCCUCCGAGGCUAAGCCAUGCAUGCCCGUGACGCAAGGAACGGCGAACGGCUCAGUAAUACUGCGAUGAUCUGCUCCGCGCGGACGAUAACUACGGGAAACUGUGGCUAAGAGCGCGGAUUGAGACGCAGCCCUAUCAGCAAGUUGGUAGUGUAACGGACUACCAAGGCGGCGACGGGUGACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUCUUGCGAGGAGGCGGUUACGAGGCGUGACGGAAGGGCGCACUGUAAAGACGUGCGCGAACGCGAUUGGAGGGCAAGUUCGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGGCACUGCGACGAAAGCGCGCUGCUCGAUGGCGCAGGCGUUGCAGGGGCUUGCGGAGCGGGCGGGGGGCACGGUAUAGGCAGGCGAGAGAUGAAAUGGCCAAGACCCUGCCUGGACCGACGGUGGCGAAGGCGGUGCCCUCGCACGCAUCUGUGGAUCAAGGACGAAGGCCGGAGGAUCGAAAGUGAUUAGAGACCGCUGUAGUUCCGGCAGUAAACGAUGCCGACACCGCGCGGCGGGGCUGCGCGGGGGGAGAAACCUUAGUGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGUGUGAAAAUUAAACGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCACCUUACCAGGGCCACGCGCGCCUGAGACCGCAUGCGCGAGGCGCGCAGGAGUGGUGCAUGGUCGUUGCAAAUUGGUGGGGCGACUUUUGGCUUAAAUGCCGGAACGAGUGAGAUCUCCGAGACGGGUGCGCGCAGCACAGGAGGGUGGAGGCGAUAACAGAUCAGUGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUCCCCGCGCGCUGCACAGAACGGUCGCGGGGGUGUGGGACCGGCGCCUGUAAGGGCGCCGCGAACGAGGAAUUCCUAGUAACGGCGGCUCACCAAGCCGCGGUGAAUGUGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGGCCGUGUCGGUGAAGGGAGCAAUCUCUGUGCCUCCGCGGCUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUCGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq new file mode 100644 index 0000000..aae8387 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.quadricornutus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGCUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGACGAUUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCUCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCGUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGCUAUUUAUUUAGUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGUCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUACCUCCGUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUUGACUCGUUGCUAAGCGAGAUUAACUUCUUAGAGGGACUUUGUGACUARACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGACUUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq new file mode 100644 index 0000000..e0d3525 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.sativa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCCGCCCGCUGAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCCUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCUUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCGCGGCCGGGCCGGUCCGCCUCACGGCAGGCACCGACCUGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUUCGUGCCUCCGGCGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGGGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUGGUCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq new file mode 100644 index 0000000..0d42d11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anophelis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUCGCCUUAAAGACUAAGCCAUGCAAGUUUGCGAGCUGAGCAGCGAACGGCUCAGUAAAACAGGGCACUCUAACGCACGGAAGAGAUAACCACGGGAAACUGUGGCUGAGAAGUGCGAUGAGGCUCUGACCUAUUAGUUUGUCGGUACGGUAAGUGCGUACGGAGACGAUGAUGGGUAACGGGGGAUCAAGUCCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGCAACUUACCCAAUGAGGAUUGAGGUAGUGACGAGGCGUAGAUUGUGAGUUGAGAGUAAAGAACUUAACGAGAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGGGCGUAUGUGUGUGUUGCUGCGGUUAAAAAGCGCGUAGUUUGUGGUGUAGCGGGUCGUUGUGGGGCGAGAUCAAUGCGUUCUGUGUGACUUAUGCUCAUUGCUAGGGAGCGCGAGACGCCGGUGGUAUUCGGUAGCGAGGGGUGAAAACUGCAGACCUACCGAGGAGCGACAGAGGCGUAAGCGGCCGGCGAGUGCGGAUCCGACGAUCAAGCGCGUGGGCAGGAGUAUCGAAGACGAUUAGAGACCGUCGUAGUUCCUGCAGUAAACGAUGCCGACAUGGUUGAAUAGAAUUGACCAAAGGGAAACUGAGUGUACGGGCUCCGGGGAGAGUACGGGCGCAAGCCAGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGCGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGGCAACUUACCCGGGCCGCAGCCUCUUGAGAGGAAACCGAUGGGGCCUCGUGGUGCAUGGCCGUUCUCAACGCGAGGGGUGACCACUGAGUUAGUUCUGGCAAGCCGUGAGGCCCCUGUACUUUUGUAGACGGCGGACGGCAAGUCCGAGGAAGCGAGGGCGUAUAACAGGUCUGUGAUGCCCGCAGAUGUCCGGGGCUCCACGCGCACUACAAUAGCAAAUGGUAGACGAGAGUAAGUUUGUUGUGGUUGGGAUUGACGCUUGUAAAUGCGUCAUGAACGAGGAAUGCCUAGUAGUUGUCUGUCAGCAGCGGACAACGAAUAAGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGCGGUGCGGAUGAAGCUGCUACGUGGCAAGAAUCCGUGCUGCUAGAUUGGAUACAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq new file mode 100644 index 0000000..bf550f0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anserina +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAUUACCUUACUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUCGGAAGGGAUGUGUUUAUUAGAUUAAAAACCAAUGCCCUCCGGGGCUCACUGGUGAUUCAUAAUAACCUCUCGAAUCGCACGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGCUGGGUCUUGGCCAGCCAUGGUGACAACGGGUAACGGGGAGUUAGGGCUCGACUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGAGGUUAAAAAGCUCGUAGUUGAACCUUGGGCCCGGCCCUCCGGUCCCCCUCACCGGGUGCACUGGCUCGGCCGGGCCUUUCCUUCUGGAGAACCGCAUGCCCUUCACUGGGCGUGCCGGGGAACCAGGACUUUUACUCUGAACAAAUUAGAUCGCUUAAAGAAGGCCUAUGCUCGAAUAGUCUAGCAUGGAAUAAUGGAAUAGGACGUGUGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGACAGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUAAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGAUUAGGGAUCGGACGGUGUUAUUUUUUGACCCGUUCGGCACCUUGCGAUAAAUCAAAAUGUUUGGGCUCCUGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACGAUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUCGUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCCGCAUCGCUUUGGCGGUGCGCCGGCUUCUUAGAGGGACUAUCGGCUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGAGCCAGCGAGUACUCCCUUGGCCGGAAGGCCCGGGUAAUCUUGUUAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCAGUGAGGCUUCCGGACUGGCCCAGGGAGGUCGGCAACGCCAACCCAGGGCCGGAAAGCUAUCCAAACUCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUCUCCGUUGGUGAACCAGCGGAGGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq new file mode 100644 index 0000000..054fe8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq @@ -0,0 +1,2 @@ +>d.16.e.P.carinii +UACCUGGUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAGUUAUACAGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUAUCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUUAUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAAUGCCUUCGGGCUUUUUGGUGAUUCAUGAUAACUUCGCGGAUCGCAUGGCCUUGUGCUGGCGAUGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUUUCGACGGGUAACGGGGAAUAAGGGUUCUAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAGAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGAAUUUAGGGAUUGGUUGCCUGGUCCUCCGAAGUUGUGUGCACUGGCGCAACUGAUCCUUCCCUCCUGGAUUACCGGCUGCCCUUCGCUGGGUGUGCCGGAUAGCCAGGGCAUUUUACUUUGAGAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCUCGAAUACAUUAGCAUGGAAUAAUAAAAUAGGACAUGUGGUUCUAUUUUGUUGGUUUCUAGGACCAUUGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUCAAUUGUCAGAGGUGAAAUUCUUAGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUCGGGCGAUGUUUUUUUCUUGACUCGCUCGGCAUCUUAUGAGAAAUCAAAGUCUUCGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGAAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCAGAUUAGCUUUUGCUGAUCGCGGGCUUCUUAGAGGGACUGUUGGCAUGAAGCCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGACAGAGCCAGCAAGUUCAUUUUCCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAAUGAGGUCUUCGGACUGGUGAUGGGUUAUUGGCAACGAUAAGCCUAUUACUGGAAAGUUGAUCAAAUUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq new file mode 100644 index 0000000..3a8ce15 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.cristatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCUAGCGAAGCCUUAUGGUGGAGCGGCGGACAGCUCAGUAAUACAGUUAUUAUUUACUCGUAGUAUGUAUACGGAUAACCAUGGUAAGCUAUGGCUAAUACGUGAACAGGUUAUUGCAUAGAUGAAACAGCGAUAACUGAGAGAGCAAUCGACUACGACUAAGUUUCUGGCCUAUCAGCUAGAUGGUAAGGUAAUGGCUUACCAUGGCUAUAACGGGUAACGGGAAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAGCGGGAGAGGUAGUGAAGAGACAUGAAGUUCUACUUAGAGACUGUACGGUAAAAUAGUACAGGAUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAACGUCCGUAGUUGAUCACAAGGUAUUCUUCUGCAUAGUAUUUGUGGAGUGUAUCUCGAUACUGUGAGAAAAAUAUGGUUCUCAAAGCGGAUUACGUGAGUAAUUUAGCAUGGGACAUGGUGAAUAUAGGAACAGAUGAUGGCAAUAGUAUUCAGCAGUUAGAGGUGAAAAUCGUUGACCUGCUGAGGACUCUCUGAAGCGAAAGCGAUUGUCAAGUAUGUCUCCGUUAAUAAAGGACUUAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACUAUGCCGACUAGGUGAGGCCGUCAGGCUGCGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCUGGGGAUAGUAUGGAUGCAAAUCUGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCCGAAUGCAUAGGAGAUCGGCUGUCUGAGAGGGUACCCGAGAUUAUGCAGGAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGGCCUGUCUGGUUAAUUCCGUAAACGCGUGAGGCCUGGGAAGCAAUUCAUUGCUUGACGGAUAGCGGCAAGCUAUAGGAAGACAGGCUAUAACAGGUCAGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGCAAUACAAUGGUAUAGUGAGACUAUGUACUGAAAAGUAUGCUUUAAGCUAUAUCGAAUCUGGGAUAAGCUCUUGUAAAUGAGUUUUGAACGAGGAAUUCCUAGUAAUCGCAGGUCAUAAUGCUGCGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGGAUGUAUCGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUAUACAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCUGUGGCAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq new file mode 100644 index 0000000..66edb7f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUAUAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAGUCUACUUGACAUUUUUAUUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAUUAUCCUUGAUUUUUAUCUUUGGAUAAGUAUUUGUUAGGCCUUAUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGUAACACGUAAUAAAUUUAUUUUAUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUGCAAGGCCAAUUUUUGGUUUUGUAAUUGGAAUGGUGGGAAUUUAAAACCUUCCCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAUUGUAACUAUUCUAGGGGAACUAUUUUAGCUUUUGGCUUUAAUACGCUUCCUCUAUUAUUAUGUUCUUUAAAUAACAAAGAUUCUUUUUAAAAUCCCCACUUUUGCUUUUGCUUUUUUGGGGAUUUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGUUAAAGCAUUUACUGUGUUUGAAUACUAUAGCAUGGAAUAACAAAAUUGAACAAGCUAAAAUUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGACAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACGAACAACUGCGAAAGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGUGUUGGAUGAAAGUGUUAAAAAUAAAAGUCAUCUUUCGAGGUGACUUUUAGAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCGAGUACACUAUAUUCUUAUUUGAAAUUGAACAUAGGUAACUAUACAUUUAUUCAGUAAUCAAAUUAGGAUAUUUUUAUUAAAAUAUCCUUUUCCCUGUUCUACUAAUAAAUUGUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUGAAAAGCUUCUUAGAGGAACAUUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUAUAUAACGAGUUUUUAAAAAUAUGCUUAUAUUUGUAUCUUUGAUGCUUAUAUUUUGCAUACUUUUCCUCCGCCGAAAGGCGUAGGUAAUCUUUAUCAAUAUAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAAAAUUGAAUUAUAUUCUUUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq new file mode 100644 index 0000000..b5b366a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCACAGAUUAAGCCAUGCAAGUGAAAGUACAUAUGUAAGUAAUAUAUUGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGAUGUUUUUAAUAUAAGGAUAACUACGGAAAAUCUGUAGCUAAUACUUGUGAAAAUACCUUUUGAUAUAUACAUAUGUAUGUAUCAUUAAGGUAUGUAUUUGUUAGAUAUAAGAAUAAAAUAAAUAUAAUUGAAUUAUAACAAAGAAGAAACACAUAAAAUAUGUGUAUUAUCAAUCGAGUAUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGACCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAAAAGAGAGGUAGUGACAAGAAAUAACAAUACAAUAUCGAAAAAUGAUUUUGUAAUUGGAAUGAUAGGAAUUUACAAGGUUCCUAGAGAAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAAUUGUUGCAGUUAAAACGUUCGUAGUUGAAUAUUAAAGAAUCCGAUGUUUCAUUUAAACUGGUUUGGGAAAACCAAAUAUAUUAUAUAUUUUGCUUUGUUCAAAAUAAGGUUUUCUAAUAAAUUAUGUUUUUAUCAGAUAUGACAGAAUCUUUUUUAAAAUCUCUUCAAUAUGCUUUUAUUGCUUUUGAGAGGUUUUGUUACUUUGAGUAAAAUUAAGUGUUCAUAACAGACGGGUAGUCAUGAUUGAGUUCAUUGUGUUUGAAUACUACAGCAUGGAAUAACAAAUAUGAAUAAGCUAAUUAUUUUUUUUUUCAUUAUUUUUUUUGAUAUUCUUAUUAGCUUAGUUACGAUUAAUAGGAGUAGCUUUGGGGGCAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACGGACUACUGCGAAAGCAUUUGCCUAAUCUAUUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUGUUGGAUGAAUAUAAAAAAUAUAUAAAUAUGUAGCAUUUCUUAGGGAAUGUUGAUUUUAUAUUAGAAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACACUAUAUUUUUAUUUGAAAUUGAAUAUAGGUUACUAUACGUUUAUUCAGUGUUCAAAUUAGGAUAUUUUUUUUAUUAAAAUAUUCUUUUCCCUGUUUUACUAAUAAUUUGUUUUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUAAAUAAAGCUUCUUAGAGGAACAGUGUGUAUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUAAACUAGGCUGCACGCGUGCUACAAUGAUAUAUAUAACAAGUUGUUAAAAAUGUACUUAUAAAUAAGUGUGUACAAUUUUUCCUGUACUGAAAAGUAUAGGUAAUCUUUAUCAGUAUAUAUCGUAAUUGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUAAAUUGUUUGGAUAUGAAUUAAAAUAAUGAAAUUUUAUAUUUCUGAUUUUUUCUAGAAGAACUGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq new file mode 100644 index 0000000..74cb22c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq @@ -0,0 +1,2 @@ +>d.16.e.P.hippoglossoideos +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUUUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCUUUUAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGUCUGAUUUGAUCUCUCGGAGUGGACAACCUCUGUAACCGGAGGCCAAAACACGGGAGGGGCAUGCAGUGGAGAUGCCCCGAGAACAUUUAGUGAGAGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAGGACGGGUACGGGGAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUGCAUUCAGGGCGGUAGUAAGGAAACGUGAAAACGAUGUGCAGGUAAAGAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGACUGCGUGACUGGCGUGAAAGACCCUUUUAUUCAUUCAAGGGGGGCGCAGCGCCGGAAAAGCAGGGAAUAAGGAGCGGCCGGGGCACAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGUGCAGGGGCGAUUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGAUGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCAGUUCUUAGACUGCGCCGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUGGUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUUGUGAGACCCCUGCUGGCGAGCCAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACACGAGUUUAUAGAUAGAAGAAAUGGUGAUCGAGAGGAAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGGUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq new file mode 100644 index 0000000..0825b4a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq @@ -0,0 +1,2 @@ +>d.16.e.P.lepisma +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUUUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCCGCAUGUUGCGUGUGCAGAGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUUUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAACGAGUACUUCCCAGCUCCGAAAGGUAGCUGGUAAUCAGCAAUAUGCAUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAAUCAUUUGGACUGCGUGAGGUUUCGUACCUCGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq new file mode 100644 index 0000000..86c7a36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.mirandellae +CACCAGGUUGAUUCUGCCUGGCGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCAUUUUGUGGAGCGGCAUAAGGCUCAGUAACGGGCGUCUAUUUGAUCUCCUGAUGUGGACAACCUCUGUAACCGGAGGCCAAUACACAUGAGGCACUGUUUCCGUUUGGUGGGGUGUCAAUAGCUAUUUAAUUUUUAUAGCGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAUAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGUGUUCGUAGUCGGGCUGCAUGACUGGCGUGAAAGACCUUCCUUUCAAGGGGGUACAGCGCGGGGAAAGCAGAGAAUAAGGAGCGUUUUGGGGUCAGGUUAUUAAGCGACGAGAGGUGAAAUUUAAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGAGCGAGUUUUAUUCGCUUCGCGGAAGAGAAAUUUAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUCAACUCAACGUGGGACAGCUUACCAGGCCGGACGACCGCACGAGUGUAGUACACGAUAGGUUGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUUACGAGUAAUGGUGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAGAUUAUUGAGAGAUAAUGGUGAUCGAGAGGGAAUGAGCUUUGUAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq new file mode 100644 index 0000000..897f945 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.palmata +UGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAGCGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAAUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUUGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGCCGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGAUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGUUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCCGCGGUUGAGGCGUUUACGCCCUGGCCGCAGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq new file mode 100644 index 0000000..a076ef4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.pulvinata +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAUUUAUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGUUACACUACCGGAUAACCGUAGUAAAUCUAGAGCUAAUACGUGCCACUAAAACGGUGAAAACCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCAAUCAUGUUUUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUAUCAUGGUCGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAUCUUAUCGAGUAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAUUUGGCGGGCGAUGUGGGGCGUCUUAACCGACGAUCUCAUGUCGGCUGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUCACUGCAUUGUUAGGUUUCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGUGAGACUGUUUUUGGCUCACCCGGCAUCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCUACUACCACUAUGGUAGUAAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAACGGGUGAGGAUGUGCGAGAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUGAACUGUGCUACACAGAUUUUUUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq new file mode 100644 index 0000000..76544cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCCUUAGCACUCUUGAUUCAUUUCUUGAGUGUGUACUUGUUAAGCCUUUUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGCGACACGUAAUGGAUCCGUCCAUUUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGGCCAAUCUGGCUUUGUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAACUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAAGCAACGCUUCUAGCUUAAUCCACAUAACUGAUACUUCGUAUCGACUUUGUGCGCAUUUUGCUAUUAUGUGUUCUUUUAAUUAAAAUGAUUCUUUUUAAGGACUUUCUUUGCUUCGGCUUGGAAGUCCUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGAUAUAGCAUUGCGCGUUUGAAUACUACAGCAUGGAAUAACAAAUUGAACAAGUCAGAAUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGGCAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACAAACAACUGCGAAAGCAUUUGCCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGCUUUGGAUGAAAGAUUUUAAAAUAAGAAUUUUCUCUUCGGAGUUUAUUCUUAGAUUGCUUCCUUCAGUGCCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCAAAUACGACAUAUUCUUACGUGGGACUGAAUUCGGUUGAUUUGCUUACUUUGAAGAAAAUAUUGGGAUACGUAACAGUUUCCCUUUCCCUUUUCUACUUAGUUCGCUUUUCAUACUGUUUCUUUUUCGCGUAAGAAUGUAUUUGCUUGAUUGUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUAUAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUUCGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUGUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAGGGGGAUUAUAUCUCCUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq new file mode 100644 index 0000000..13a90ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUACAUGCAUAUUUUUAUAUGCGGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAAUGCUCUCGACGAAUGUCUUGGGCAUGUACUUGUUAAGCCUUUAUAAGAAAAAAGUUAAUAACUUAAGGAAUGAUAACAAAGAAGUGACACAUAGAAGGACCUGCGUCCAUUUAUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUUGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGACCAAAACUGGUUUUGUAAUUGGAAUGAUGGGAAUUUAAAUCCUUCCCAUAAUACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAACCAAUAUUUUAAUAACGCCGUUAGCUAGAUCCACAAGGGGUUGAGCCAAUCACGGUUUCGGCUUCUGUGCGCAUCCUACCUAUCAAGCGUUUUUUUAAUUAAAGUGUUUCUUUUUAAAAUCUUCUUUACCUUAACCAUAUGGAAGAUUUUGUUACUUUGAGUAAAUUAAAGUGUUCAUAGCAAACAGAUACAGCAUUGCGCGUUUUGAAUACUACAGCAUGGAAUAACAAAAUUGAACAAGUCAAAACUAUGUUUCUUUUUUUUUAUUUUUGGCUUAGUUACGAUUAAUAGGAGUAGUUUGGGGACAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACAAACAACUGCGAAGGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUUUUGGAUGAAAGUUAAACAAAUAAGGAUAGUCUCUUCGGGGAUAGUCCUUAGAUUUCUUCCUUCAGUACCCUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUGAGAGCUCUUUCUCGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACGACAUAUUUUUAUGUCGGAUUGGAUCUGGAUGAUUUGCUUAUAUUGAGGUGCAAUCUAAAUAGGGGAUUGCAAUUAUACUUCGUGUCGGUGUUUCUUAAUCGAAUAGCUGAUGCGUUUGGUAUAUUGCUUUCCUUUUUUUUAUUUCUGCGCUUCUUUACUUGGCUUAUCGUACCGUUUCCUUUUUGUGUAGAAAUGUAUUUGCAUUAUAUUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUACAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUACGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCACGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAAGGGGAUUAUAUCUUCUUUUUUCUGGAAAAACCGUAAAUCCUGUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq new file mode 100644 index 0000000..64ca28d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq @@ -0,0 +1,2 @@ +>d.16.e.P.weissei +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCGCCAAUGUCCGCUGAUUGCGUGUGCAGCGGUGCCCUCUCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUAGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUAAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACCGCGAAGUCCUCGUGGCUUUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq new file mode 100644 index 0000000..7479150 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq @@ -0,0 +1,2 @@ +>d.16.e.Ple.lanceolata +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCUUCGGCUUUGCCAGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACCCGUUGCUAAGCGGGAAUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGAUCUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq new file mode 100644 index 0000000..093c07a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq @@ -0,0 +1,2 @@ +>d.16.e.R.carriebowensis +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUAAGUGAUUCUGAUGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAACUUACUAUUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAAUGCGGGGUUUCGGCUCCGUGGUGCCAAUUAGAUAACAACACCAACAUUUGGUGAUUCAUAAUUUUCUUUCUGAUCGCUGCAUGCAUUGCGGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCGAUGGGUGCCCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAGUUGGUGGUCUUGCGGGUGCGCGCGUUGAGCGUACGCCUGUCGAGGCUGCUUUUGUGGAUUGCGCGCACGGGCGGCUUUAGUGUCGAACGUGUUGGGUUUCGCUGCUUUGGCGUUCACGCGGCAGAGCGGCGGAGGCGCAGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUUUUCCUAUUUUGUUGGUGUUGUGAGGGGCGAGUAAUGAUUAAGAGGGACAGUUGGGGGCACUUGUAUUCCGGCGCUAGAGGUGAAAUUCUUAGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGUGGAAUUGCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUAUUACCGCUUUUUUUGGUAGUGAGAGCUUUUUUGACCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAGCGGGCGAGGAUGCGCGAAAGCGUUUCCUAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGGUUGCAAUUCUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAUUGUCGUGAGGGGAGCGUUUGCGCUCGUUUCGUGAAGAAAACUUGGUCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq new file mode 100644 index 0000000..99deaaf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq @@ -0,0 +1,2 @@ +>d.16.e.R.leptophylla +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGACGACUCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCACUUUCGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACUUGCCUCGUCCUCGCGGAUGUUGGCAGGUCGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUUCUUUACUGCAUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGAAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUCAUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCGCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGCGAGGAUGUGCGAGAGCAUUUCCAAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAAAUGGACUGUGUUCUCACGGACCGUUUGGCCCAAACUUGGCCAAGCCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq new file mode 100644 index 0000000..8a1603d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.e.R.norvegicus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGUGGGGGGGACGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq new file mode 100644 index 0000000..b728e04 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq @@ -0,0 +1,2 @@ +>d.16.e.S.alba +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGUGCUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUUUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGCCCGGUCCGCGUUUGGUGAGCACCGGUCGGCUUGUCCCUUCUGUCGGCGAUACGCUCCUGGCCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGGACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAAGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGUCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUACUCGGAUCGCGGCGACGUGGGUGGUUCGCCGUCCGCGACGUCGCGAGAAGUUUUCUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq new file mode 100644 index 0000000..7eb6818 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.cerevisiae +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq new file mode 100644 index 0000000..3697105 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lemnae +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCAUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGCGCCAAUGUCCGAUGUUUCGUGUGCAGCGGUGCCUCUCCAUCCUUCAGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCUGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGCGGUCCUCGUGACUGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq new file mode 100644 index 0000000..2908cfd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lophii +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGAUUUAGCCAUGCAUGUGUAAGCGAAGCGAUUAGUGAAGCGGCGGAAGGCUCAGUAACGGGCGAGUAUUUUAAUCUCUAGAACCGGACAACCUCAGGAAACAGAGGGGAAAACGGAGUAAGAGCAUGUGUUGUUAGCAUGUGAUGAGAACAACAGUGCAGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUAUUUAGACGUAGACGGGUACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCAAGAGGGCGGUAGUGAAGAGACGUGAAAACAAGUGUGUGUAAAAACCACAUGAGUAACUGUGGAGGGUCAAGGCUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAGAACAGUACUUGUUUGUAAUGUGGCUUAUCGAGAGCCGAAUAGAACGAGAAGAGUUCAGAGUAAGGAGYGAAGGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUUUGAUGACCUGCUUUAGGAGUAACAGAGGCGAAAGCGCUAGUCAAGAACGAAUCCGAUGAUCAAGGACGUAGGCUGGAGGAUCGAAGACGAUUAGAGAGACCGUAGUAGUUCCAGCAGUAAACGAUGCCUACGCUGUUGUGGUUAUGAGCACGGCAGAAGAGAAAUCUAGUAGGGCUUUGGGGAGAGUACGCGCGCAAGCGAUAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAUACCCGAUGGCCGUGUGAGCGUAGUACGCGAUAGGUCAGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGCCGAAGUAGUGAGAUCCCUAGGAUACGAAAGUUAUCGACAGGUGUUAAAAACACAGGAAGGAAGGGGCAAGAACAGGGUCAGUGAUGCCCUUAGAUGGUAUGGGCUGCACGCGCACUACAGUGGUCACAGCAGAAACGGAUAGAAGUAAAUGUGAUCGAGAGGGAAUGAGCACUGUAAUGUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUAUCUCAUUAAGAAGCGAUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCAGGUGCGAACAAGUGAAAGCGAGUGAGUGCAGGGUUCYAGAUCUGAUACAAGUCGUAACAAGGCAGCUGUAGGAGAACCAUUAGCAGGAAGCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq new file mode 100644 index 0000000..022bce8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq @@ -0,0 +1,2 @@ +>d.16.e.S.mytilus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCAACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGUGCCAAUGUCCGAUUGUUUCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGUUCCGGUGAACCAUUUGGACCACGCGGUCUUCGUGACUGUGAGGAAAAUCUAGUAAACCAUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq new file mode 100644 index 0000000..3e571a9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq @@ -0,0 +1,2 @@ +>d.16.e.S.tuberosum +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACAAAUUCAGACUGUGAAACUGCGAAUGGCUCAUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCAUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUAUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGAUGGCACGGCCGGUCCGCCCUAGGUGUGCACCGGUCGUCUUGUCCCUUCUGUCGGCGAUGCGCUCCUGGCCUUAAUGUGCCGGGUCGUGCCUCCGGCGCUGUUACUUGAAGAAAUUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUCGGUCCUAUUUACGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACCGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGGUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGAAGGUAUCCCUUCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGCUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq new file mode 100644 index 0000000..9a3b981 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.16.e.T.cruzi +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUUUCAAGGACUUAGCCAUGCAUGCCUCAGAAUCACUGCAUUGCAGGAAUCUGCGCAUGGCUCAUUACAUCAGACGUAAUCUGCCGCAAAAAUCUUGCGGUCUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGAUGUUCUCUGUUCCGGCGGCAGGGCAACCUGCUGCCAUGGGACGUCCAGCGAAUGAAUGAAAGUAAAACCAAUGCCUUCACCGGGCAGUAACACUCAGAAGUGUUGAUUCAAUUCAUUCCGUGCGAAAGCCGGGUUUUUUAUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCCAGCGAUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCAAAAAAAAAAGAUGAGGCAGCGAAAAGAAAUAGAGCCGACAGUGCUUUUGCAUUGUCGUUUUCAAUGGGGGAUAUUUAAACCCAUCCAAAAUCGAGUAACAAUUGGAGGACAAGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGAAUUGAGGGCCUCUAAGGCGCAAUGGUUUAGUCCCAUCCACUUCGGAUUGGUGACCCAUGCCCUUGUGGUCCGUGAACAGACAUAUUCAGAAACAAAAAACACGGGAGUGGUACCUUUUCUGAUUAUCGCAUGUCAUGCAUGCCAGAGGGCGCCCGUGAUUUUUUACUGUGACUAAAAAAGUGUGACCAAAGCAGUCAUUCGACUUGAAUUAGAAAGCAUGGGAUAACAAAGGAGCAGCCUCUGGGCCACCGUUUCGGCUUUUGUUGGUUUUAAAAGUCCAUUGGAGAUUAUGGGGCAGUGUGACAAGCGGCUGGGUGGUUAUUCCACACACACGCACACUCCUUUUUUGGAUGUUGUGUCUCUGUGUGUGUGGCACUCGUCGCCUUUGUGGGAAAUCCGUGUGGCACUUGUUUGGUGUUGUUGGCAGACUUCGGUCUUGCCUUCACACACGUUUCACAUGUGUCAUGCCUUCCCUCAACUCACGGCAUCCAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGUGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGGGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAGUUUUUGGUCGUAGGCGUGGUCGGGCUUGAUUAUAUUAUUUUUCAUCCCGUUCCUCGUCUCGCCAAUGAAUAUAUUAAAUUUACGUGCAUAUUCUUUUUGGUCUUCGUUUUUUUACGGCGAGGACCUUUAACGGGAAUAUCCUCAGCACGUUAUCUGACUUCUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUUGACUCAACACGGGGAACUUUACCAGAUCCGGACAGGGUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGAUCCCCUGAAUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGCUGCCCAGUAGGAUUCAGAAUUGCCCAUAGGAUAGCAAUCCCUUCCGCGGGUUUUACCCAAGGGGGGGCGGUAUUCGCUUGUAUCCUUCUCUGCGGGAUUCCUUGUUUUGCGCAAGGUGAGAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUCAAUGUUCUGGGCGACACGCGCACUACAAUGUCAGUGAGAACAAGAAAAACGACUCUUGUCGGACCUACUUGAUCAAAAGAGUGGGAAAACCCCGGAAUCACGUAGACCCACUUGGGACCGAGUAUUGCAAUUAUUGGUCGCGCAACGAGGAAUGUCUCGUAGGCGCAGCUCAUCAAACUGUGCCGAUUACGUCCCUGCCAUUUGUACACACCGCCCGUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGUCGAGUGCUUCACUUGACCGAAAGUUCACCGAUAUUUCUUCAAUAGAGGAAGCAAAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCAGAAGGAUCAAGCUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq new file mode 100644 index 0000000..c3f9ae2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.e.T.gondii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCUAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGGUCUUUACUACAUGGAUAACCGUGGUAAUUCUAUGGCUAAUACAUGCGCACAUGCCUCUUCCCCUGGAAGGCAGUGUUUAUUAGAUACAGAACCAACCCACCUUCCGGUGGUCCUCAGGUGAUUCAUAGUAACCGAACGGAUCGCGUUGACUUCGGUCUGCGACGGAUCAUUCAAGUUUCUGACCUAUCAGCUUUCGACGGUACUGUAUUGGACUACCGUGGCAGUGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACAACACUGGAAAUUUCAUUUCUAGUGAUUGGAAUGAUAGGAAUCCAAACCCCUUUCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGGAAGCAGCCAGUCCGCCCUCAGGGGUGUGCACUUGGUGAAUUCUAGCAUCCUUCUGGAUUUCUCCACACUUCAUUGUGUGGAGUUUUUUCCAGGACUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUGUCGCCUUGAAUACUGCAGCAUGGAAUAAUAAGAUAGGAUUUCGGCCCUAUUUUGUUGGUUUCUAGGACUGAAGUAAUGAUUAAUAGGGACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUAGGAAAACGUCAUGCUUGACUUCUCCUGCACCUUAUGAGAAACCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGGAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGGAUCAGGAACUUCGUGUUCUUGUAUCACUUCUUAGAGGGACUUUGCGUGUCUAACGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAACGAGUUUAUAACCUUGGCCGAUAGGUCUAGGUAAUCUUGUGAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUCAACGAGGAAUGCCUAGUAGGCGCAAGUCAGCACGUUGCGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGUUCCGGUGAAUUAUUCGGACCGUUUUGUGGCGCGUUCGUGCCCGAAAUGGGAAGUUUUGUGAACCUUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq new file mode 100644 index 0000000..22f2555 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq @@ -0,0 +1,2 @@ +>d.16.e.T.hominis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGGGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUGUAAACGGAGGCCAAAACACAGGAGCGCCGUGUACAGAGACGGUGCGAGAACCGGAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGCAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGUAAGCGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUAAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGGGUUUAAGGCCCGCUAUCGAGGCGGGCAGUGCGCCAGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGGUCGCAUGAGUGUUGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGUGCCGGGACAGGUGCGCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUGGCAGAGGUAGCCUGAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq new file mode 100644 index 0000000..15995cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq @@ -0,0 +1,2 @@ +>d.16.e.T.thermophila +AACCUGGUUGAUCCUGCCAGUUACAUAUGCUUGUCUUAAAUAUUAACCCAUGCAUGUGCCAGUUCAGUAUUGAACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUUAAAGAUUACAUGGAUAACCGAGCUAAUUGUUGGGCUAAUACAUGCUUAAAAUUCCGUGUCCUGCGACCGGAACGUAUUUAUUAGAUAUUAGACCAAUCGCAGCAAUGUGAUUGAGAUGAAUCAAAGUAACUGAUCGGAUCGAGGUUUACCUCGAUAAAUCAUCUAAGUUUCUGCCCUAUCAGCUCUCGAUGGUAGUGUAUUGGACUACCAUGGCAGUCACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAACUACGGUUCGGCAGCAGGGAAGAAAAUUGGCCAAUCCUAAUUCAGGGAGCCAGUGACAAGAAAUAGCAAGCUGGGAAACUUACGUUUCUACGGCAUUGAAAUGAGAACAGUGUAAAUCUCUUAGCGAGGAACAAUUGGAGGGCAAGUCAUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGUUCAGGUUCAUUUCGAUUCGUCGUGUGAAACUGGACAUACGUUUGCAAACUAAAAUCGGCCUUCACUGGUUCGACUUAGGGAGUAAACAUUUUACUGUGAAAAAAUUAGAGUGUUCCAGGCAGGUUUUAGCCCGAAUACAUUAGCAUGGAAUAAUGGAAUAGGACUAAGUCCAUUUUAUUGGUUCUUGGAUUUGGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUAGUCAGAGGUGAAAUUCUUGGAUUUAUUAAGGACUAACUAAUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAACUAUACCGACUCGGGAUCGGCUGGAAUAAAUGUCCAGUCGGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGAAGUAUGGUACGCAAGUCUGAAACUUAAAGGAAUUGACGGAACAGCACACCAGAAGUGGAACCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACGAGCGCAAGACAGAGAAGGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGUCUGCUUGUAAAUAACAGGUUGUACUUCUUAGAGGGACUAUUGUGCAAUAAGCCAAUGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCCUAGACGUGCUCGGCCGCACGCGCGUUACAAUGACUGGCGCAAAAAGUAUUUCCUGUCCUGGGAAGGUACGGGUAAUCUUAUUAAUACCAGUCGUGUUAGGGAUAGUUCUUUGGAAUUGUGGAUCUUGAACGAGGAAUUUCUAGUAAGUGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCGUUUGUACACACCGCCCGUCGCUUGUAGUAACGAAUGGUCUGGUGAACCUUCUGGACUGCGACAGCAAUGUUGCGGAAAAAUAAGUAAACCCUACCAUUUGGAACAACAAGAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq new file mode 100644 index 0000000..627b884 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq @@ -0,0 +1,2 @@ +>d.16.e.T.violacea.1 +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGCUAACUUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAACACGCGGGGCAACCCGUGGUACCAAUUAGAUAUCAAGCCAACAUAUGGUGAUUCAUGAUUGUUUUUCUGAUCGCACGCGCAGUGCGACGCAUCGUUCAAGUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUCUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGCGGCCGGCGCUGUGCGCGUAAAUGCGUGCGGCGUUAAAGAAAAAAUUUAUUUUUUUUCGGGCGUGCUUUUGUGGAGGGCGACACGUGGUGGCUUGAUUGUUGCUGCGGGUCGGCGCCACUUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGUCGUGAAUACGUUAGCAUGGGAAAAUGGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGAGCAUUACGAUGACUCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCUGUUACACAUGUUUGUGUAGCUCAGAAGCAAUAGAGGUUUUUUCUUUUCUUUUCUUUUCUUUCUUUUUUUCCUUUGAGCAAUUGAAGGGGGAGAGGUUUGAAAAAGGAAUGGAACGGAGACUCCUUACUCAUGUUGUUUUGUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUGGAUGCGCGAGAGCGUUUCCUAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGAUUGCUGCGAUCGGAGUGUUUACGCUCUGGCCGCGGUGAAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq new file mode 100644 index 0000000..f847076 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq @@ -0,0 +1,2 @@ +>d.16.e.U.gallina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUCGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGAAUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGGGUCUCGUGCCUCGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq new file mode 100644 index 0000000..8506647 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.grandis +AACCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGAUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUCAAGGAAAGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCAUAGUCUUUGGCUGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAGAAAUAACGGACUGAGCCUUUGGUUCAGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACCAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGGGGGUGACAAAGUCCGCUGAUGCGUGUGCUGCGUCGCCCCUUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGGUCUCCUUUGUUGGUUUGAGGGACUCUAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGUGUGUAUUAUCCACCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUUAUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACGCAAUCUUAUUGCAUUUGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAGCGAGUACUUUCCAGCUCCGAGAGGCUGCUGGUAAUCAGCAAUAUGCAUCGUGCUUGGGAUUGAUCUUUGGAAUUAUAGAUCAUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUUCGGUGAACCUUUUGGACAGCGUUAGUUUCGGCUGAUGCUGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq new file mode 100644 index 0000000..e4d1fb5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.maydis +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUACGCAAAUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGUUUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCGUAAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAACCAUCCUCCUCGGAGUUUGGUGAUUCAUAAUAACUUCUCGAAUCGCACGGCCUUGUGCUGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUUGCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACGAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAGUUUGGUCUCGGACGCUGGGUCUGCUUAAUUGCAUGUACUUGACGGUCCGAGACUUCCUUCUUGGUGAACGGCCGCCCUCGGGUGGUCCGGAACCAGGACUAUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCAUAGGCCCGAAUAUAUUAGCAUGGAAUAACAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGAACUGCCGUAAUGAUUAAAAGGGACAGCCGGGGGCAUUAGUAUUUGCACGCUAGAGGUGAAAUUCUUGGAUUGUGCAAAGACUUCCUACUGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAGGUUAGGGUAUCGAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACUAUGCCGACUCCGAAUCGGUCGAUGCUCAUUUCACUGGCUCGAUCGGCGCGGUACGAGAAAUCAAAGUUUUUGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCGGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUGGCGCUUUCAUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGACCUGCUAAAUAGACGGGUUGACAUUUUGUUGGCCCCUUAUGUCUUCUUAGAGGGACAAUCGACCGUCUAGGUGAUGGAGGCAAAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCCGGGCUGCACGCGCGCUACACUGACAGAGACAACGAGUGGAGCCCCUUGUCCGAAAUGACUGGGUAAACUUGUGAAACUUUGUCGUGCUGGGGAUGGAGCUUUGUAAUUUUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGACUUGGGAGAGUACAUCGGGGAGCCAGCAAUGGCACCCUGACGGCUCAAACUCUUACAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq new file mode 100644 index 0000000..7e0d307 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq @@ -0,0 +1,2 @@ +>d.16.e.U.pisces +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUAUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCAUGUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCUCGUUUUAUCAGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGGUGGCUUCGUGCCAACUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq new file mode 100644 index 0000000..9cf06ee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq @@ -0,0 +1,2 @@ +>d.16.e.V.acridophagus +CACCAGGUUGAUUCUGCCUGUUAUAUGUACUAGUGUCGAAGAUUUAGCCAUGCAUGCUUUACGAAUUCACAAGAAGAAGUGGCGGACAGCUCAGUAAUACAGUUAUAAUAUACUCUCUACUAAAGGAUAACCGCGGUAAGCUGCGGGUAAAACUUCAAGCUAUGUGUUUCAUGAAAGAAUUUAUAGUUCAGAGUGUUAGUUUCUGGCCUAUUAGUUAGUAGGUAAUGUAAGGGAUUACCUAGACUAUUAUGGGUAACGGGAGAUGAAUGUCUGAUACCGGAGAGGAAGCCUUAGAAACCGCUUUCACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUCGUUUUUUAAGACGGAGGUAGUUAUGACACAUGUGAAUUAUUCACGAGGAAGAUCAAUAAAUCAGAUUUUUUUUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGUGCAUAUACAUGCUGUAGUUAGAAAGUUUGUAGCCGUAUAAGCUUGAAUCAGAGGAAAGGAGGACUCUUAAGGUAAACUUUAACUCUGGUCAAUGCUUAUAUUCGAAGCGGAUGGAGGCACUUGUAUUCAAUAGCGAGAGGUAAAAUUUGAUGACCUAUUGAGGACAAUCAGUAGCGAAAGCGAGUGUCUAGUACGCGUUUGAGGGUCAAGAACGUUAGCCGGAGGAUCGAAGAUGAUUAGAUACCGUUGUAGUUCCGGCCGUAAACCAUGCCUACUUGCCUUGUACAUAGUAUGAAGCAUAGAGAAAUUAAGAGUUUUUGGGCUCUAGGGAUAGUAAUCCGGCAACGGACAAACUUAAAGAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUCAACUUGACUCAACACGGGAAAUCUUACCAGGGUCUGUAUAUGUGAGACUGUCCCAUUUAUGGUGGUACACGAUAAUAUACUGAGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUUAUUCCGGUAACGUGUGAGGUCACAGUAUUAAUAAGUAUUUUAAUAGACAGCUAAUGGUAAAUUAGAGGAAGUGUGACGAUAACAGGUCAGUGAUGCCCUUAGAUACCCUGGGCUGCACGCGCAAUACAUUGAGUAAGUCAUUUACAAUAGUAAUUUUGAAACUUACUCGCUACUGGGAUCAUCCUUUGUAAUUGGGAUGUGAACGUGGAAUUCCUAGUAAUCGUAGCUCACUAAGUUACGAUGAAUGUGUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUAAGAUGGAUGUUGAUAUGAAAUUGCUGCUUGAAUGUGAGGUACUUGAGUAUUAACAACUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGAAGAAUCUGUGGCAAGAUCAUAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq new file mode 100644 index 0000000..b9bf68b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq @@ -0,0 +1,2 @@ +>d.16.e.V.corneae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUAAGAUUAAGCCAUGCAUGUUUCCUCAAUCAGGGACGAAUAGCUCAGUAAAACUGCGAUGAUUUAGUCUGGCUGUGUAGAUAACACGUGAAAAUGUAGCUAAGGGAAGGCAGAAUAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACAGUGACGGUUGACGGGAAAUUAGGGUUUUGUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUUUGCAGGAGGCAGUUAUGAGACGUGAAGAUGAGUAUCUUGUAAAGAGGGAUAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCAUAGAAGGGCAAAGAGAGAUGCGAGGUCUCACAGUGCGAUGAUGGAGGAGCCGAUGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAGGCGAUGUUCUUGUAGGCAUUCGGUGAUCAAGGACGAAGGCUGGAGUAUCGAAAGUCAUUAGAUACCGCAGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCAUUGGACACAGUGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAACUUACCAGGGCCAAGUACUUGUGUAGAAACGAGCAAUACAGGAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGACCUUAAAUGGUUGAAUGAGUGAGAUCUUUUGGACAUGUUCCGCACGGAACAGGAAGGAAAAGGCUAUAACAGAUCCGAGAUGCCCUCAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCAGGUAGAGAGAGAGACAGGAAGGUGCUCAGAUGGACUAUGUGCUGUAAGGCACAUACGAAAGAGGAAUUCCUAGUAAGUGUGUAUCAACAAUGGAUAUUGAAUAAGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGUUUUUCAGGAUGAAGAGUCCAGGCUCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUUGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq new file mode 100644 index 0000000..32ce19a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq @@ -0,0 +1,2 @@ +>d.16.e.V.culicis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGAGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUAUAACCGGAGGCCAAAACACAGGAGGCGCGUGACACGGGCACGGGCGUGCAACCGGCAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGGAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGACGAUUGUUGCAGUUAAAGAGUUCGUAGUCGGGCUGCAUGACCGGCGCUGAAGGCUCCCUAUCGAGGGGGGCAGGGCGCCGGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGCAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGACAGCUUACCAGGCCCGACGGUCGCACGAGUGUGGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGCGCCGGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUCAGUGCCCGAGCGGCAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACACGGUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq new file mode 100644 index 0000000..ddad56b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq @@ -0,0 +1,2 @@ +>d.16.e.V.imperfecta +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUACUCUAAGAUUAACCCAUGCAUGUUAUUGAAUAUAAAGAAAAGACGAACAGCUCAGUAACUCUUAUUUGAUUUGAUGUAUUAGGACUCUAACUAUGUUAAAUUAUAGGUAACAAUAAUACAAUAAGAAUAAGAUCUAUCAGUUAGUUGUUAAGGUAAUGGCUUAACAAGACUAUGACGGAUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGAUUGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGAUAUUAUAUUGAGGCAGUUAUGAGUAGUAUUUUAUAAUUAUUGUAAUAUUGUAAGUACAUAUUACAAGAUAAAUCGGAGGGCAAAUCGAGUGCCAGCAGCCGCGGUAAUACUUGUUCCGAUAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCUGUAGUUUAUUUAUAAUAAGCAUUGUAAGGUAUACUGUAUGGUUAGGAGAGAGAUGAAAUGUGAUAACCCUAACUGGAUGAACAGAAGCGAAAGCUGUAUACUUAAAUGUAUUAUUAGAACAAGGACGUAAGCUAGAGGAUCGAAGAUGAUUAGAUACCAUUGUAGUUCUAGCAGUAAACUAUGUUGAAUCAUAGAUAUAUUUUGAUAUAUAUUUGUGUAGAGAAAUUAAGAUUAUAUUGACUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGUAAUUUACCAGGUAUAACAUGGUAUAAUAUUUUAUCAUGAUAGUGGUGCAUGGCCGUUUCCAAUGGAUGCUGUGAAGUAAUGAUUAAUUUCAACAAGAUGUGAGACCCUCAUUUAGACAGAUGUAGUGAUACAUAUGAAGGAGAGGAUUAAAACAGGUCCGUUAUGCCCUAAGAUAAUCUGGGUUGCACGCGCAAUACAAUAAUAUUUGAUAUUAUAAGGGAUAAUAUAAUGUAAGAUAUAUUUGAACAUGGAAUUGCUAGUAAAUUUUAUUUAAUAAGUAGAAUUGAAUGAGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUAUUAUCUAUGAACAAAUUUAUAAAGUGAAUAGAUAGUACUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq new file mode 100644 index 0000000..1ae37da --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq @@ -0,0 +1,2 @@ +>d.16.e.V.necatrix +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGAUAUGGAAAAAUGGACUGCUCAGUAAUACUCACUUUAUUUAAUGUAUUAAAUUAGUAUAACUGCGUUAAAGUGUAGCAUAAGACAUAUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUAUCUGAGGCAGUUAUGGGAAGUAAUAUUCUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUAUUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCGACGAUGUGAUAUGAUAUUAAUUGUAUUAGAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCAGAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUCAGAGAAGAUUUUCGAUCUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCACCAAGACGUGAGACCCUUUUAUUAAUAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUGUGAAAUUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq new file mode 100644 index 0000000..ae6d794 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq @@ -0,0 +1,2 @@ +>d.16.e.Vairimorpha.sp.C21 +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGACAUUUGAAAAAUGGACUGCUCAGUAAUACUUACUUUAUUUAAUGUACAUUUGAAAAUAACUACGUUAAAGUGUAGAUAAGAUGUGUACAGUAAGAGUAAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAGUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUUUCUGAGGCAGUUAUGGGAAGUAAUAUUAUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUGAUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAAAAAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCAACGAUGUGAUAUGAUAUUAAUUGUAUUACAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUAUUCUGAGAUAAUUUUCCAAUUUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCAACAAGACGUGAGACCCUUUUUUAUAUAAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUAUGAAAAUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq new file mode 100644 index 0000000..780471c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.borealis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCAAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCAACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq new file mode 100644 index 0000000..ec9c5bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.laevis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGACCAAAACCAAUCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCGAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCCACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq new file mode 100644 index 0000000..6dcff46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.e.Z.mays +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCCCGCCGAUCCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCGUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGCCGGGUGCCGCCGCCGUACGGGCAGAACCGACCGGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGUGUUACUAAUAGGACCCCGCUGGCCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGUAGUUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCGCGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUUGGCCGACAGGCCGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAGCUCGGCCGCACCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq new file mode 100644 index 0000000..3994c56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq @@ -0,0 +1,2 @@ +>d.16.m.A.americana +CAUAGGUUUGGUCCCAGCCUUCCUAUUGACUACUAAUAGACUUACACAUGCAAGCAUCCGCACCCCAGUGAAGACGCCCUUUAAAUCCACCUGAACCAAAAGGAGCUGGUAUCAAGCACACAUUUGUAGCUUAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUGGACGAAAGUCUGACUAAGUCAUAUUGAUAAGGGUCGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCUAGUUAAUAGGAAUACGGCGUAAAGAGUGUUAAAGCAUCACACUAAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCACAGCUGUAAUAAAAAUAGACAACGAAAGUGACUCUACAACCGCUGAUCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACACAGGUAAUUGUAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGAACAAGAGUAAGCAUAAUAAUAGCACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUAUUUCAAGAACACUCAACACGAAAGUUAUUAUGAAACUGAUGACUAAAGGAGGAUUUAGUAGUAAACUAAGAAUAGAGCGCUUAGUUGAAUUAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAACACGAUACACCUAAACUUAUUCACACGUAUUAACCGUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq new file mode 100644 index 0000000..487d01e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq @@ -0,0 +1,2 @@ +>d.16.m.A.cahirinus +AAUAGGUUUGGUCCUAGCCUUAUAAUUAGCUGAAAGUAAAAUUACACAUGCAAGACUCCCCACACCAGUGUCAAAUCCCUUAGAACUAGACAGCUAACCUAAGGAGAGGAUAUCAAGCACAUUAAUAUAGCUCAAGACAUCUCGCCAAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCAAUGAACGAAAGUUUGACUUAGUUAUACUUCCAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUACGGCGUAAAAGGUGUUAUAUCUAAAACAAAUAGAAUUAAAACCUGACUUAUAUGUGAAAAUUCAUUGUCAGACAAAAACACAACCACGAAAGUGAUUCUAAUAAACCAAACACGAAAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAAAUAAUUAAUAACAAAAUUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAUACCCCGUUACACCUCACCACCCCUUGCUAAUCCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGACACACAGUAAGCAAGAGCACAAACAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGAGGUGGGAAGUAAUGGGCUACAUUUUCUUAAAAAGAACACACGAAACCCUUUAUGAAAUUAAAGGAUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUGCGCACACACCGCCCGUCACCCUCCUCAAACUAAUCUUCAAGUAAAAUAAAUAAAAUUAAACUAACUAGAAUACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq new file mode 100644 index 0000000..eeb9896 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq @@ -0,0 +1,2 @@ +>d.16.m.A.fulgens +CAAAGGUUUGGUCCUAGCCUUCCCGUUAGUUCUUAAUAAAAUUACACAUGCAAGUAUCUACACCCCAGUGAAAAUGCCCUCCAAAUCACUAGUUGAUUAAAAGGAGCAGGUAUCAAGCACACUUUACAUAAGUAGCUCACAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUUAUAUUAAUAGAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAAACUAACGGGCAUCCGGCGUAAAACGUGUUAAAGAAUCUACUCACAUUAAAGUUAAAACUUAAUCAGGCCGUAAAAAGCUACCGUUAACAUAAAAUACCUUACGAAAGUAACUUUAUUAAUUCUGAUUACACGACAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUUAGUAUAACAAAACUAUUCGCCAGAGAACUACUAGCAAUAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUUACCACUUCUAGCUACUUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGAAGCAAAGUAAGCAUAAUGAUUCCUGCAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAACAAGAACACUAUACGAAAAUUUUUAUGAAAUUAAAACCUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAGUUGAAUUGGGCUAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAACGUCAAGAUUUAAACCCAAUAUAUAAUCACAACAGACUAAACGCAAGAGGAGACAAGUCGUAACAAGGUAAGCGUACUGGAAGGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq new file mode 100644 index 0000000..2249b46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq @@ -0,0 +1,2 @@ +>d.16.m.B.brevicauda +UAAAGGUUUGGUCCCAGCCUUCCUAUUAAUUGUUAGCAAAUUUACACAUGCAAGUAUCCGCGCCCCUGUGAGAAUACCCUUUAAAUCACCUAUGACUGAAAGGAGUAGGUAUCAAGCACACUUAUUUAUAAGUAGCUAAUCACACCUUGCUUAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUGCUAAUAUUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGGUAGCGGCGUAAAGCGUGUUAAAGAACACUAAAUAAAAUAAAGAUAAAACUUGACUAGGCUGUAGAAAGCAACAGUCAAGACUAAAAUAAACUACGAAAGUGACUUUAUUACUUUUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAGGUAAUUUAAUUAACAAAACUACUCGCCAGAGGACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCGCCCCUUGCUAAUACAGCUUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCUUAAAUAUUUCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGGCGGGAAGAAAUGGGCUACAUUUUCUAUAACUAGAAUAUUCACGAAAGUUUCUAUGAAACUAGAAACCAAAGGAGGAUUUAGUAGUAAGUUAAGAAUAGAGCGCUUAACUGAACCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUUUAAGUCUACUGAUAUAUAAUCUCAGACUAACUAAUAUUAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq new file mode 100644 index 0000000..f3a2a28 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq @@ -0,0 +1,2 @@ +>d.16.m.B.taurus +CAUAGGUUUGGUCCCAGCCUUCCUGUUAACUCUUAAUAAACUUACACAUGCAAGCAUCUACACCCCAGUGAGAAUGCCCUCUAGGUUAUUAAAACUAAGAGGAGCUGGCAUCAAGCACACACCCUGUAGCUCACGACGCCUUGCUUAACCACACCCCACGGGAAACAGCAGUGACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUUAUAUUAAUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGCUAACAGGAGUACGGCGUAAAACGUGUUAAAGCACCAUACCAAAUAGGGUUAAAUUCUAACUAAGCUGUAAAAAGCCAUGAUUAAAAUAAAAAUAAAUGACGAAAGUGACCCUACAAUAGCCGACGCACUAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUACAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAAAAAAAGUAAGCGUAAUUAUGAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGAAAUGGGAAGAAAUGGGCUACAUUCUCUACACCAAGAGAAUCAAGCACGAAAGUUAUUAUGAAACCAAUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAGAUUCAGUGCAUCUAACCCUAUUUAAACGCACUAGCUACAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq new file mode 100644 index 0000000..ca47b03 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq @@ -0,0 +1,2 @@ +>d.16.m.C.elegans +UAAAGUUUUCUUUCAGGGAAUUAAAAUUUGAUCAUGGUUUAAGAUGAUUUAAAAUGGUAUUAUCUAAAUUUGAUUUACAGAGUAGGCAAUAAAAAUUUACCUCGGCAAUUUAUCGCUUGUAAAAUACUUGUUCCAGAAUAAUCGGCUAGACUUGUUAAAGCUUGUACUUUAAUUGAUGUUAAUUAUGAAAUUAUUAUAUUUUCUUUUAGAUCUAUGGUAGAAUUUGGAUUUAUAUUAGUGAAUUUUCAUAAUUUUAAGAUUUGUUGAACAAAGCAGAUUAGUACCUGGUUAGACAAAAAUUAAAAGAGCAGGAGUAAAGUUGUAUUUAAACUGAAAAGAUAUUGGCAGACAUUCUAAAUUAUCUUUGGAGGCUGAGUAGUAACUGAGAACCCUCAUUAACUACUUAAUUUUUUGACUCGUGUAUGAUCGUUUAUUUUAUUCUUAAGGAUUAUAAUAAAAAAUUUUUAAUUUAUUAAAAUAGAUAUAUACCCGGUUUAUGAUUUAAGAAACAUUUGGCCUACAAUAUUUUAUAUUAUGGAUUUUAGUUUUAGUUAACUAAAUGAAAUUGUAAAAGACAGUAAAAAAUUCUUAAUGUAUUUUUGAAGAUUAUCUAGAAGUGGUACAAAUCAUCCAUCAAUUGCCCAAAGGGGAGUAAGUUGUAGUAAAGUAGAUUUAGGGGAACCUGAAUCUAGUAAUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq new file mode 100644 index 0000000..9bb815f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq @@ -0,0 +1,2 @@ +>d.16.m.D.dugon +UAAAGGUUUGGUCCUGGCCUUCUUAUUGGUUCUUAGCGAGCUUACACAUGCAAGUAUCCGCGCGCCAGUGAGAAUGCCCUUUAAAUCACUCCCGAUCAUAAAGGAGCAGGUAUCAAGCACACACUCAUGUAGCUCAUAACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAGAAAUUUAGCCAUAAACGAAAGUUUGACUAAGCUACGCUAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAAUUAAUAAGUACCGGCGUAGAGCGUGUUUAGGAGAAGACCCAUAAAUAAAGUUAAAUCAGAUCCAAGCCGUAGAAAGCUAAAGAUCAGACAAAAAUAAUCCACGAAAGUGACUUUAUCAGCUCUGAACACACGAUAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCGAUAGCUUCCAACAAAGCUACCCGCCAGAGAACUACUAGCAAAAGCUUAAAACUCAAAGGACUUGACGGUGCUUCACAUCCCCCUAGAGGAGCCUGUCCCAUAAUCGAUAAACCCCGAUAAACCUCACCCCCACUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUUAAAAGGUGCAAAAGUAAGCUCAAUGAUAGCCAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGUGGAGGUCUAAGAUGGGCUACAUUUUCUCUUAGAGAACAAUCAACCAACGGACGUCACUAUGAAACAAGUGACCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUCAUAACCAUUCCACCAUAUAUGAUCCUAAUAGCAUAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq new file mode 100644 index 0000000..a39ca60 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq @@ -0,0 +1,2 @@ +>d.16.m.D.geoffroii +CAGAGGUUUGGUCCUGGCCUUACUGUUAAUUUUUAUUAGACCUACACAUGCAAGUUUCCGCAUCCCAGUGAGUAUGCCCUUUUAGCUUCACUGAAGUAUAAAGGAGCUGGUAUCAGGCACACUUAAUUAAGCAGCCCAUGACACCUUGUUUAACCACACCCCCACGGGUAACAGCAGUGACUAACAUUGAGCUAUAAACGAAAGUUUGACUAAAUCAUAAUAAAUAAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAACAGAAAAACGGCGUAAAGGGUGUUUAAGCAUAAACCUCAUAAAUAAAGUUAAAACUCAACUAUGCUGUAAUACGCCCUAGUUGGCAUUAAAAUAUACAACUUACGUGACUUUACUACUGCUGAAGACACUAAAGCUAAGGUACAAACUGGGAUUAGAGACCCCACUAUGCUUAGCCGUAAACCUAGGUAAUUAAAUAACAAAAUUACUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCCCUAGACCCUCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUAGCUUAACAGUCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGCCCCAAAGUGAGCAAAAUCAUCUAAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAUAUUAGAACAUAACGGAUUGUCUACUGAAAUAGAGGCAUGAAGGAGGAUUUAGUAGUAAAUUAAGAGUAGAGAGCUUAAUUGAAAUAGGCAAUAGGGUGCGUACACACCGCCCGUCACCCUCCUCGAUAAAGUAACCUUCAAUACCUAAUUAGAAUACGCUAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq new file mode 100644 index 0000000..e7d211c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq @@ -0,0 +1,2 @@ +>d.16.m.D.novemcinctus +CACAGGUCUGGUCCUAGCCUUACUAUUAAUUCAUAACAAAAUUACACAUGCAAGUAUCAGCACACCAGUGAGAAUGCCCUCUAACUCUUAUAGAUCAAAAGGAGCAAGCAUCAAGUACACACAGCCCUUACAGUAGCUCAUAACGCUUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCAAUAAGCGAAAGCUUGACUAAGUUAUGUUAUUAUAAGGGUUGGUAAAUUUCGUGCCAGCAACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUUAUCGGCGUAAAGCGUGUUUAAGACACCUAGACAAUAGAGUUAAACCCUUACUACGCUGUAAAAAGCCUUAGUAGGACCAUAAACCCUUCAACGAAAGUGACUCUAAUUUAUCUGACUACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUAAAACAGUUCACAAACAAAACUGUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAUACCUCACCACCCCUUGCUAAUACAGCCUAUAUACCGCCAUCUUCAGCAGACCCUAGUAAGGCACCACAGUGAGCACAAUAACAUACAUAAAGACGUUAGGUCAAGGUGUAGCUUAUGGGGUGGGAAGAAAUGGGCUACAUUUUCUAAUAAAGAGCAAAUACAAAAAACUUAAUGAAACAAUUUAAGACUAAGGUGGAUUUAGUAGUAAGCUAAAAAUAGAGAGUUUAGCUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAUUAUAAGCGCCACAUAAACUAAAACACAUUAAUUCAGUAGCAACUAUAUAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq new file mode 100644 index 0000000..5620601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq @@ -0,0 +1,2 @@ +>d.16.m.D.virilis +AUAAAGUUUUAUUUUGGCUUAAAAGUUUGUUAUUAAUUUGAUUUAUAUGUAAAUUUUUGUGUGAAUAUUUAAUAAUUUAAAAAAUUAUUAAAUUUAUUAUAAUCGCAGUAAUUAAUUUUAUUAGUUAAAGAAAUUUAGAAAUAGCAAUAUUAAAGAGUAUAGAUUAAAUUGGUGCCAGCAAUCGCGGUUACACCAAUUAUACAAAUGAAUUUUUUUAGUAAAAGUUAAAUUGGUUUAAUUUAAAUAUAAUUAAAUUUAUUAAGUGAAAUUUUAAAUUUAAAAUUUUUAUUAAGUGAAUAAUUGAAACUUGAAAAUUUUAAAUAAAAACUAGGAUUAGAUACCCUAUUAUUUAAAAUGUAAAUAUAAAUACUUAAGUAGUAAUAGUUAAGUUCUUGAAACUUAAAAAAUUUGGCGGUAUUUUAGUCUAUCCAGAGGAACCUGUUUUGUAAUCGAUAAUCCACGAUGGACCUUACUUAAGUUUGUAAUCAGUUUAUAUACCGUCGUUAUCAGAAUAUUUUAUAAGAAUAUUAAUAUUCAAUAAUUUUUAUUAAAAUUUAUAUCAGAUCAAGGUGUAGCUUAUAUUUAAGUAAUAAUGGGUUACAAUAAAUUUAUUUAAACGGAUAAAAUUAUGAAAAAAUUUUUGAAGGUGGAUUUGGUAGUAAAAUUAUAAAGAUUAAUAAUUUGAUUUUAGCUCUAAAAUAUGUACACAUCGCCCGUCGCUCUUAUUAUUAAGGUAAGAUAAGUCGUAACAUAGUAGAUGUACUGGAAAGUGUAUCUAGAAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq new file mode 100644 index 0000000..52bb4a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq @@ -0,0 +1,2 @@ +>d.16.m.E.rufescens +CAAAGGUUUGGUCCUAGCCUUAUUAUUAGUUGUCAGUAAGAUUAUACAUGCAAGUAUCCGCCAACCAGUGAAAAUGCCCUCAUACUCGUCCACUACAAACGAUCCCAAAGGAGCCGAUAUCAAGCACACCCACGGUAGCUCAAGACAUCUUGCUCAGCCACACCCCCACGGGAUACAGCAGUAGUAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUGAUUAGGGUUGGUCAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAAUUAAUGAUUAAACGGCGUAAAGUGUGGUUAAACACUUACCAAUGUAAAUAAAGUUAAACUAGCUCUCAGCUGUAAAAAGCUAAAGAUCUAUGGUAAAUAGACUAUUAAUGUAACUUUACUUAUAGUGAACCCACGAUAGCUAAGAUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACUUUGAUAAUUACUAACAAAAAUAUCCGCCAGAGAACUACAAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCCUAGAGGAGCCUGUUGCAUAAUCGAUAAACCCCGAUAAACCCUACCAUCACUUGCUAAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAUAAGGAACAAUAGUAAGCUUAAACGCCCCCGCAAAAACGUUAGGUCAAGGUGUAACCUAUGUGAUGGAAAACAAUGGGCUACAUUUUCUACAUAAGAACACACGAACUCUUAUAUGAAAUUAUCAGAUAAAGGAGGAUUUAGAAGUAAGCCAGGAAUAGAGAGCCUGACUGAACUUGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGUUUAAGACUAACAACCCUAUUACACUAAUACAAACAUAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAGUAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq new file mode 100644 index 0000000..ec6581f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq @@ -0,0 +1,2 @@ +>d.16.m.G.gorilla +AAUAGGUUUGGUCCUAGCCUUUCUAUUAACUCUUAGUAGGAUUACACAUGCAAGCAUCCCCGCCCCAGUGAGUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGUACGCAGAAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUGAGUUGUAAAAAACUCCAGCUGAUAUAAAAUAAACUACGAAAGUGGCUUUAAUAUAUCUGAACACACAAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUUCAACAGUUAAAUUAACAAGACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCACAUCCUUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACGAAGGCCACAAAGUAAGCACAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACUUCAGAAAACUACGAUAACCCUUAUGAAACCUAAGGGUAGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUCUAUAUAGAGGAGAUAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq new file mode 100644 index 0000000..bb4f2d2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq @@ -0,0 +1,2 @@ +>d.16.m.H.amphibius +UACAGGUUUGGUCCCAGCCUUUCUGUUAAUUUUUAAUAGAAUUACACAUGCAAGUAUCCACACCCCAGUGAGAAUGCCCUCUAAAUCACCCAGAUCAAAAGGAGCGGGUAUCAAGCACACCAUACACCGUAGCUCAAAACGCCCUGCUCAGCCACACCCCCACGGGAAACAGCAGUGACCAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGCCAUAUUAACCAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAAACUAACAGAAAUACGGCGUAAAGCGUGUUAAAGAAUUAAAAGUACAAAUAAAGUUAAAUUCUAACUAAACUGUAAAAAGCCCUAACUAGAAUAAAAAUCUACUACAAAAGUGACUUUAACAAUACUGACCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUCCAAAAACAAAACUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUCCAGUCUAUAUACCGCCAUCUCCAGCAAACCCUAAAAAGGACUAAAAGUAAGCUCAACUAUUACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGGCUGGGAAGAAAUGGGCUACAUUUUCUAGAACAAGAACACAACCCACCCGAACGAAAACUCCUAUGAAAGCUAGGAACUAAAGGAGGAUUUAGUAGUAAAUCAAGAGUAGAGUGCUUGAUUGAACAAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAACACAAACCCAUAAACAUAAUAGCUAGACAAAACCAAAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq new file mode 100644 index 0000000..5a42913 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.auropunctatus +CAAGGGUUUGGUCCUGGCCCUUCCAUUAGUUACUAAUAGGAUUACACAUGCAAGCCUCCGCAUCCCGGUGAAAAUGCCCUCUAAGUCAUAACUGACCUAAAGGAGCAGGUAUCAAGCACACAAAAUGUAGCUCAUAACGCCUUGCUCAGCCACACCCCCACGGGCUACAGCAGUGACAAAAAUUAAGCCAUGAAUGAAAGUUCGACUAAGCCAUAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAGACUAAUAGACACACGGCGUAAAGCGUGUUCCAGAAACAACCUACCACUAAAGUUAAACCUUAACUAAGCCGUAAAAAGCCACAGUUAACAUGAAAAUACAACACGAAAGUAACUUUAAUACCCCAACUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAAUCUAGAUAGUUAACUUAACAAACCUAUCCGCCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCAAAAGUAUCUUAACAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGAAAGCAAUGGGCUACAUUUUCUACACAAGAACAUCUUACGAAAGUUUUUAUGAAAUCAAAAACUAAAGGAGGAUUUAGCAGUAAGCUGAGAAUAGAGCGCUCAGCUGAAUCGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACACAAACCCAAACAUAACCUAUUAAAAUCACACUUAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq new file mode 100644 index 0000000..d10d756 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.2 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq new file mode 100644 index 0000000..88f8a65 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq new file mode 100644 index 0000000..6d7bbbc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.moschatus +CAUAGGUUUGGUCCUGGCCCUACUGUUAAUUGUAAUUAGACCUACACAUGCAAGCUUCCACAAUCCGGUGAGAUAUGCCCUACAGAUUACUUACCAUAAUCGUUAAGGAGCGGGCAUCAGGCACACCACAGGUAGCCCAUCACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAAUAUUAAGCCAUAAACGAAAGUUUGACUAAAUCAUAAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAGUUAACAGAAAACCGGCGUAAAGCGUGUUUAAGCACAAACCUACAAAUAAAGCUAAGACGCAACUAAGCUGUAAUACGCUAUAGUCAACAUUAAAAUACACUACAAAAGUGGCUUUAAUACCGCUGAAGACACGACAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUCAGCUUUAAACCAAGAUAAUUAAACAACAAAAUUAUUCGCCAGAGAACUACUAGCAAUCGCUUAAAACUCAAAGGACUUGGCGGUGUCCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCACGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUGGCCCCAACACGGGUAAUAAAGCAGCAAGAUUACUCAACCGUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAAAUUAGAACAAACGAAUUAUCUUAUGAAACCUAAGACAUAUGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGCACACACCGCCCGUCACCCUCCUCGAUAAAACUGGAUAAAUAACUAAUAACUCCGAGCACAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGAACAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq new file mode 100644 index 0000000..790ca18 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.5 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAACCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACAGAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq new file mode 100644 index 0000000..7292f31 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq new file mode 100644 index 0000000..dfde3d8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq @@ -0,0 +1,2 @@ +>d.16.m.L.catta +UAUAGGUUUGGUCCUGGCCUUACUAUUAGUUUACAGUAAGAUUACACAUGCAAGUAACCGCAUCCCAGUGAGAAUGCCCUCCAAAUCCCCUGAUUAAAAGGAGCAGGUAUCAAGCACACCAAUAGGUAGCUCACCACACCUUGCUAAACCACACCCCCACGGGAUACAGCAGUGAUUGAACUUAAGCAAUAAACGAAAGUUUGACUAAGCUAUACUGACACUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUAUUUCCCGGCGUAAAGUGUGUUUAAGAUUUAUAUAAAUAAAGUUAAUUUUUAUCCAAGCCGUAAAACGCCCCAGCUAAAACAAAACUAACCUACGAAAGUGACUUUAAUACUCUGAAGACACGACAACUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACCUAAGUAAUUAACAAACAAAAUUACUCGCCAGAGCACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACUUCUUGCUAAUUCAACUUAUAUACCGCCAUCCCCAGCAAACCCUAUUAAGGCCCCAAAGUAAGCAAAAACACAUACAUAAAGACGUUAGGUCAAGGUGUAGUCAAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAUAUUAGAACAACACCCCAACAGAAGCCUUUAUGAAACUAAAAGCCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCACCAAUUAUUAAUUCACUAAUUCUACUAAACUCUAAACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq new file mode 100644 index 0000000..5f34aee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.auratus +AAAAGGUUUGGUCCUAGCCUUAUAGUUAGUUAGAGGUAGAGUUACACAUGCAAAUCUCUAUAAACCAGUGUCAAAUCCCUAGGUUUUACUUUAAACCCUAAGGAGAGGGUAUCAAGCACAUACACAUAUAUAGCUAAAGACACCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUUAGUCAUACCUCAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACUAUUCUCCGGCGUAAAAUGUGUUUUUAUUACGAACAUAAUAGAAUUAAAACCCAACUAAUAUGUGAAAAUUCAUUGUUGGACUUAAAAUCAAUAACGAAAGUAAUUCUAAUUAUAUUAAUACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUAAGUGAUUAAAUAACAAAAUCACUUGCCUGAGAACUACUGGCCACAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAUACCUUACCACCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCUUAAAAAAGAACAAGAGUAAGCAAGAGAAUACCCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUGGGCUGGGAAGUAAUGGGCUACAUUUUCUUCUAAAGAACAGUUACGCUAUCCUCUAUGAAACUUAGAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGUACACACCGCCCGUCACCCUCCUCAAAUUAAGCUAACUGUUAACUAUACCUAAUAUUGACUCAUAAACUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq new file mode 100644 index 0000000..1091d21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.musculus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUAGAGGUAAAAUUACACAUGCAAACCUCCAUAGACCGGUGUAAAAUCCCUUAAACAUUUACUUAAAAUUUAAGGAGAGGGUAUCAAGCACAUUAAAAUAGCUUAAGACACCUUGCCUUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACCUCUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUCUUCGGCGUAAAACGUGUCAACUAUAAAUAAAUAAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAACUCAAUAACGAAAGUAAUUCUAGUCAUUUAUAAUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACCUAAAUAAUUAAAUUUAACAAAACUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGCUCUACCUCACCAUCUCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGUAUUAAAGUAAGCAAAAGAAUCAAACAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGAAAUGGGAAGAAAUGGGCUACAUUUUCUUAUAAAAGAACAUUACUAUACCCUUUAUGAAACUAAAGGACUAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUUGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAAAUUAAACUUAACAUAAUUAAUUUCUAGACAUCCGUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq new file mode 100644 index 0000000..276037b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq @@ -0,0 +1,2 @@ +>d.16.m.M.putorius +CAAAGGUUUGGUCCUAGCCUUCCUAUUGAUUAUUAACAGAAUUACACAUGCAAGUCUCUACACCCCAGUGAGAAUGCCCUCCAAAUCUAUAUGUUGAUUAAAAGGAGCGGGUAUCAAGCACACUAAAUUAGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGCCAUGUUAACAAAGAGCUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAGCCCGAAUCAAUAGGCAAACGGCGUAAAACGUGUUAAGGAUUAUAUUAUAUUAAAGUUAAAAUUUGACAAGGCUGUAAAAAGCUACUGUUAAUAUAAGAUAAACCACGAAAGUGACUUUAUUACUUCCAUCAACACGAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACAUAAAUAAUUAUCACAACAAAAUUAUCUGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUCACCACUUCUAGCUUAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAAGAAAAGUAAGCACAAUAAUAUUACAUAAAAAAGUUAGGUCAAGGUGUAACCUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAACCAAGAACACACUCACGAAAGUUUUUAUGAAAACUAAAAACUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAACACACUCAAAUACUACAUAAUAAAAGUAAACCUAAAGCAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGGUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq new file mode 100644 index 0000000..c971496 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq @@ -0,0 +1,2 @@ +>d.16.m.Manis.sp +CAUAGGUUUGGUCCCAGCCUUUUUAUUAGUUUAUGAUAAAAUUACACAUGCAAGUAUCCGCCCUACGGUGAAAACGCCCUUUAGCCUUUACAAGUCAAAAGGAGCUGGUAUCAAGCACGCCAAUUUAAGGCAGCUAGUGACACCUUGCUUACGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAACCAUUAACGAAAGUUAGAUUUAGUUAUAUCAUUUAUGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAAUUAAUAAAAAACCGGCGUAAAAAGUGUCAAAGUGUAUUUAAAUCAAAUAAAAUUAAGCCCUAAUCAAGCUGUAAAAAGCCUCGAUUAUAGUAAAAAUAAACUAUGAAAAUAAUUUUAAUAAAACCCACACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCUUAAACCUAAAUAAUUAAUUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAAUAGCUUGAAACUCAAAGGACUUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUCCUAUAAACGAUAAACCCCGAUAAACCUCACCAAUCCUAGCUAAUGCAGCCUAUAUACCGCCAUCCUCAGCAAACCCUAAUAAAGGAACCAUAGUAAGCAAGAUCAUUGAAACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGAUUGGGAAGAGAUGGGCUACAUUUUCUAAAACAGAAUAAGACGAAUACCCUUAUGAAAAUAAGGGUUAAAGGAGGAUUUAGUAGUAAGACAAGAAUAGAGAGCUUGACUGAAUUAGGCCCUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUUUCCAAAAAACAGUAAAUAUAUUAAUGAAUAACAAGAAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAGGUGUGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq new file mode 100644 index 0000000..4a5338a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq @@ -0,0 +1,2 @@ +>d.16.m.O.afer +AUAAAGGUUUGGUCCUAGCCUUUCUAUUAGUUGACAGUAAAUUUAUACAUGCAAGUAUCUGCCUCCCAGUGAAAUAUGCCCUCUAAAUCCUUACCGGAUUAAAAGGAGCCGGUAUCAAGCUCACCUAGAGUAGCUCAUGACGCCUUGCUAAACCACGCCCCCACGGGAUACAGCAGUAAUAAAAAUUUAGCAAUGAACGAAAGUUUGACUAAGUUAUACUAUAACUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUAAUACGGCGUAAAGCAUGAUUAGGGAAUAAUAUAAAUAAAGUUAAAUGUAAAUCAAAGCUGUAAAAAGCUCCUGAUUAACUUAAAAUAAAACACGAAAGUUACUUUACCACUCCUGAAUUCAUGAUAGCUAGGAUACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUAAAUAUUUCUCAACAAAAUUAUUCGCCAGAGAACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUAUGUAAUCGAUAAACCCCGAUAUACCUCACCAUCACUUGCCAAUACAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUACAAGGAAUAAUAGUAAGCCAAAUUAUUACCAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGUGAUGGCAAUAAAUGGGCUACAUUUUCUAUUUUAAGAACAUAUCCCUACGAAAACCCAAAUGAAACCAAGGCUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAACUACUAGUAUUACUAAAAAUAUUUCACUACAUAAACGUACUAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq new file mode 100644 index 0000000..fb058b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.anatinus +UAAAGGUUUGGUCCUAGCCUUACUGUUAGAUUUGAUUAGAUUUAUACAUGCAAGUAUCCGCAACCCAGUGAGAAUACCCUAAAAACUCUUAACAAGUUAGAAGGAGUAGAUAUCAGGCACACUAAAGUAGCCCACAACAUCUUGCCCUAGCCACACCCCCACGGGACACAGCAGUAAUAGAAAUUAGUCAAUAAACGCAAGUUUGAACAAGUCAUAAUCAAUAAGAGUCGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAACCUAACAAAUAACGGUGUAAAACGUGUUUAAAAACUUAAACUAAUAAGAUUAAAGUAGAACUAAACUGUGAUAAGUCAUAGUUAAUACUAAAGCCAUCUACGAAAGUGAUCUUAGACUAAUUGAAUACACGAUAGCUAAGGUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUCAAGUCGUUUAAUAACAAAACUACUCACCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCAUCUUUUGCCACUACUGUCUAUAUACCGCCAUCGUCAGCCAACCCUAAAAAGGAACAAAAGUAGGCGUAAUCAUUUUUCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAAGAUGGAAGAAAUGGGCUACAUUUUCUACAUUAGAACAUACGAAAAACUCUAUGAAACUAGAGUAUUAAGGAGGAUUUAGUAGUAAGCCAAGAAUAGAGAGCUUGACUGAACUGGGCAAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCAAGCAACACAAACAUUCCUAAAAUCCCAACGCUUUUCAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACCGGAAGGUGUGCUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq new file mode 100644 index 0000000..d11a7f6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq @@ -0,0 +1,2 @@ +>d.16.m.O.aries +UAUAGGUUUGGUCCCAGCCUUCCUGUUAACUUUCAAUAGACUUAUACAUGCAAGCAUCCACGCCCCGGUGAGUAACGCCCUUCGAAUCACACAGGACUAAAAGGAGCAGGUAUCAAGCACACACUCUUGUAGCUCACAACGCCUUGCUUAACCACACCCCCACGGGAGACAGCAGUAACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUCAUAUUGACCAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAGCUAACAGGAGUACGGCGUAAAGCGUGUUAAAGCAUCAUACUAAAUAGAGUUAAAUUUUAAUUAAACUGUAAAAAGCCAUAAUUAUAACAAAAAUAAAUGACGAAAGUAACCCUACAAUAGCUGAUACACCAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAAAUAAUUAUAAAAACAAAAUUAUUCGCCAGAGUACUACCGCAACAGCCCGAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGGACAAAAGUAAGCUCAAUAAUAACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGAGUGGGAAGAAAUGGGCUACAUUUUCUACCCAAGAAAAUUUAAUACGAAAGCCAUUAUGAAAUUAAUAGCCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAAUAUGAUAUACUUAAACCUAUUUACAUAUAUCAACCACACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq new file mode 100644 index 0000000..018a895 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.cuniculus +UAAAGGUUUGGUCCUGGCCUUUUUAUUGUUUUGUAGCAACCUUACACAUGCAAGACUCCUCACGCCAGUGAGAAUGCCCUUAACAUCAAACUAGAUCAAGAGGAGCGGACAUUAAGCACACUAAUCAGUAGCUCAAGAUGCCUUGCUUAACCACACCCCCAAGGGAUACAGCAGUGAUAAAUAUUUAGCAAUGAACGUAAGUUUGACUAAGUUAUGCUACUUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAAAUAUCCGGCGUAAAGCGUGAUUAGAAUAAACAACAAAAUAAAAUCAAAUAACAACUAAGCUGUAGAAAGUAAUAGUUGCAAACAAAAAUAAACAACGAAAGUGAUUUUAUACUCUUCGAACUCACGAUAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUUGAUAAUUUCAUAACAAAAUUAUUCGCCAGAGAACUACAAGCCAAAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCACCUAGAGGAGCCUGUUCCGUAAUCGAUAAACCCCGAUAAACCCUACCACUCUUUGCCAACUCAGCCUAUAUACCGCCAUCUUCAGCGAACCCUAAAAAGGAGCAAAAGUAAGCUCAAUUACCACCGUAAAAACGUUAGGUCAAGGUGUAGCCCAUAGAGUGGAGAGCAAUGGGCUACAUUUUCUACUUCAGAAUAUACGAAAGCCCUUAUGAAACUCUAAGGGCCAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAACAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGACAAAUAUUUACUUAUACCUAAUUACAUAAAUAGACAAGCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq new file mode 100644 index 0000000..bfc3821 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.virginianus +CAGAGGUUUGGUCCCAGCCUUCCUAUUAAUCCCUAGCAGACUUACACAUGCAAGUAUCCUCAUCCCAGUGAAAAUGCCCUCCAAGUCAAUAAAACUAAGAGGAGCUGGUAUCAAGCUCACACCCGUAGCUCAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUCAUGCUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGUUAAUAGGCACACGGCGUAAAGCGUGUUUAAGCACUAUGCCAAAUAGAGUUAAACUCCAAUUAAGCUGUAAAAAGCCAUAAUCAAGACGAAAAUAAAUAACGAAAGUAACUUUACAACCGCUGAAACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUAUAUAAACAAAACUAUUCGCCAGAGUACUACCGGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCACCCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAAAGUAAGCACAAUCAUUAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGAGUGGAAAGAAAUGGGCUACAUUUUCUAAUCUAAGAAAACUCUUUACGAAAGUUACUAUGAAAUUAGUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUAGGCACAAUACACUUAAAUUUAAUUAUACGUAUUAAUCAUAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq new file mode 100644 index 0000000..d59ad6b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq @@ -0,0 +1,2 @@ +>d.16.m.P.cinereus +UAAAGGUUUGAUCCUAGCCUUACUGUUAGUUUUAAUUAAACUUACACAUGCAAGUUUCCGCAACCCAGUGAGAAUGCCCCCAAAAUUUAUACACAAUUUAGCAGGAGCAGACAUCAGGUUCACUACAAAGUAGCCCAUAACGUCUUGUCCAACCACACCCCCACGGGAUACAGCAGUGAUUAACAUUAAGCUAUAAACGAAAGUUUGACUAAAUUAUAAUUAUCUAGGGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACCCAAACUAACAGAUGUCGGCGUAAAGCGUGUACAAUCCAACAACCAAAAUAAGGCUAAAACUCAAUCAUGCUGUAAUACGCUAUAGCUAACAUUAAAAAAUGCAACCAAAGUGGCCUUAAUACUGACCAAAACACGACAGCUAAGACUCAAACUGGGAUUAGAUACCCCAUUAUGCUUUAGCGUAAACUUAGAUAGUUUAAUAACGAAACUAUUCGCCAGAGAACUACUAGCCAGCGCUUAAAACUCAAAGGACUUGACGGUGUCCUAAGCCCAUCUAGAGGAGCCUGUCCUAUAACCGAUGAACCCCGAUACACCCCACCUCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCCUACCCCAAUAGGGACCAAAAGUAAGCAAAAUCAUCAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGAGGAAAGUGAUGGGCUACAUUUUCUAACAUAGAAAAUUACGGACUAUCUUAUGAAACCUAAGAUAUACGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGUACACACCGCCCGUCACUCUCUUCAACAUAAACAAACCAAAUAACUAAUAAAAUAAAUAAAUAAAGAAGAGAAAAGUCGUAACAUGGUAAGUGUACCGGAAGGUGCACUUGGAUCAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq new file mode 100644 index 0000000..f347a38 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq @@ -0,0 +1,2 @@ +>d.16.m.P.polycephalum +GUUUUAAUAUAAUAAUGAGUUUGAUCCUGGCUCCGAGAGAAUGCUAGCAACUUACUUGAUACAUGCUAGUCGAACGCUUAUAUGAGCGUGGCGUACGAGCGACAAGGGCAAAGAUAGAAAAUACAUCAGUCAAGGGAAAUCCUAGAUUUAAAAGAUUAUAUCGCUGAAUGUAAGGUCUUUGUGAGAUUAGGUUGUUGGUAAGAUAAAAGCCUACCAAGCCGAUGAUCUCUAGCUGGUCUGAGAGGAUGUACAGCCGCGUCGGAAAUGCAAUAAGGUCCGGACUCCCUCGGGAGGCUGCAGUAGGGAAUCGUGAACAAUGUGCUAACGCUUGAUUCUAUAAUGUUGCGUGGGGGAUACAAAAAACAUUAUUUUAUACUUAUUGUUUUAUAAACAAAUUUAUAUAUAAAAUAGUGAUAAUUCUAGCAACGACUUAAGCGCAAUAAAAGUUUCCGUAAAAAGAGAUUUUUAUCUGUGUCUUCUGUAGCGUGCCUUUCUAGUAGACGGCAAGUUGUCUUAAACCCCUUUUUUUACGAUUAUAAUGACUGUAGUUAGUAUAUAUCUAUUUAUCAAGAUGAGGGUUGGUAAAUUACAUUUUGUUUGUUAGACUAAAAUACUCGAGCAAAAAUGCCUUAUGCUGCUUUGCUUAAAAAUAUCAAACCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAAACGGGGGGGGUUAGUGUUAUUCGUGAUGACUGGGCGUAAAGGGUACGUAGGCAGAUAAUUGAAAAUACAGUAAAAAACUGAGGUAAACCCUCUUCAUUCUGUAUUCACUCAUUAUCUUGAGUUCAGAAGGCGGUUUAUUGAAUUCUCGAAGGAAGGGUGAAAUCUGUUGAUAUCUGGAAGACAUUCGAUAGCGAAAGCAACAUCCGAUUCUGAUCUAACGCUCAGGUACUAAAGUAUGGGGAUCAAAUAGGAUUAGAGACCCUAGUAGUCCAUACCUUAAACAAUGAGUGUUCAACGUCUUUAAUAUAGUCAAUAUAUUUAGGGGGUUUAAAGCUAACGCGUGAAACACUCCGCCUGGGGAAUGUGGCCGCAAGGUCUAAACUCAAAGGAAUUGACGGUGACUUAUACAAGGGGUGGAGCAUGUGGUUUAAUUCGACAUACCGCGCAAAACCUUACCAAUUUUUGUAUCUGGUUUCUUUUCGUUAGCCAUUUAUUUGGUUAGCCUUCUUCUUUCUGUUGAAGGUCUACUACGAUAUCGAUUGAAGAUGUGGGUGUUUCUAUGCGUAAGCAUGAUCUAGCUAUUUUCAAUUAACGGUAACCAAUGACAAGAGCUGCAUGAUUGUCGUAAGUUCGUGCCGUGAGGUGUUGGGUUCAUUCCAUAAACGAACGCAACCCUUUUGAUUAGUUGCAUAAUGGAUGAAAGUUUAAACUGGAUAUCCAUGUUCACUAGUUCAACCAGCCCUUCUACCUUUAGGGAUUAAGGACAGGUCCACGUCAAAUCAUUAUGGCCUUAAUAGAUUGGGCUACACAUGUGCUACAUUGAUGAUCGACAACAAGAAGCAAUGGCGUGAGCCUGAGCAAAUCUUUAAAAGACAUUUCAGUCCGAAUUGUUCUUUGAAACUCAAGAGCAUGAAGCCGGAAUCUCUUGUAAUCGUGGAUCAUUACGCCACGGUGAAUUAGUACAAAAGUCACGUACAGACCGCCCGUCAUGCUAUGGAAACUAUUUGAAGUAGAAGUUACAAGGUUUCAAUUGUUUCGAUAGACCACCUUAUUGAAAGUUUUCAUAAGGCCUUGACAUUCUGUUGGCUUUGUACACGACUCUUUAUUUAGGGACUGGAGUAAAGUCGAAACAGGGUAGUGGUAGAAGAAUCUGCUGCUGGACCAUUAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq new file mode 100644 index 0000000..a016faf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.m.R.norvegicus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUGGAGGUAAGAUUACACAUGCAAACAUCCAUAAACCGGUGUAAAAUCCCUUAAAGAUUUGCCUAAAACUUAAGGAGAGGGCAUCAAGCACAUAAUAUAGCUCAAGACGCCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUGAACGAAAGUUUGACUAAGCUAGUACCUCUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUCGGCGUAAAACGUGCCAACUAUAAAUCUCAUAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAGCCCAAUAACGAAAGUAAUUCUAAUCAUUUAUAUAAUGCACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUUAAUAAUUAAACCUACAAAAUUAUUUGCCAGAGAACUACUAGCUACAGCUUAAAACACAAAGGACUUGGCGGUACUUUAUAUCCGUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUCUACCUUACCCCUUCUCGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGCACUAAGUUAGCACAAGACAACAUAAAACGUUAGGUCAAGGUGUAGCCAAUGAAGCGGAAAGAAAUGGGCUACAUUUUCUUUUCCCAGAGAACAUUACGAAACCCUUAUGAAACUAAAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAGAUUGACAUUCACAUAUACAUAAUUUCACUAACAAAUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq new file mode 100644 index 0000000..1a6dfd1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq @@ -0,0 +1,2 @@ +>d.16.m.R.unicornis +CAUAGGUUUGGUCCUAGCCUUUCUAUUAACUAUUAGUAAAAUUACACAUGCAAGUAUCCGCACUCCAGUGAGAAUGCCCUCUAAAUCACCCAUAACGAUUAAAAGGAGCAGGUAUCAAGUACACUAAUAACAGUAGCUAACAACACCUUGCUCAACCACACCCCCACGGGAGACAGCAGUGACAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUAAGCAGAGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACUCAAAUUAAUAGAACCUCGGCGUAAAGCGUGUCAAAGAUAUAACCCCUAAUAAAGUUAAAAACAUAGUUAAGCUGUAAAAAGCUAUAACCAAGAUAAAAUAAACCACGAAAGUGACUUUAAUAUAUCACCCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCCAAACUCAAAUAAUUCUUCCCAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCCCUAGAGGAGCCUGUUCCAUAACCGAUAAACCCCGAUAAACCUUACCAGCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUAAAAAGGAACCAAAGUAAGCACAAGUAUAAGACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGAUGGAGAGAAAUGGGCUACAUUUUCUACUUCAAGAACAACAACUACCCAAACGAAGGCUUUUAUGAAAUUAAAAGCUAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUUAAAUAUCAUAAACCACAACACAACAUAUUAACGUACGUUGAACAUAUAAAAGGAGACAAGUCGUAACAAGGUAAGUGUACUGGAAAGUGCGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq new file mode 100644 index 0000000..ec9dd34 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aestuans +UAUAGGUUUGGUCCUAGCCUUUUUAUUAAUUCUUAGUAGACUUACACAUGCAAGUAUCCCCGCCCCAGUGAGAAUGCCCUCUAUCUCCAUAAGGAUCUAAAGGUGCAGGUAUCAAGUACGCUCUCUCGAGCAGCUCAUGACACCUUGCUACACCACACCCCCACGGGACACAGCAGUGAUUAAAAUUGAGACAUAAACGAAAGUUUGACUGAGUUAUACUAAUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAGUUAAUAAAACACGGCGUAAAGCGUGAUUAAGGAAUAACCCCAAAUAAGAUUAAGCUCUGACUAAGCUGUAAAAAGCCUUAGUUAAAAUAAAAAUUUAUAAACGAAAGUAAUCUUACAACCCCUGAAUUCACGAUAGCUAAGGCCCAAACCGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUACUCAAAUAACAAGAGUAUUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAAACCUCACCACUCUUUGCAAUGUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAUAAGGUAUCGCAGUAAGCACAAGAAUUCUGCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAGAGUGGGAAGAAAUGGGCUACAUUUUCUAAUUUCUUUAGAACAUUUCACGAUAGCUGUCAUGAAACAUGAUCAGCCCAAGGAGGAUUUAGUAGUAAGUUGGGAAUAGAGUGCCCAACUGAAUUGGGCAAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAGCAUCCAUGAUAACCCAUAUAAAUAAUACAAAAAUCUCCUAAUGCAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq new file mode 100644 index 0000000..e30ce56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aquaticus +UAAAAGGUUUGGUCCUGGCCUUUCUAUUAGCUGUCAGUAAAAUUACACAUGCAAGUAUCCGCGCCCCAGUGAAAAUGCCCUUGAAGUCAUCAUAGACAUAAAGGAGCCGGCAUCAAGUACACCAUAAUGGUAGCUAACGACGCCUUGCUUAGCCACGCCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCUAUGAACGAAAGUUUGACUAAGUUAUACUGAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAAUAACCCAAGUUAAUAGAUACACGGCGUAAAGAGUGUUAAAGAACCUGGCAUUGUAAAUAAAGCUAAGACUUAACUAAGACGUAAAAAUCUCCAGUUAAAGUAAAAACAAACUACGAAAGUGGCUUUAUAUUAUUCUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUAAGACAAUCCAACUAACAAGAUUGUUCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAGCCACAGUAAGCACAAGUAUAUACAUAAAAACGUUAGGUCAAGGUGUAGCUAAUGAGUUGGGAAGAAAUGGGCUACAUUUUCUAUAUCUAGAACACUUUAACGAAAGUCUUUAUGAAACGAAAGACUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACUAAAGCCAGUCAAUAUACAUAAUAUAUAGGCAAUAAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq new file mode 100644 index 0000000..af65bac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq @@ -0,0 +1,2 @@ +>d.16.m.S.scrofa +CACAGGUUUGGUCCUGGCCUUUCUAUUAAUUCUUAAUAAAAUUACACAUGCAAGUAUCCGCGCCCCGGUGAGAAUGCCCUCCAGAUCUUAAAGAUCAAAAGGAGCAGGUAUCAAGCACACCUAUAACGGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGUUAUAUUAAUUAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGAUCCACGGCGUAAAGAGUGUUUAAGAAAAAAAAAUCACAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCCUAGUUAAAAUAAAAUAACCCACGAAAGUGACUCUAAUAAUCCUGACACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACCCAAAUAGUUACAUAACAAAACUAUUCGCCAGAGUACUACUCGCAACUGCCUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCAACCCUUGCCAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAUAGUAAGCACAAUCAUAGCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUACAUAAGAAUAUCCACCACACGAAAGUUUUUAUGAAACUAAAAACCAAAGGAGGAUUUAGCAGUAAAUCAAGAAUAGAGUGCUUGAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAUGUAGUAAUAAAAAUAACCUAUAUUCAAUUACACAACCAUGCAAGAAGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq new file mode 100644 index 0000000..5a2d1d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.sinuspaulianus +AAAAGAAAGAAUUUAAUUUUGGUUCCGAUUGAACGUUUUUCAGUAGUUUUAAGACAUGCAAAUCGUUAUUUCUGAAAGUAAAUUUUUAUUUAAAAUUAUAUAAAUAAUAACUAAAUAAAAAUGAUAAUAUGAAAUAAGGUGUAGAGGUGAGGAUAGUAAAUAAGAUACCCUGUAGUCUUCAUAGAUAGAAGAUAUUAUUCUAAGUAAAUUUUUUAAAUUUAUUACUAGUAUUUUUAAAUUAAUUUGCUUGCAUUAUAUAAAAUUAUAAUUGUUUUUCAUUAAUUGCAAAAAUUUAAAUAAAAAUGACUAAAGCAAAAAAAUUAUUUAAAUAACAAUAAUGUAAAAUAAAUGAAUAAAAUAAAAAAGCUAUUUUUAUUAAAAAAAGGAAAUUUUCUGCUAUAGGAUUCUAUUUAUUUUGAUUAGGUAGUUGGUAUGGGUAAAGGCCUACCAAGCCGACAAUCAAUAGCCAUGCUUGACAGAGCAGAUGGCCACAUUGGGAAUGAAAUCUCCCAAGUAGUUUUAUACUACCAGCAGUCAAGAAUAUUAGUCAAUGCUCGUAAGAGUGAACUAGCUAACUGAAAUCGCAAAUGUGUCAUUUGUGAUAAAGUAAGAGAAAAUUAUGAUAUUAUCUUACUACUAGUGCUGUCCAAAACUGGUGCCAGAAGACUCGGUAAGGCCAGAGGCGCAAACGUUAGUCGUCCUAAUCAGGCGUAAAGGGUUUGUAGGCUGCUUUGAAAGUCUUAUUAUUAUAAUAGCUAUUAAAUGAUAAGAUGAAUUGAAGCUAGAAUCUAAUAGAGGGUAAAACAAAUAAUAUUUAAAGUAAGGAUUAAAUCUCAAGAGUUUAGAUGGAAUACUAACGGUUAAAGCUUUUAUCUAUCUACAGAUUGACGCUGAGAAACGAAAGGGAGGUAAGGAAACAGGAUUAGAUACCCAACUACUGCUCCCUGUCAACGAUGAAUGGUGGUUGCUAGUUAUAACUACUUUAAGUAAAUAUUUUAUAUUAUAUAAGAUAAAAUAAGUAGUUAAAAUGACUGGUAGCGAUGCUAACGCGUUAACCAUUCCGCCUUGUGAGUACGACUGCAAAGUUGAAAACAAAAAAAUUAGUCGGUUUCGAAGCAAACGAAGUGAAGCAUGUUAUUUAAUACGAUAAUCCGCGUAAAAUCUUACCAGUUCUUGCAUACAAACUUUUUUUAUAAUAAUUUAAAUUAAAUUUUAAAUAGUUAUUUAAAAAGGAGUGUUUUUACUUUUUUAAAAAUACUUAGAUACAGGUGUUGCAUGGCUGUCGUCAGUCCGUGCUGUGAGAAGUUUGGUUAAAUCCGCUAACGGACAAAAUCCCUGUUGUUAAUUUAUACUUAACAAUUAAUGAUACUGAUAGAGCAUCAUUUGGGGCGAAGACAAGUCGUUAUGGCCCUCAUGAACUGGGCUAUAGACGUGCCACAAAGACUUUAACAAAGUGAAGCGAUACUGUUCCCUUAAUAUUUUUCUAAAGAAUUUUAUUAGAUUUAAUUAUAACAAUUAAAUUAUAGGGAAUUUAAGGAGGAGCUAAUCAUUAAAAAAAGUCAAACUAUUAAAUAUAGUCGGAUUGUCAUCUGAAACUCGGGGACAUGAAGAAGGAAUUUCGAGUAAUCGUUGAUCACUACGCAACGGUGAAGCUAGCAUUCGGAAUGAACUAACCGUCUGUCGCUGGGAAGGAGCUUAACUUGGUGGAAACUGGAAUGAAGUUUUAACUUUUACAAAAAUUAAAUUUUUAUUUAGUAUCUUUGAUAUUUUAUUUUUAAUUUAUUAGUUUUUUUUUCGUUAGAUUUUUUUUAAUUUAUUGCUUAAUUAAAAAGUAUUAUUUUUGUUUAAAGAAUAAAUACUUGUCUAACAAUGUUAAAUUUAAAACGAUUUUGUUAAGCAAAUUAGCUCUAGUUAAACCAAUUAAGUAACAUCUCAAAAGUCAUAGCAAGGUAGCCGUACUGGAAAGUGCUGCUGUAAAAUAAAACGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq new file mode 100644 index 0000000..e00de33 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq @@ -0,0 +1,2 @@ +>d.16.m.V.ursinus +CAAAGGUUUGGUCCUAGCCUUACUGUUAAUUUUAAUUAAGCCUACACAUGCAAGUUUCCGCUGCCCAGUGAGAAUGCCCUCAAAAUUCUACAAUCGAAUCAACAGGAGCAGGUAUCAGGCACACCCAUCCCGGUAGCCCAUAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAACUUUAAGAUAUGAACGAAAGUUUGACUAAAUUAUAAUUAUACAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAAUUAACAGAACACCGGCGUAAAGCGUGUUUAAGCGCAAAUCUCAAAAUAAAGUUAAUACUUAACUAAACUGUAAUACGCCCUAGUUAACAUUAAAAUAAACAACUAAAGUGACUUUAAUUUCGCUGAAUACACGACAACUAAGACUCAAACUGGGAUUAGAUACCCCACUAUGCUUAGUCAUAAACCUAGGUAAUCCGAUAACAAAAUUAUUCGCCAGAGAACUACUAGCCACCGCUUAAAACUCAAAGGACUUGGCGGUGCUCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGAACAAAAGUGGGCAAAAUCAUUCACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGUAAUGGGCUACAUUUUCUAAAUUAGAAAACCAACGAACUAUCUCAUGAAACCCUGAGUCAUACGAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAAUAGGCAAUAGAGCGCGCACACACCGCCCGUCACCCUCCUCAACACAAACCGUCACAUUAACUAAUAAGUUAUCCAAAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAGGUGCACUUGGAGUAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq new file mode 100644 index 0000000..dc25fe7 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.m.X.laevis +UAAAGGUUUGGUCCUAGCCUUAUUAUCAACUUUUUCUGAACUUACACAUGCAAGCAUCCGCACUCCCGUGAAAAUGCCCUUAAGCCUCUUAAACAGGGGAUAAGGAGCCGGUAUCAGGCACAACUAAUAGCCCAUGACACCUUGCUCUGCCACACCCACAAGGGAAUUCAGCAGUGAUAAACAUUGAACAUGAGCGACACAAAGCUCGAUUCAGUUACAGUAAAUAGAGUUGGUCAAUCUCGUGCCAGCCGCCGCGGUUAUACGAGAAACUCAAGUUGAUCAUUUUCGGCGUAAAGCGUGAUUAAAGUAACCCAAACUAGAGUCAAACUCCAACCAAGCUGUCGCCGCUUUCGUUGGUUUGAAGAACACUCACGAAAGUAACUCUACCCAUAUUACACUUGAACUCACGACCGCUAGGAAACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUUGACUACUUACGCAAAAAUCCGCCAGAACUACGAGCCUAAGCUUAAAACCCAAAGGACUUGGCGGUGCUCCAAACCCACCUAGAGGAGCCUGUUCUGUAAUCGAUACCCCUCGCUAAACCUCACCACUUCUUGCCAAACCCGCCUAUAUACCACCGUCGCCAGCCCACCUCGUGAGAGAUUCUUAGUAGGCUUAAUGAUUUUUCAUCAACACGUCAGGUCAAGGUGUAGCAUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAUACCUUAGAAUAAACGCAAGAUCUCUAUGAAACCAGAUCGGAAGGCGGAUUUAGCAGUAAAGAGAAACAAGAGAGUUCUCUUUAAAACGGCCCUGGAGCGCGCACACACCGCCCGUCACCCUCUUCUACAAAAAUCAACCAAUUUUAUAAACACACAAUUAACACAAAGAAGAGGCAAGUCGUAACAUGGUAAGCACACCGGAAGGUGUGCUUGGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq new file mode 100644 index 0000000..47e7bd4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.californianus +CAAAGGUUUGGUCCUAGCCCUUCCGUUAGUUUUUAAUAAAAUUAUACAUGCAAGCUUCCACGCCCCAGUGAGAAUGCCCUUCAGAUCCCUACAGCCGAUCAAAAGGAGCGGGUAUCAAGCACACUCAACGAGUAGCUCACAACGCCUUGCUCAACCACACCCCCACGGGACACAGCAGUAAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUAUUAAUCAUAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACGGGCUCACGGCGUAAAGCGUGUAAAAGAUCUACCUACACUAAAGUUAAAAUUUAACCAAGCCGUAAAAAGCUGCCGUUAAUACAAAAUAUACUACGAAAGUGACUUUAAUAAUUCUGAUUACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAAUUCACUUAACAAAAUUAUCCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUCCAGUCUAUAUACCGCCAUCCUCAGCAAACCCUUAAAAGGAAAGAAAGUAAGCAUAAUCAUCGCACGUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGGAAGAAAUGGGCUACAUUUUCUAAACAAGAACACACCGUACGAAAGUUAUUAUGAAACUAAUAACUAAAGGUGGAUUUAGUAGUAAACUAAGAAUAGAGAGCUUAAUUGAACUGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAAUAACCUCAAAGCACAUACAUAAAUCAAUAUAAAACCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq new file mode 100644 index 0000000..10bd605 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.mays +AAAAUCUGAGUUUGAUCCUGGCUCAGAAGGAACGCUAGCUAUAUGCUUAACACAUGCAAGUCGAACGUUGUUUUCGGGGAGCUGGGCAGAAGGAAAAGAGGCUCCUAGCUAAAGUUGUCUCGCCCUGCCUGCAGGGCGCGCGCAACGGCUUUGACCUAACGGCCUCCGUUUGCUGGAAUCGGAAUAGUUGAGAACAAAGUGGCGAACGGGUGCGUAACGCGUGGGAAUCUGCCGAACAGUUCGGGCCAAAUCCUGAAGAAAGCUCAAAAGCGCUGUUUGAUGAGCCUGCGUAGUAUUAGGUAGUUGGUCAGGUAAAGGCUGACCAAGCCAAUGAUGCUUAGCUGGUCUUUUCGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCGGACUCCCACGGGGGGCAGCAGUGGGGAAUCUUGGACAAUGGGCGAAAGCCCGAUCCAGCAAUAUCGCGUGAGUGAAGAAGGGCAAUGCCGCUUGUAAAGCUCUUUCGUCGAGUGCGCGAUCAUGACAGGACUCGAGGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGGGGGGGCAAGUGUUCUUCGGAAUGACUGGGCGUAAAGGGCACGUAGGCGGUGAAUCGGGUUGAAAGUGAAAGUCGCCAAAAAGUGGCGGAAUGCUCUCGAAACCAAUUCACUUGAGUGAGACAGAGGAGAGUGGAAUUUCGUGUGUAGGGGUGAAAUCCGUAGAUCUACGAAGGAACGCCAAAAGCGAAGGCAGCUCUCUGGGUCCCUACCGACGCUGGGGUGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAGUGUUCGCCCUUGGUCUGUCUACGCUACGCUACGCGGAUCAGGGGCCCAGCUAACGCGUGAAACACUCCGCCUGGGGAGUACGGUCGCAAGACCGAAACUCAAAGGAAUUGACGGGGGCCUGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUACAACGCGCAAAACCUUACCAGCCCUUGACAUAUGAACAACAAAACCUGUCUUUAACGGGAUGGUACUUACUUUCAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUCAAGUCCUAUAACGAGCGAAACCCUCGUUUUGUGUUGCUGAGACAUGCGCCUAAGGAGAAAUAGCCGAGGAGCCGAGUGACGUGCCAGCGCUACUACUUGAUUGAGUGCCAGCACGUAGCUGUGCUUUCCGCAAGAAUUUCACCAUUGGGAGCCUCGAAGCACUUUCACGUGUGAACCGAAGUCGUCUUGCCGAACUCAAGACCCACGGAGACCUACCUAUAGUGACGUCAAAGUACCAGUGAGCAUGGAGGUUUGGUUAGGCUUGGUUACGACGACGUCGAGUUGGCGGCGGAGGAAGACUCGGCAUGAAGGCCAGCCGCCCGGUGGUGUGGUACGUAGUGGUAAUAGUACGCGCCCCGCUCCGAAACAAAGAAAAAGGUGCGUGCCGCACUCACGAGGGACUGCCAGUGAGAUACUGGAGGAAGGUGGGGAUGACGUCAAGUCCGCAUGGCCCUUAUGGGCUGGGCCACACACGUGCUACAAUGGCAAUGACAAUGGGAAGCAAGGCUGUAAGGCGGAGCGAAUCCGGAAAGAUUGCCUCAGUUCGGAUUGUUCUCUGCAACUCGGGAACAUGAAGUAGAAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUAUGUACCCGGGCCCUGUACACACCGCCCGUCACACCCUGGGAAUUGGUUUCGCCCGAAGCAUCGGACCAAUGAUCACCCAUGACUUCUGUGUACCACUAGUGCCACAAAGGCCUUUGGUGGUCUUAUUGGCGCAUACCACGGUGGGGUCUUCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGUGGCUGGAUUGAAUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq new file mode 100644 index 0000000..48e9291 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.y.C.paradoxa +UACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGAUCGCAAGAUCUUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUACCCUUAGGAGGGGGACAACAGUUGGAAACGACUGCUAAUACCCCAUAUGCCAUUCGUGGUGAAAAGAGUAAUCUGCCUGAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAAGACGGCCUGUGGGUUGUAAACCUCUUUUCUUAGGGAAGAAUCAAUGACGGUACCUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCAUUGGGCGUAAAGAGUUCGUAGGUGGCUAAGCAAGUCUGUUGUUAAAGGCUGGGGCUUAACCCCAAAAAGGCAAUGGAAACUGUUUGGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCGUUACUGACACUGAGGAACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGGUGUUGUGCGUAUCGACCCGUACAGUACCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCGCGAAUUUUCUUGAAAGAGAAAAGUGCCUUCGGGAACGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAAAGAGACUGCCGGUGACAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUAUACCCUGGGCUACACACGUACUACAAUGGUCGGGACAAUAGGUUGCCAACUUGCGAAAGUGAGCUAAUCCGUUAAACCCGGCCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGUCGGCCAUGCCCGAAGUCGUUACCCUAACCAUUUCGGAGGGGGAUGCCUAAGGCAGGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq new file mode 100644 index 0000000..84b1c04 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq @@ -0,0 +1,2 @@ +>d.5.a.D.mobilis +ACGGUGCCCGACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAUCGGGCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq new file mode 100644 index 0000000..d202539 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq @@ -0,0 +1,2 @@ +>d.5.a.H.marismortui +UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq new file mode 100644 index 0000000..1bfbb69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.mediterranei.1 +AUUAGGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq new file mode 100644 index 0000000..637ed19 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.1 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq new file mode 100644 index 0000000..1dd9dcf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.2 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq new file mode 100644 index 0000000..dba1e06 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq @@ -0,0 +1,2 @@ +>d.5.a.H.saccharovorum +GGCAGCGGCCAUAGCGGUGGGGCGACACCCGUACCCAUUCCGAACACGGAAGUUAAGCCCACCAGCGUACCGGGAAGUACUGGAGUGAGCGAUCCUCUGGGAAGCGGGGUUCGCCGCCUGCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq new file mode 100644 index 0000000..13aca4b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.1 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq new file mode 100644 index 0000000..cd1707d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.2 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq new file mode 100644 index 0000000..149b7b4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.5.a.H.volcanii +UUAAGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq new file mode 100644 index 0000000..aa89660 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq @@ -0,0 +1,2 @@ +>d.5.a.M.barkeri +GGAGUUUGGCGCCAUAGCGGCAGUGUAACUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUACUGUACUGAAGUGUGCGAGCCUUCGGGAACUCUGGAUCGCUGCCAUACUCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq new file mode 100644 index 0000000..014e2e9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq @@ -0,0 +1,2 @@ +>d.5.a.M.fervidus +GGGUACGGCGACCAUAGCGGGGGGGCCACACCUGAACCCGUUCCGAUCUCAGAAGUUAAGCCCCCCUGCGUUGGAGGUGGUACUGCAACGUUAGUUGCGGGAAGCCUCCAACGUCGCCGGCCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq new file mode 100644 index 0000000..0d9789e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq @@ -0,0 +1,2 @@ +>d.5.a.M.formicicum +AGGUUGGCGGCCAUAGCGGAGGGGCCAUACCUGGUCUCGUUUCGAUCCCAGAAGUGAAGUCCUCCUGCGUUUUGUUGUUGUACUGUGGACGAGAGUCUAUGGGAAGCUCAUAACGCUGCCGGCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq new file mode 100644 index 0000000..173a5b8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnA +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACGCCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq new file mode 100644 index 0000000..8df9051 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnB +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACACCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq new file mode 100644 index 0000000..ac65026 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermautotrophicus.1 +GGGGCAUGGCGGUCAUGGCGCAGGGGUUAUACCUGAUCUCGUUUCGAUCUCAGUAGUUAAGUCCUGCUGCGUUGUGGGUGUGUACUGCGGUUUUUUGCUGUGGGAAGCCCACUUCACUGCCAGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq new file mode 100644 index 0000000..2c27595 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermolithotrophicus.2 +UGAUAUAACGGUCAUAGCGGAGGAGCCACAUCCGAUCCCGUCCCGAUCUCGGAAAUUAAGCCCUCCAGCGAUACCCUAAGUACUGCCAUUUGGUGGGAACAGGGUGACGCUGUUGAUCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq new file mode 100644 index 0000000..bc9a31f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.tindarius.1 +GGAGUUUGGCGGCCAUAGCGGCGGGGCAAUUCCUGUACCCAUCCCGAACACAGAAGAUAAGCCCGCCUGCGUUCUAUACUGUACUAAAGUAUGAGAGUCUUUGGGAAAUAUGGAACGCUGCCAUCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq new file mode 100644 index 0000000..2289727 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq @@ -0,0 +1,2 @@ +>d.5.a.M.vacuolata +GAUCUGGCAGCCAUAGCGGCAGGUGUAAUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUGCCUGUACUGAAGUGUGCGAGCUUCGGGAACUCUGGAUCGUGCCAUAUCAGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq new file mode 100644 index 0000000..1e9fb96 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq @@ -0,0 +1,2 @@ +>d.5.a.N.magadii +UUAAGGCGGCCAUCGCGGCGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCUGCCUGCGUAUUGGUGAGUACUGGAGUGGGAGACCCUCUGGGAGAGCCGAUUCGCCGCCCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq new file mode 100644 index 0000000..35940f9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.aerophilum +GCCCCUAACCCGGCCAUAGGCGCCGGUGAUACGCCCGGUCUCAUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGCUCGGGAGUACUGGGCUCCGCGAGGGCCCGGGAAACCGGCGUGCUGGGAGGGGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq new file mode 100644 index 0000000..fe1e44d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.occultum +UGGCCCGACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAUCGGGCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq new file mode 100644 index 0000000..0db6b35 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq @@ -0,0 +1,2 @@ +>d.5.a.P.woesei +GGUACGGCGGUCAUAGCGGGGGGGCCACACCCGGUCUCAUUUCGAACCCGGAAGUUAAGCCCCCCAGCGAUCCCGGCUGUACUGCCCUCCGAGAGGGGGCGGGAACCGGGGACGCCGCCGGCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq new file mode 100644 index 0000000..5e79dbe --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq @@ -0,0 +1,2 @@ +>d.5.a.S.solfataricus +GCCCACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq new file mode 100644 index 0000000..993246c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq @@ -0,0 +1,2 @@ +>d.5.a.Sulfolobus.sp.B12 +GCCCACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq new file mode 100644 index 0000000..a7dad6b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.T.acidophilum +GGCAACGGUCAUAGCAGCAGGGAAACACCAGAUCCCAUUCCGAACUCGACGGUUAAGCCUGCUGCGUAUUGCGUUGUACUGUAUGCCGCGAGGGUACGGGAAGCGCAAUAUGCUGUUACCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq new file mode 100644 index 0000000..91d9b16 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq @@ -0,0 +1,2 @@ +>d.5.a.T.celer.1 +GGUACGGCGGUCAUAGCGGCGGGGUCACACCCGGUCUCGUUUCGACCCCGGAAGUUAAGCCCGCCAGCGAUCCCGGUUGUACUGCCCUCCGGGAGGGGGCGGGAAGCCGGGGACGCCGCCGGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq new file mode 100644 index 0000000..758f2f3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.5.b.A.tumefaciens +CGACCUGGUGGUCAUCGCGGGGCGGCUGCACCCGUUCCCUUUCCGAACACGGCCGUGAAACGCCCCAGCGCCAAUGGUACUUCGUCUCAAGACGCGGGAGAGUAGGUCGCUGCCAGGUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq new file mode 100644 index 0000000..42aafa3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.b.D.radiodurans.rrnB +ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq new file mode 100644 index 0000000..c43add3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.5.b.E.coli +UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq new file mode 100644 index 0000000..215d002 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.2 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq new file mode 100644 index 0000000..c061b92 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.3 +CCUAGUGACAAUAGCGAGAGAGGAAACACCCGUCUCCAUCCCGAACACGAAGGUUAAGCUCUCCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUUGUCGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq new file mode 100644 index 0000000..c3fb93d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.4 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGCCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq new file mode 100644 index 0000000..f3cf935 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.5.b.M.genitalium +UUUUGUUUGGUGCUAAUAUCGCUGUGGAAACACCUGGAACCAUCCCGAACCCAGCAGUUAAGCACAGUGGAGCUAAAUGUAGGUAGUAAUACUGAGAAUAGGUAAGCACCAAGCAAAA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq new file mode 100644 index 0000000..2eb8001 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aquaticus +GUCAACGGCCAUACCACGUUGAAAGCACCGCUUCUCGUCCGAUCAGCAAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq new file mode 100644 index 0000000..4691f30 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aurita.2 +GCCUACGACUAUACCACCAUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGUAUGGUAGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCCGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq new file mode 100644 index 0000000..21ffcae --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.domesticus +GCCAACGUCCAUACCACGUUGAAAGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAGCGUCGGGCGCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAACCCCGCGUGACGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq new file mode 100644 index 0000000..e343cc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.equina +GUCUACGGCCAUACCACCGGGAAAAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCCCGGUAGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq new file mode 100644 index 0000000..0b3da01 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.A.immersus.1 +ACAUACGGCCAUAGAUUGAAGAAUAUACGGGAUCCCGUCCGCUCUCCCAUAGUCAAGCUUCUAAUCGCCAAGUUAGUACUGCGGUGGGUGACCACGCGGGAAUCCUUGGUGCUGUAUGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq new file mode 100644 index 0000000..336539c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq @@ -0,0 +1,2 @@ +>d.5.e.A.magnoliae +GGCAACGACCAUACCACGUUGAAUACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCGUAGUUAGUACUUGGAUGGGUGACCGCUUGGGAACACUACGUGCCGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq new file mode 100644 index 0000000..8b924c3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq @@ -0,0 +1,2 @@ +>d.5.e.A.pernyi +GACAACGUCCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCGCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGCGUGACGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq new file mode 100644 index 0000000..bd70eab --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.salina +ACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq new file mode 100644 index 0000000..311e3c2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq @@ -0,0 +1,2 @@ +>d.5.e.A.tabira +GCUUACAGCCAUACUGUCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGACAAGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq new file mode 100644 index 0000000..b3d1240 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.napus +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq new file mode 100644 index 0000000..c94dd69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq @@ -0,0 +1,2 @@ +>d.5.e.B.neritina +GUUUACGGCCAUAUCACGUUGAAAACGCCAGUUCUCGUCCGAUCACUGAAGCUAAGCAACGUCGAGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq new file mode 100644 index 0000000..0f615ff --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.taurus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq new file mode 100644 index 0000000..7d2da47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vorax +GUUAUCGGCCAUACUAAGCCAAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCAUGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGCCCAUGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq new file mode 100644 index 0000000..a05bd88 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vulgaris +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq new file mode 100644 index 0000000..32ee26d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq @@ -0,0 +1,2 @@ +>d.5.e.C.carpio +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq new file mode 100644 index 0000000..91c3d86 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.1 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq new file mode 100644 index 0000000..4a4584e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.2 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq new file mode 100644 index 0000000..4eef3e3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq @@ -0,0 +1,2 @@ +>d.5.e.C.quinquecirrha +GCCUACGACCAUACCACCAUGAGUAUACCGGUUCUCGUCCGAUCACCGGAGUCAAGCAUGGUCGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCUGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq new file mode 100644 index 0000000..0a9db8c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq @@ -0,0 +1,2 @@ +>d.5.e.C.revoluta +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGUUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUAAUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq new file mode 100644 index 0000000..b9bba74 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq @@ -0,0 +1,2 @@ +>d.5.e.C.vicina +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq new file mode 100644 index 0000000..fe798c7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq @@ -0,0 +1,2 @@ +>d.5.e.D.mauritiana +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq new file mode 100644 index 0000000..2a8d663 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.1 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq new file mode 100644 index 0000000..05ba8f8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.2 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGAGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq new file mode 100644 index 0000000..e715502 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq @@ -0,0 +1,2 @@ +>d.5.e.E.eurystomus +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCUUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq new file mode 100644 index 0000000..c73a6b7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.1 +GAGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCGGGUUAGGCCCAGUUAGUACUGAGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq new file mode 100644 index 0000000..895e4e4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.2 +GGCGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCUGGUCAGGCCCAGUUAGUACUGAGGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq new file mode 100644 index 0000000..33c38fc --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq @@ -0,0 +1,2 @@ +>d.5.e.E.kokanica +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq new file mode 100644 index 0000000..2b22082 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq @@ -0,0 +1,2 @@ +>d.5.e.E.woodruffi +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCAUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq new file mode 100644 index 0000000..946b73c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq @@ -0,0 +1,2 @@ +>d.5.e.F.hygrometrica +UGAUGCGGUCAUACCAAGGCUACUACACCAGAUCCCAUCAGAACUCUGAAGUUAAGCGCCUUUGGGCCGGAAUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUGCUGCAUCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq new file mode 100644 index 0000000..30eaebf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.F.neoformans.1 +AUCCACGGCCAUAGCCUUCAUAGAGCACCCUGCCCCGUCCGAUCCAGGAAGUUAAGCUGAACAGCGCUCGGUUAGUACCACGGUGGGGGACCACGUGGGAAUCCCGGGUGCCGUGGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq new file mode 100644 index 0000000..7b952b0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq @@ -0,0 +1,2 @@ +>d.5.e.G.arboreum +GGGUGCGAUCAUACCAGCACUAAACCACCGGAUUCCAUCAGUGCUCCCCAGUUAAGCGUGCUUGGCCGAGAGUAGAACUAGGGUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq new file mode 100644 index 0000000..cb7eb79 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq @@ -0,0 +1,2 @@ +>d.5.e.G.biloba +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCCAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq new file mode 100644 index 0000000..178c783 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq @@ -0,0 +1,2 @@ +>d.5.e.G.gnemon +GGGUGCGAUAAUACCACCGCUAACGUAUCGGAUCCGAUCAGAACUCCGUAAUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCUCGGGAAGUCCUAGUGUUGCACCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq new file mode 100644 index 0000000..1d478a3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq @@ -0,0 +1,2 @@ +>d.5.e.G.riobambae +GCCUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq new file mode 100644 index 0000000..f67da34 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq @@ -0,0 +1,2 @@ +>d.5.e.H.japonica +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq new file mode 100644 index 0000000..49bf2a1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq @@ -0,0 +1,2 @@ +>d.5.e.H.oculata +GCCUGCGGCCAUACCACGUUGAAUGCACCGGUUCCCAUCUGAACACCGAAGUUAAGCAACGUCGGGCCAGCUUAGUACCUGGAUGGGUGACCGCCUGGGAAUCGCUGGUGCUGCAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq new file mode 100644 index 0000000..55c19b9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sanguinea +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq new file mode 100644 index 0000000..517c965 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.1 +AUCUAUGGCUGUACCGCUCUGAACGUGCACUAUCUCUUCUGAUCUCAAAAGCUAAGCAGGGUCAGGCCUGGUUAGUACUGGAAUGGGAGACCACAUGGGAAAACUGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq new file mode 100644 index 0000000..1b449fa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq new file mode 100644 index 0000000..d82f578 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq new file mode 100644 index 0000000..fdcdc80 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.4 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq new file mode 100644 index 0000000..627f910 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.5 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq new file mode 100644 index 0000000..01812e1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.6 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq new file mode 100644 index 0000000..a8577d9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Hemicentrotus.sp +GUUUACGACCAUACCAUGCUGAAUAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAGCAUAGGGCCCGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGUUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq new file mode 100644 index 0000000..fb02dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq @@ -0,0 +1,2 @@ +>d.5.e.I.iguana +GCCUACGGCCAUACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq new file mode 100644 index 0000000..39aa1e2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq @@ -0,0 +1,2 @@ +>d.5.e.I.illecebrosus +GCUUACGGCCAUAUCACGCUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGAGCCUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAAUACUAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq new file mode 100644 index 0000000..9a40744 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq @@ -0,0 +1,2 @@ +>d.5.e.L.decidua +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUAGAGUAGUGCUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq new file mode 100644 index 0000000..2d9f606 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq @@ -0,0 +1,2 @@ +>d.5.e.L.edodes +AUCCACGGCCAUAGGACUCUGAAAGAACCGCAUCCCGUCUGAUCUGCGCAGUUAACCAGAGUGCCGCCUAGUUAGUACCACGGUGGGGGACCACGCGGGAAUCCUAGGUGCUGUAGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq new file mode 100644 index 0000000..73c1db0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.geniculatus +GUCUACGACCAUAUCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGAGCGUGGUUAGUACGUGGAUGGGUGACCGCCUCGGAAUACCACGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq new file mode 100644 index 0000000..83e9877 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.japonicum +GCCUACGACCAUAUCACCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGAGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq new file mode 100644 index 0000000..9d33a3c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.luteus +AGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq new file mode 100644 index 0000000..2e8a669 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.usitatissimum +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGAAGUUAAACGUGCUUGGGCGAGAGUAGUACUAAGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCACCCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq new file mode 100644 index 0000000..dfa7faa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.auratus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq new file mode 100644 index 0000000..046a55c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq @@ -0,0 +1,2 @@ +>d.5.e.M.fossilis +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGUUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq new file mode 100644 index 0000000..1d4c204 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.glyptostroboides +GGGUGCGAUCAUACCAGCGUUAGUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCCGGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq new file mode 100644 index 0000000..fa29c33 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.musculus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq new file mode 100644 index 0000000..3101592 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.salmoides +GCUUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUCGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq new file mode 100644 index 0000000..df2ff9f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq @@ -0,0 +1,2 @@ +>d.5.e.N.dofleini +GUCUACGACCAUACCACAAUGAACACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAUUGUCGGGCCAGGAUAGUACCUGGAUGGGGGACCGCCUGGGAACGCCUGGUGUCGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq new file mode 100644 index 0000000..a966f10 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq @@ -0,0 +1,2 @@ +>d.5.e.N.viridescens +GCUUACGGCCAUACCACCCUGAAAGCACCUGAUCUCGUCUGAUCUCAGAAGUUAAGCAGGGUCGGGCCUGGUUAGUACCUGGAUGGGAGACCGCCUUGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq new file mode 100644 index 0000000..0f05eee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq @@ -0,0 +1,2 @@ +>d.5.e.O.mykiss +GCUUACGGCCAUACCAGCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq new file mode 100644 index 0000000..614084f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.1 +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq new file mode 100644 index 0000000..bb31e0b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.2 +GGAUGCGAUCAUACGAGGACGAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq new file mode 100644 index 0000000..9c4e025 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq @@ -0,0 +1,2 @@ +>d.5.e.P.brevicirris +GCCUACGGCCAUACUACGUUGAAAACACCGGUUCUCGUCUGAUCACCGAAGUUAAGCAACGUCGGGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq new file mode 100644 index 0000000..035e1ec --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq @@ -0,0 +1,2 @@ +>d.5.e.P.coxalis +GUCAACGGCCAUACCACGUUGAAAGCACCACUUCUCGUCCGAUCAGCGAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq new file mode 100644 index 0000000..bb21939 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq @@ -0,0 +1,2 @@ +>d.5.e.P.gouldii +GCCUACGACCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq new file mode 100644 index 0000000..cee3f47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.1 +GGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq new file mode 100644 index 0000000..4b4969f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.2 +AGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGCUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq new file mode 100644 index 0000000..0fe2e5f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.radiata +GGGUGCGAUCAUACCAGCGUUAAUGCACCGAAUCCCAUCAGAACUCCGCAGUUUAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq new file mode 100644 index 0000000..48aafa5 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.reticulata +GAUAGCGUCCAUACCACACUGAAAACACCGGUUCUCGUCCGAUCACCGCAGUUAAGCAGUGUCGGGCCCAGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACUGGGUGUCGCUACCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq new file mode 100644 index 0000000..ac85b0c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq @@ -0,0 +1,2 @@ +>d.5.e.P.tetraurelia +GUUGGUGGCCAUACUAAGCCUAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCGAGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCUCGUGUUGACAACCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq new file mode 100644 index 0000000..686043c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq @@ -0,0 +1,2 @@ +>d.5.e.P.waltl +GCCUACGGCCAUACCACCCUGAAUGCGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq new file mode 100644 index 0000000..7356089 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Phytomonas.sp +GGGUACGACCAUACUUGGCUGAAAGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACCCUCCACAACACUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq new file mode 100644 index 0000000..4611843 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq @@ -0,0 +1,2 @@ +>d.5.e.Q.petraea +GGGUGCGAUCAUACCAACACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGUUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq new file mode 100644 index 0000000..b317aac --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.1 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq new file mode 100644 index 0000000..9bfefd4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq new file mode 100644 index 0000000..97d8ffd --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq new file mode 100644 index 0000000..91ab62d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq @@ -0,0 +1,2 @@ +>d.5.e.S.aggregatum +ACAGCCGUUCAUACCACACGGAGAAUACCGGAUCUCGUUCGAACUCCGCAGUCAAGCCGUGUCGGGCGUGCUCAGUACUACCAUAGGGGACUGGGUGGGAAGCGUGCGUGACGGCUGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq new file mode 100644 index 0000000..f821f70 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq @@ -0,0 +1,2 @@ +>d.5.e.S.canicula +GCCUACGGCCAUACUAGUCUGAAAACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGAUUCAGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCAGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq new file mode 100644 index 0000000..99153a7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cerevisiae +GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUGUUAAGCUGGUAGAGCCUGACCGAGUAGUGUAUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq new file mode 100644 index 0000000..7301bd3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cynthia.XBM +GCCAACGUCCAUACCAUGUUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAACAUCGGGCGUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACUACGUGAUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq new file mode 100644 index 0000000..c309c20 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq @@ -0,0 +1,2 @@ +>d.5.e.S.kowalevskii +GCCUACGGCCAUACCACGUAGAAUGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCUGCGUCGGGCGUGGUUAGUACUUGCAUGGGAGACCGGCUGGGAAUACCACGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq new file mode 100644 index 0000000..fbcd514 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq @@ -0,0 +1,2 @@ +>d.5.e.S.officinalis +GCUUACGGCCAUAUCACGCUGAAAACACCGGUUCUCGUCCGAACACCGAAGUUAAGCAACGUAGAGCCUGGUGAGUACUUGGAUGGGUGACCGCUUGGGAAUACCAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq new file mode 100644 index 0000000..45e16c8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq @@ -0,0 +1,2 @@ +>d.5.e.S.pombe.1 +GUCUACGGCCAUACCUAGGCGAAAACACCAGUUCCCGUCCGAUCACUGCAGUUAAGCGUCUGAGGGCCUCGUUAGUACUAUGGUUGGAGACAACAUGGGAAUCCGGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq new file mode 100644 index 0000000..dacd0d4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.aestivum +GGAUGCGAUCAUACCAGCACUAAGGCAUCGGAUCCCGUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACAAGGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq new file mode 100644 index 0000000..91d76b6 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq @@ -0,0 +1,2 @@ +>d.5.e.T.borreli +GGGUACGUCCAUACUUGGCUGAAAGCACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUUGGGAACCCUAAGUGUCGUACUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq new file mode 100644 index 0000000..b4fe443 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.5.e.T.cruzi +GGGUACGACCAUACUUGGCCGAGUGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCGGCCACAGGCCUCGUUAGUACGGCGAUCAGUGAUGGCGCUGGAACCCGGGGUGCCGUACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq new file mode 100644 index 0000000..0d095ee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.monococcum +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCUGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUCGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq new file mode 100644 index 0000000..2846ec9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq @@ -0,0 +1,2 @@ +>d.5.e.T.thermophila.2 +GUUGUCGGCCAUACUAAGGUGAAAACACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGCCUUAAGGCUGGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCCAGUGUCGAUAGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq new file mode 100644 index 0000000..5b30dba --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq @@ -0,0 +1,2 @@ +>d.5.e.U.unicinctus +GUCUACGGCCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCGGGUGCUGUAGACUU From f5c75dd91e7ecc155417925e933b7063495da821 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 7 Oct 2011 15:26:41 -0400 Subject: [PATCH 159/187] Merge the README file. --- gtfold-mfe/tests/README | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 gtfold-mfe/tests/README diff --git a/gtfold-mfe/tests/README b/gtfold-mfe/tests/README new file mode 100644 index 0000000..7e55fcb --- /dev/null +++ b/gtfold-mfe/tests/README @@ -0,0 +1,4 @@ +This directory contains the Test Framework for GTFold. +The complete documentation can be accessed here: +http://goo.gl/OliVA + From aac4e4ae96a2eccdaedbaa179c70aa8a55d72574 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 7 Oct 2011 16:13:20 -0400 Subject: [PATCH 160/187] Rename PseudoKnotDetection Tests to ExitCode Tests. --- .../default.expectedresult | 1 + .../data/exitcodes_sequences/seq1.constraint | 4 +++ .../tests/data/exitcodes_sequences/seq1.ct | 20 +++++++++++++++ .../exitcodes_sequences/seq1.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq1.seq | 1 + .../data/exitcodes_sequences/seq2.constraint | 2 ++ .../exitcodes_sequences/seq2.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq2.seq | 1 + .../data/exitcodes_sequences/seq3.constraint | 3 +++ .../exitcodes_sequences/seq3.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq3.seq | 1 + .../data/exitcodes_sequences/seq4.constraint | 4 +++ .../exitcodes_sequences/seq4.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq4.seq | 1 + .../data/exitcodes_sequences/seq5.constraint | 1 + .../exitcodes_sequences/seq5.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq5.seq | 1 + .../data/exitcodes_sequences/seq6.constraint | 5 ++++ .../exitcodes_sequences/seq6.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq6.seq | 1 + .../data/exitcodes_sequences/seq7.constraint | 4 +++ .../exitcodes_sequences/seq7.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq7.seq | 1 + .../data/exitcodes_sequences/seq8.constraint | 4 +++ .../exitcodes_sequences/seq8.expectedresult | 1 + .../tests/data/exitcodes_sequences/seq8.seq | 1 + .../{PseudoKnotDetection.pm => ExitCodes.pm} | 25 ++++++++++++++----- 27 files changed, 83 insertions(+), 6 deletions(-) create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult create mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq rename gtfold-mfe/tests/scripts/{PseudoKnotDetection.pm => ExitCodes.pm} (61%) diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint new file mode 100644 index 0000000..2a01386 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct new file mode 100644 index 0000000..da642b1 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct @@ -0,0 +1,20 @@ +19 dG = 10.1 +1 C 0 2 0 1 +2 C 1 3 0 2 +3 C 2 4 0 3 +4 C 3 5 0 4 +5 A 4 6 0 5 +6 A 5 7 0 6 +7 G 6 8 0 7 +8 A 7 9 0 8 +9 A 8 10 0 9 +10 G 9 11 0 10 +11 C 10 12 0 11 +12 A 11 13 0 12 +13 A 12 14 0 13 +14 A 13 15 0 14 +15 G 14 16 0 15 +16 A 15 17 0 16 +17 A 16 18 0 17 +18 G 17 19 0 18 +19 G 18 0 0 19 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint new file mode 100644 index 0000000..2a8e728 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint @@ -0,0 +1,2 @@ +F 1 19 2 +F 15 21 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq new file mode 100644 index 0000000..23023c5 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq @@ -0,0 +1 @@ +CCAAAAAAAAAAAACAAGGAG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint new file mode 100644 index 0000000..bcbe409 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint @@ -0,0 +1,3 @@ +F 1 19 2 +F 3 10 2 +F 15 23 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq new file mode 100644 index 0000000..6b590de --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGAAAACAAGGAAAG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint new file mode 100644 index 0000000..cece32a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 18 1 +F 4 7 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint new file mode 100644 index 0000000..7029d7d --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint @@ -0,0 +1 @@ +F 1 8 8 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq new file mode 100644 index 0000000..0984ecd --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq @@ -0,0 +1 @@ +CCCCCGGGGGGAAAGGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint new file mode 100644 index 0000000..adb4fdb --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint @@ -0,0 +1,5 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 +F 24 25 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq new file mode 100644 index 0000000..9a1d7d8 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGGCCCACGAAAA diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint new file mode 100644 index 0000000..2ce893a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint @@ -0,0 +1,4 @@ +F 0 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint new file mode 100644 index 0000000..65ea20f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 24 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm b/gtfold-mfe/tests/scripts/ExitCodes.pm similarity index 61% rename from gtfold-mfe/tests/scripts/PseudoKnotDetection.pm rename to gtfold-mfe/tests/scripts/ExitCodes.pm index 1bdfc38..fbe7079 100755 --- a/gtfold-mfe/tests/scripts/PseudoKnotDetection.pm +++ b/gtfold-mfe/tests/scripts/ExitCodes.pm @@ -1,5 +1,5 @@ #!/usr/bin/perl -package PseudoKnotDetection; +package ExitCodes; use strict; use warnings; use File::Basename; @@ -17,10 +17,10 @@ sub test() my $key; my $value; - + my %new_hash = (%local_sequences, %Sequences); # For testing pseudoknot detection logic # we may only test the sequences specified in local_sequences - while (($key, $value) = each(%local_sequences)) { + while (($key, $value) = each(%new_hash)) { my $seqname=$key; my $path; @@ -32,14 +32,27 @@ sub test() my $gtout = "$workdir$seqname-gt"; my $gtoutfilename = $workdir."$seqname-gt.ct"; - my $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1"; + my $gtcmd; + if (-e $constraint_file) { + $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1"; + } + else { + $gtcmd = "$gtdir/gtfold -m $seqfile -o $gtout > /dev/null 2>&1"; + } + my $x = system("$gtcmd") >> 8; my $expected_result_file = "$dirname/$seqname.expectedresult"; - my $expected_result = `head -n 1 $expected_result_file`; + my $expected_result; + if (-e $expected_result_file) { + $expected_result = `head -n 1 $expected_result_file`; + } + else { + $expected_result = 0; + } if ($expected_result =~ $x) { - $logger->error("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result"); + $logger->info("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result"); } else { $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result"); From 8ed1a048238fd79197b4ee2d8112b42d24500e3c Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 7 Oct 2011 16:17:00 -0400 Subject: [PATCH 161/187] Remove pseudoknot detection sequences --- .../seq1.constraint | 4 ---- .../pseudoknot_detection_sequences/seq1.ct | 20 ------------------- .../seq1.expectedresult | 1 - .../pseudoknot_detection_sequences/seq1.seq | 1 - .../seq2.constraint | 2 -- .../seq2.expectedresult | 1 - .../pseudoknot_detection_sequences/seq2.seq | 1 - .../seq3.constraint | 3 --- .../seq3.expectedresult | 1 - .../pseudoknot_detection_sequences/seq3.seq | 1 - .../seq4.constraint | 4 ---- .../seq4.expectedresult | 1 - .../pseudoknot_detection_sequences/seq4.seq | 1 - .../seq5.constraint | 1 - .../seq5.expectedresult | 1 - .../pseudoknot_detection_sequences/seq5.seq | 1 - .../seq6.constraint | 5 ----- .../seq6.expectedresult | 1 - .../pseudoknot_detection_sequences/seq6.seq | 1 - .../seq7.constraint | 4 ---- .../seq7.expectedresult | 1 - .../pseudoknot_detection_sequences/seq7.seq | 1 - .../seq8.constraint | 4 ---- .../seq8.expectedresult | 1 - .../pseudoknot_detection_sequences/seq8.seq | 1 - 25 files changed, 63 deletions(-) delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult delete mode 100644 gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint deleted file mode 100644 index 2a01386..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.constraint +++ /dev/null @@ -1,4 +0,0 @@ -F 1 19 2 -F 3 10 1 -F 4 8 1 -F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct deleted file mode 100644 index da642b1..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.ct +++ /dev/null @@ -1,20 +0,0 @@ -19 dG = 10.1 -1 C 0 2 0 1 -2 C 1 3 0 2 -3 C 2 4 0 3 -4 C 3 5 0 4 -5 A 4 6 0 5 -6 A 5 7 0 6 -7 G 6 8 0 7 -8 A 7 9 0 8 -9 A 8 10 0 9 -10 G 9 11 0 10 -11 C 10 12 0 11 -12 A 11 13 0 12 -13 A 12 14 0 13 -14 A 13 15 0 14 -15 G 14 16 0 15 -16 A 15 17 0 16 -17 A 16 18 0 17 -18 G 17 19 0 18 -19 G 18 0 0 19 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult deleted file mode 100644 index 573541a..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.expectedresult +++ /dev/null @@ -1 +0,0 @@ -0 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq deleted file mode 100644 index 0964dc3..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq1.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint deleted file mode 100644 index 2a8e728..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.constraint +++ /dev/null @@ -1,2 +0,0 @@ -F 1 19 2 -F 15 21 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq deleted file mode 100644 index 23023c5..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq2.seq +++ /dev/null @@ -1 +0,0 @@ -CCAAAAAAAAAAAACAAGGAG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint deleted file mode 100644 index bcbe409..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.constraint +++ /dev/null @@ -1,3 +0,0 @@ -F 1 19 2 -F 3 10 2 -F 15 23 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq deleted file mode 100644 index 6b590de..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq3.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAAAGGAAAACAAGGAAAG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint deleted file mode 100644 index cece32a..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.constraint +++ /dev/null @@ -1,4 +0,0 @@ -F 1 19 2 -F 3 18 1 -F 4 7 1 -F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq deleted file mode 100644 index 0964dc3..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq4.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint deleted file mode 100644 index 7029d7d..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.constraint +++ /dev/null @@ -1 +0,0 @@ -F 1 8 8 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq deleted file mode 100644 index 0984ecd..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq5.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCCGGGGGGAAAGGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint deleted file mode 100644 index adb4fdb..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.constraint +++ /dev/null @@ -1,5 +0,0 @@ -F 1 19 2 -F 3 10 1 -F 4 8 1 -F 11 15 1 -F 24 25 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq deleted file mode 100644 index 9a1d7d8..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq6.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAGAAGCAAAGAAGGCCCACGAAAA diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint deleted file mode 100644 index 2ce893a..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.constraint +++ /dev/null @@ -1,4 +0,0 @@ -F 0 19 2 -F 3 10 1 -F 4 8 1 -F 11 15 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq deleted file mode 100644 index 0964dc3..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq7.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint deleted file mode 100644 index 65ea20f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.constraint +++ /dev/null @@ -1,4 +0,0 @@ -F 1 19 2 -F 3 10 1 -F 4 8 1 -F 11 24 1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult deleted file mode 100644 index d00491f..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.expectedresult +++ /dev/null @@ -1 +0,0 @@ -1 diff --git a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq b/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq deleted file mode 100644 index 0964dc3..0000000 --- a/gtfold-mfe/tests/data/pseudoknot_detection_sequences/seq8.seq +++ /dev/null @@ -1 +0,0 @@ -CCCCAAGAAGCAAAGAAGG From 7b4289c25806a2dd07d68c9f543a78c3af6b7554 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Thu, 13 Oct 2011 22:17:44 -0400 Subject: [PATCH 162/187] Test to Compare CT structure returned by GTFold and UNAFold. --- gtfold-mfe/tests/config/test-params.conf | 8 +- .../tests/scripts/CompareGTCTwithUNACT.pm | 64 ++++ gtfold-mfe/tests/scripts/compare_ct.pl | 339 ++++++++++++++++++ 3 files changed, 407 insertions(+), 4 deletions(-) create mode 100755 gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm create mode 100755 gtfold-mfe/tests/scripts/compare_ct.pl diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf index d1fdec2..5b649f8 100644 --- a/gtfold-mfe/tests/config/test-params.conf +++ b/gtfold-mfe/tests/config/test-params.conf @@ -1,9 +1,9 @@ # Important directory variables G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ -#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ -G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/ G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/ @@ -14,7 +14,7 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test- #G_INCLUDE_SEQUENCES=d.16.e.B.g* #G_INCLUDE_SEQUENCES=d.16.e.B.m* #G_INCLUDE_SEQUENCES=d.16.e.B.h* -#G_INCLUDE_SEQUENCES=d.16.e.G.va* +#G_INCLUDE_SEQUENCES=d.16.e.E.bieneusi #G_EXCLUDE_SEQUENCES=d.16.e.A.* #G_EXCLUDE_SEQUENCES=d.16.e.B.ma* #G_INCLUDE_SEQUENCES=acc1 @@ -24,4 +24,4 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test- # Local Sequence Directories # Directory containing sequences for testing pseudoknot detection logic -L_PSEUDOKNOTDETECTION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/pseudoknot_detection_sequences/ +#L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ diff --git a/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm new file mode 100755 index 0000000..ddabcdc --- /dev/null +++ b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm @@ -0,0 +1,64 @@ +#!/usr/bin/perl +package CompareGTCTwithUNACT; +use strict; +use warnings; +use Error; +use File::Basename; +use Exception::Class; + +require "compare_ct.pl"; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[4]; + + my $epsilon = 0.001; + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + + my @result; + eval { + @result = compare_ct_structures($gtoutfilename, $unaoutfilename); + }; + my $exception; + if ($exception = Exception::Class->caught('CompareCTException')) { + $logger->error("Test Failed: $seqname: $exception\n"); + next; + } + + my $diff1 = abs(1 - $result[0]); + my $diff2 = abs(1 - $result[1]); + if ($diff1 < $epsilon || $diff2 < $epsilon) { + $logger->info("TEST PASSED: $seqname: Specificity = $result[0], Selectivity = $result[1]"); + } + else { + $logger->info("TEST FAILED: $seqname: Specificity = $result[0], Selectivity = $result[1]\n". + "More Information: $result[2] $result[3]"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/compare_ct.pl b/gtfold-mfe/tests/scripts/compare_ct.pl new file mode 100755 index 0000000..7196ffe --- /dev/null +++ b/gtfold-mfe/tests/scripts/compare_ct.pl @@ -0,0 +1,339 @@ +#!/usr/bin/perl + +use paul_specials; +use Error; +use Exception::Class('CompareCTException'); + +sub compare_ct_structures() +{ +my $ref_filename=$_[0]; +my $filename=$_[1]; + +open(REF, "< $ref_filename"); +open(RNA, "< $filename"); + +#printf "opened files $ref_filename and $filename\n\n\n"; + +@ref_struct = read_struct_ct(*REF); +@struct = read_struct_ct(*RNA); + +my $rlen = length($ref_struct[0]); +my $slen = length($struct[0]); +my $ref_seq = $ref_struct[0]; +my $seq = $struct[0]; + +$ref_struct[0]=$rlen; +$struct[0]=$slen; + +my $ref_dotb = table_to_bracket(\@ref_struct); +my $dotb = table_to_bracket(\@struct); + +$dotb =~ s/\(/\{/g; +$dotb =~ s/\)/\}/g; + + $_ = $ref_seq; + my $ref_nogaps = tr/\-//; + $_ = $seq; + my $nogaps = tr/\-//; + + + if (($rlen-$ref_nogaps) != ($slen-$nogaps)){ + CompareCTException->throw(error => "seq lengths aren't equal (reference = $rlen, prediction = $slen)! +$rlen-$ref_nogaps ne $slen-$nogaps +ref_nogaps = $ref_nogaps +nogaps = $nogaps + +>ref +$ref_seq +$ref_dotb +>str +$seq\n\n\n"); + } + +#print ">ref1 +#$ref_seq +#$ref_dotb +#>str1 +#$seq +#$dotb\n\n\n"; + +#If different lengths, gap or delete as appropriate: +while ($rlen != $slen){ + + for (my $i = 0; $i < length($ref_seq); $i++){ + if ( substr($ref_seq,$i,1) =~ '\-'){ + + if (substr($ref_dotb,$i,1) =~ '\.' ){ + substr($ref_seq,$i,1) = ""; + substr($ref_dotb,$i,1) = ""; + $i--; + } + elsif ((substr($seq,$i,1) ne substr($ref_seq,$i,1)) && (substr($ref_dotb,$i,1) ne '\.') ) { + substr($seq,$i,0) = "."; + substr($dotb,$i,0) = "."; + + substr($ref_seq,$i,1) = "."; + + + } + } + } + + + for (my $i = 0; $i < length($seq); $i++){ + + if ( substr($seq,$i,1) =~ '\-'){ + + if (substr($dotb,$i,1) =~ '\.' ){ + substr($seq,$i,1) = ""; + substr($dotb,$i,1) = ""; + $i--; + } + elsif (substr($seq,$i,1) ne substr($ref_seq,$i,1) && (substr($dotb,$i,1) ne '\.')) { + substr($ref_seq,$i,0) = "."; + substr($ref_dotb,$i,0) = "."; + substr($seq,$i,1) = "."; + + } + } + + } +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq +#$dotb\n\n"; + @ref_struct = make_pair_table($ref_dotb); + @struct = make_pair_table($dotb); + + #Update lengths after gapping + $rlen = length($ref_seq); + $slen = length($seq); + +} + + + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; + + + +my $rcount = 0; +my $scount = 0; +my $true_pos = 0; +my $true_neg = 0; +my $false_neg = 0; +my $false_pos = 0; +my $conflict = 0; +my $contradict = 0; +my $temp = 0; + +for (my $i=1; $i<=$rlen; $i++){ + + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + + if ($ref_struct[$i]>0 && $ref_struct[$i]>$i){ + $rcount++; + #print "$rcount: $i-$ref_struct[$i]\n"; + } + + if ($struct[$i]>0 && $struct[$i]>$i){ + $scount++; + } + + if (($ref_struct[$i]==$struct[$i]) && $ref_struct[$i]>0 && $ref_struct[$i]>$i){ + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + $true_pos++; + $temp = $struct[$i]; + substr($dotb,$i-1,1) = '('; + substr($dotb,$temp-1,1) = ')'; + } + elsif (($ref_struct[$i]!=$struct[$i]) && $struct[$i]>0 && $struct[$i]>$i){ + + #print "struct: $i . $struct[$i]\n"; + + $prime5 = $i; + $prime3 = $struct[$i]; + + if ($ref_struct[$prime3]>0 || $ref_struct[$prime5]>0){ + #print " ref: $ref_struct[$prime3] . $ref_struct[$ref_struct[$prime3]] : $ref_struct[$prime5] . $ref_struct[$ref_struct[$prime5]]\n"; + $contradict++; + + substr($dotb,$prime5-1,1) = '<'; + substr($dotb,$prime3-1,1) = '>'; + + + } + else { + #check nested! + $j=$prime5; + $b=1; + while ($b && $j<$prime3 ) { + + if ( ($ref_struct[$j]>0 && $ref_struct[$j]<$prime5) || $ref_struct[$j]>$prime3 ) { + $b=0; + $conflict++; + #print "conflict $ref_struct[$j] . $j\n"; + + substr($dotb,$prime5-1,1) = '['; + substr($dotb,$prime3-1,1) = ']'; + + } + $j++; + } + + } + + + } + + for (my $j=$i+4; $j<=$rlen; $j++){ + + my $x = substr($ref_seq,$i-1,1); + my $y = substr($ref_seq,$j-1,1); + + if (ispair($x,$y) ){ + $true_neg++; + #print "$x $i $y $j\n"; + } + + } + + +} + + +#$false_pos = $scount - $true_pos; +$false_pos = $conflict + $contradict; +$false_neg = $rcount - $true_pos; + +$true_neg=$true_neg-$true_pos-$false_pos; + +my $sensitivity = 0; +my $selectivity =0; +if ($rcount>0){ + $sensitivity = $true_pos/($false_neg + $true_pos); #$rcount; +} +if ($scount>0){ + $selectivity = $true_pos/($false_pos + $true_pos); #$scount; +} + +my $approx_corr = ($sensitivity + $selectivity)/2; +my $N = $true_pos + $false_pos + $false_neg + $true_neg; + +my $corr_coeff = 0; +if ($true_pos>0){ +$corr_coeff = ($N*$sensitivity*$selectivity - $true_pos)/sqrt(($N*$sensitivity - $true_pos)*($N*$selectivity - $true_pos)); +} + + +my $MCC = 0; +my $MCCquotient = (($true_pos+$false_pos)*($true_pos+$false_neg)*($true_neg+$false_pos)*($true_neg+$false_neg)); + +if ($MCCquotient>0){ +$MCC = ($true_pos*$true_neg - $false_pos*$false_neg)/sqrt( $MCCquotient ); +} + +$old_false_pos = $scount - $true_pos; +$compatable = $old_false_pos - $false_pos; + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; +#print "$dotb\n"; + +my $comparison_result = " +seq length = %6d +num of bps in ref = %6d +num of bps in sub = %6d +Basepair distance = %6d +true positives = %6d +true negatives = %6d +false positive = %6d +\t contradict = $contradict +\t conflict = $conflict +\t compatable = $compatable +false negative = %6d +sensitivity = %1.3f +selectivity = %1.3f +Approximate correlation = %1.3f +Correlation Coefficient = %1.3f +Matthews Corr. Coeff. = %1.3f + +\n\n", $rlen, $rcount, $scount, $false_pos+$false_neg+$compatable, $true_pos, $true_neg, $false_pos, $false_neg, $sensitivity, $selectivity, $approx_corr, $corr_coeff, $MCC; + +my $latex_comparison_result = "LaTeX: +Subj. File & BPs in Ref. & BPs in Subj. & TPs (sens.)& FPs (select.) & Matthews Corr. Coeff. (approx. corr.) & \\\\ +$filename & %d & %d & %d (%2.1f) & %d (%2.1f) & %1.3f (%2.1f) \\\\ \n\n", +$rcount, $scount, $true_pos, $sensitivity*100, $false_pos, $selectivity*100, $MCC, $approx_corr*100; + +#printf "%1.4f\t%1.4f\n", +#$sensitivity, $selectivity; + + return ($sensitivity, $selectivity, $comparison_result, $latex_comparison_result); +} + +sub read_struct_ct{ + +$fileptr = $_[0]; +my $seq = ""; + +my $i=-1; +while ( <$fileptr> ){ + + @F = split; + + #if ((/ = /) && ($#F!=5)) { + # next; + #} + + if ($i>=0){ + + $seq .= $F[1]; + $table[$i] = $F[4]; +} + $i++; + + #if ($F[4]==0) {$s .= "."; next} + #$s .= "(" if ($F[0]<$F[4]); + #$s .= ")" if ($F[0]>$F[4]); +} + + + $seq =~ tr/a-z/A-Z/; +#print "2: $seq\n\n"; + +return ($seq, @table); + +} + +sub ispair{ + my ($x, $y) = @_; + + if ( ($x eq 'A' && $y eq 'U')||($x eq 'U' && $y eq 'A') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'C')||($x eq 'C' && $y eq 'G') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'U')||($x eq 'U' && $y eq 'G') ) { + + return 1; + } + + else { + return 0; + } +} + +# End of file +1; From 82ca1b236138b1bbb3260a192cb4da0ae13d3832 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Thu, 13 Oct 2011 22:56:43 -0400 Subject: [PATCH 163/187] Added meaningful names to some sequence files. --- .../{seq5.constraint => base_pair_distance1.constraint} | 0 .../{seq2.expectedresult => base_pair_distance1.expectedresult} | 0 .../exitcodes_sequences/{seq5.seq => base_pair_distance1.seq} | 0 .../{seq6.constraint => base_pair_distance2.constraint} | 0 .../{seq3.expectedresult => base_pair_distance2.expectedresult} | 0 .../exitcodes_sequences/{seq6.seq => base_pair_distance2.seq} | 0 .../{seq4.constraint => duplicate_base1.constraint} | 0 .../{seq4.expectedresult => duplicate_base1.expectedresult} | 0 .../data/exitcodes_sequences/{seq1.seq => duplicate_base1.seq} | 0 .../{seq7.constraint => invalid_base_number1.constraint} | 0 .../{seq5.expectedresult => invalid_base_number1.expectedresult} | 0 .../exitcodes_sequences/{seq4.seq => invalid_base_number1.seq} | 0 .../{seq8.constraint => invalid_base_number2.constraint} | 0 .../{seq6.expectedresult => invalid_base_number2.expectedresult} | 0 .../exitcodes_sequences/{seq7.seq => invalid_base_number2.seq} | 0 .../{seq1.constraint => normal_struct1.constraint} | 0 .../{seq1.expectedresult => normal_struct1.expectedresult} | 0 .../data/exitcodes_sequences/{seq8.seq => normal_struct1.seq} | 0 .../{seq2.constraint => pseudoknot1.constraint} | 0 .../{seq7.expectedresult => pseudoknot1.expectedresult} | 0 .../tests/data/exitcodes_sequences/{seq2.seq => pseudoknot1.seq} | 0 .../{seq3.constraint => pseudoknot2.constraint} | 0 .../{seq8.expectedresult => pseudoknot2.expectedresult} | 0 .../tests/data/exitcodes_sequences/{seq3.seq => pseudoknot2.seq} | 0 24 files changed, 0 insertions(+), 0 deletions(-) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.constraint => base_pair_distance1.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.expectedresult => base_pair_distance1.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.seq => base_pair_distance1.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.constraint => base_pair_distance2.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.expectedresult => base_pair_distance2.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.seq => base_pair_distance2.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.constraint => duplicate_base1.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.expectedresult => duplicate_base1.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.seq => duplicate_base1.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.constraint => invalid_base_number1.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq5.expectedresult => invalid_base_number1.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq4.seq => invalid_base_number1.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.constraint => invalid_base_number2.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq6.expectedresult => invalid_base_number2.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.seq => invalid_base_number2.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.constraint => normal_struct1.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq1.expectedresult => normal_struct1.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.seq => normal_struct1.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.constraint => pseudoknot1.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq7.expectedresult => pseudoknot1.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq2.seq => pseudoknot1.seq} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.constraint => pseudoknot2.constraint} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq8.expectedresult => pseudoknot2.expectedresult} (100%) rename gtfold-mfe/tests/data/exitcodes_sequences/{seq3.seq => pseudoknot2.seq} (100%) diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq5.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq4.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq6.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq1.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq7.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq2.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.constraint rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq8.expectedresult rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq similarity index 100% rename from gtfold-mfe/tests/data/exitcodes_sequences/seq3.seq rename to gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq From 0926b47ff7c9b954f8a1aad5deab7f030477ed6f Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Thu, 13 Oct 2011 22:59:11 -0400 Subject: [PATCH 164/187] Cleanup - Delete a file. --- .../tests/data/exitcodes_sequences/seq1.ct | 20 ------------------- 1 file changed, 20 deletions(-) delete mode 100644 gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct b/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct deleted file mode 100644 index da642b1..0000000 --- a/gtfold-mfe/tests/data/exitcodes_sequences/seq1.ct +++ /dev/null @@ -1,20 +0,0 @@ -19 dG = 10.1 -1 C 0 2 0 1 -2 C 1 3 0 2 -3 C 2 4 0 3 -4 C 3 5 0 4 -5 A 4 6 0 5 -6 A 5 7 0 6 -7 G 6 8 0 7 -8 A 7 9 0 8 -9 A 8 10 0 9 -10 G 9 11 0 10 -11 C 10 12 0 11 -12 A 11 13 0 12 -13 A 12 14 0 13 -14 A 13 15 0 14 -15 G 14 16 0 15 -16 A 15 17 0 16 -17 A 16 18 0 17 -18 G 17 19 0 18 -19 G 18 0 0 19 From 594093c6caf8b373ea49db9388649232bae75675 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 14 Oct 2011 01:34:07 -0400 Subject: [PATCH 165/187] Merge Suboptimal Structure matching test. --- gtfold-mfe/tests/config/test-list.conf | 4 +- gtfold-mfe/tests/config/test-params.conf | 4 +- .../tests/data/subopt_sequences/combseq.seq | 1 + .../tests/data/subopt_sequences/combseq3.seq | 1 + .../tests/data/subopt_sequences/combseq4.seq | 1 + .../tests/data/subopt_sequences/cs1.seq | 1 + .../tests/scripts/SuboptMatchStructures.pm | 70 +++++++++++++++++++ 7 files changed, 80 insertions(+), 2 deletions(-) create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq.seq create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq3.seq create mode 100644 gtfold-mfe/tests/data/subopt_sequences/combseq4.seq create mode 100644 gtfold-mfe/tests/data/subopt_sequences/cs1.seq create mode 100755 gtfold-mfe/tests/scripts/SuboptMatchStructures.pm diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf index 827ab10..fbc5593 100644 --- a/gtfold-mfe/tests/config/test-list.conf +++ b/gtfold-mfe/tests/config/test-list.conf @@ -1,2 +1,4 @@ #Scoregtwithunafold -PseudoKnotDetection +#ExitCodes +#CompareGTCTwithUNACT +SuboptMatchStructures diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf index 5b649f8..98f99cc 100644 --- a/gtfold-mfe/tests/config/test-params.conf +++ b/gtfold-mfe/tests/config/test-params.conf @@ -1,6 +1,7 @@ # Important directory variables G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ +G_RNAFOLD_DIR=/usr/local/bin/ G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ #G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ @@ -24,4 +25,5 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test- # Local Sequence Directories # Directory containing sequences for testing pseudoknot detection logic -#L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ +L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/ diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq new file mode 100644 index 0000000..ac737d0 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq @@ -0,0 +1 @@ +CCCAAAAGGGAAAACCCAAAAGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq new file mode 100644 index 0000000..c2722ec --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq @@ -0,0 +1 @@ +CCCCAAAACCCCAAAAGGGGAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/cs1.seq b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq new file mode 100644 index 0000000..5e4009c --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq @@ -0,0 +1 @@ +CAAAAGAAAACAAAAG diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm new file mode 100755 index 0000000..1697a46 --- /dev/null +++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm @@ -0,0 +1,70 @@ +#!/usr/bin/perl +package SuboptNumStructures; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $rnadir = $Config{"G_RNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences); + # For testing pseudoknot detection logic + # we may only test the sequences specified in local_sequences + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $gtout = "$workdir$seqname-gt"; + my $rnaout = "$workdir$seqname-rna"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $energy; + for ($energy = 1; $energy <=10; ++$energy) { + + my $gtfile = $gtout.$energy; + my $rnafile = $rnaout.$energy."_ss.txt"; + my $gtcmd; + my $rnacmd; + $gtcmd = "$gtdir/gtfold --subopt $energy $seqfile -o $gtfile > /dev/null 2>&1"; + $rnacmd = "$rnadir/RNAsubopt -s DAT -e $energy < $seqfile > $rnafile"; + + system("$gtcmd"); + system("$rnacmd"); + + my $gtsubopt_file = $gtfile."_ss.txt"; + my $rnasubopt_file = $rnafile; + + my $gtsorted = $gtsubopt_file."_sorted"; + my $rnasubopt_sorted = $rnafile."_sorted"; + `cat $gtsubopt_file | sed '/[A-Z]/d' | sort -o $gtsorted`; + `cat $rnasubopt_file | sed '/[A-Z]/d' | sort -o $rnasubopt_sorted`; + #`sort $gtsubopt_file -o $gtsorted`; + #`sort $rnasubopt_file -o $rnasubopt_sorted`; + + my $diff_str = `diff $gtsorted $rnasubopt_sorted`; + #print $diff_str; + + if ($diff_str eq "") { + $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched"); + } + else { + $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched\n $diff_str"); + } + } + } +} +1; From d966815f1590f2bda3891a251ec493fdac15ef8d Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 14 Oct 2011 01:39:41 -0400 Subject: [PATCH 166/187] Output formatting for saving suboptimal structures to a file changed to match rna subopt. --- gtfold-mfe/src/main.cc | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 952aba1..89ba476 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -44,7 +44,7 @@ #include "subopt_traceback.h" #include "shapereader.h" -//#define DEBUG 1 +#define DEBUG 1 using namespace std; @@ -227,11 +227,11 @@ void save_subopt_file(string outputFile, ss_map_t& ss_data, outfile.open(outputFile.c_str()); char buff[1024]; - sprintf(buff,"%s\t%0.2f", seq.c_str(), energy/100.0); + sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0); outfile << buff << std::endl; for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) { - sprintf(buff,"%s %0.2f", (it->first).c_str(), it->second/100.0); + sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0); //outfile << it->first << '\t' << it->second/100.0 << std::endl; outfile << buff << std::endl; } From d069c655169184e8d32f4908f9c6bcd0be701584 Mon Sep 17 00:00:00 2001 From: Manoj Soni Date: Fri, 14 Oct 2011 14:21:22 -0400 Subject: [PATCH 167/187] Few Bug removed from partition function and options for getting structure count by partition function added --- gtfold-mfe/include/energy.h | 3 +- gtfold-mfe/include/options.h | 1 + gtfold-mfe/include/partition-func.h | 9 +- gtfold-mfe/src/energy.c | 1 + gtfold-mfe/src/main.cc | 66 ++++---- gtfold-mfe/src/options.cc | 7 +- gtfold-mfe/src/partition-func.c | 239 +++++++++++++++++----------- 7 files changed, 203 insertions(+), 123 deletions(-) diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index f742042..b4beeb3 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -19,7 +19,8 @@ extern int **PP; #define WMU(i,j) WM[i][j] #define WML(i,j) WM[j][i] #define VBI(i,j) VBI[indx[j]+i] -#define RT ((0.00198721 * 310.15) * 100.00) +//#define RT ((0.00198721 * 310.15) * 100.00) +extern const float RT; #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index f0499a9..7965698 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -24,6 +24,7 @@ extern bool UNAMODE; extern bool RNAMODE; extern bool CALC_PART_FUNC; extern bool RND_SAMPLE; +extern bool PF_COUNT_MODE; extern string seqfile; extern string constraintsFile; diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index 6532bea..b2e8c80 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -22,8 +22,15 @@ extern double ** u1; extern int part_len; double ED3_new(int i, int j, int k); double ED5_new(int i, int j, int k); +double EA_new(); +double EB_new(); +double EC_new(); +double eS_new(int i, int j); +double eL_new(int i, int j, int p, int q); +double eH_new(int i, int j); +double auPenalty_new(int i, int j); double f(int j, int h, int l); -void calculate_partition(int len); +void calculate_partition(int len, int pf_count_mode); void free_partition(); #ifdef __cplusplus diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index bc71d37..314d35a 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -18,6 +18,7 @@ int *indx; int **PP; int alloc_flag = 0; +const float RT = ((0.00198721 * 310.15)*10000); //* 100.00); void create_tables(int len) { V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 77a23a5..07f6b19 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -287,43 +287,47 @@ int main(int argc, char** argv) { if (CALC_PART_FUNC == true) { printf("\nComputing partition function...\n"); - calculate_partition(seq.length()); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + calculate_partition(seq.length(),pf_count_mode); free_partition(); free_fold(seq.length()); exit(0); } if (RND_SAMPLE == true) { - printf("\nComputing partition function...\n"); - calculate_partition(seq.length()); - - int* structure = new int[seq.length()+1]; - srand(time(NULL)); - - if (num_rnd > 0 ) { - printf("\nSampling structures...\n"); - for (int count = 1; count <= num_rnd; ++count) - { - memset(structure, 0, (seq.length()+1)*sizeof(int)); - rnd_structure(structure, seq.length()); - - std::string ensemble(seq.length()+1,'.'); - for (int i = 1; i <= (int)seq.length(); ++ i) { - // printf("%d %d\n",i,structure[i]); - if (structure[i] > 0 && ensemble[i] == '.') - { - ensemble[i] = '('; - ensemble[structure[i]] = ')'; - } - } - std::cout << ensemble.substr(1) << std::endl; - } - } - - free_partition(); - free_fold(seq.length()); - delete [] structure; - exit(0); + printf("\nComputing partition function...\n"); + int pf_count_mode = 1; + //if(PF_COUNT_MODE) pf_count_mode=1; + calculate_partition(seq.length(),pf_count_mode); + + int* structure = new int[seq.length()+1]; + srand(time(NULL)); + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + for (int count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (seq.length()+1)*sizeof(int)); + rnd_structure(structure, seq.length()); + + std::string ensemble(seq.length()+1,'.'); + for (int i = 1; i <= (int)seq.length(); ++ i) { + // printf("%d %d\n",i,structure[i]); + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } + std::cout << ensemble.substr(1) << std::endl; + } + } + + free_partition(); + free_fold(seq.length()); + delete [] structure; + exit(0); } printf("\nComputing minimum free energy structure...\n"); diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index b600088..8a9082f 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -20,6 +20,7 @@ bool RNAMODE = false; bool b_prefilter = false; bool CALC_PART_FUNC = false; bool RND_SAMPLE = false; +bool PF_COUNT_MODE = false; string seqfile = ""; string constraintsFile = ""; @@ -74,6 +75,7 @@ void help() { printf("\nBETA OPTIONS\n"); printf(" --bpp Calculate base pair probabilities.\n"); printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); @@ -186,7 +188,10 @@ void parse_options(int argc, char** argv) { help(); } else if (strcmp(argv[i],"--partition") == 0) { CALC_PART_FUNC = true; - } else if (strcmp(argv[i],"--sample") == 0) { + } else if (strcmp(argv[i],"--pf_count") == 0) { + CALC_PART_FUNC = true; + PF_COUNT_MODE = true; + } else if (strcmp(argv[i],"--sample") == 0) { RND_SAMPLE = true; if(i < argc) num_rnd = atoi(argv[++i]); diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index 51ceede..fcd1b1d 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -6,34 +6,7 @@ #include "algorithms-partition.h" #include "global.h" #include "utils.h" - -#ifdef _OPENMP -#include "omp.h" -#endif - -//#define DEBUG_PF 1 - -#ifdef DEBUG_PF - #undef Ec - #undef Eb - #undef Ea - #define Ec 0 - #define Eb 0 - #define Ea 0 - #define eS StackE - #define eH HairE - #define eL ILoopE - #define Ed3 D3 - #define Ed5 D5 - #define auPenalty Etp -#endif - -int StackE(int i, int j) { return 0; } -int HairE(int i, int j) { return 0; } -int ILoopE(int i, int j, int ip, int jp) { return 0; } -int D3(int i, int j, int k) { return 0; } -int D5(int i, int j, int k) { return 0; } -int Etp(int i, int j) { return 0; } +//#include "options.h" double ** u; double ** up; @@ -47,6 +20,7 @@ double ** s3; double ** u1; int part_len; +int PF_COUNT_MODE_; static void create_partition_arrays(); static void init_partition_arrays(); @@ -113,21 +87,71 @@ void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAn void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;} void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;} +double myExp(double arg){ + double posArgMultRT = (-1)*arg*RT; + if(posArgMultRT>=INFINITY_){ + //printf("WARN: posArgMultRT is greater than or equal to INFINITY_, hence returning zero\n"); + return 0; + } + return exp(arg); +} + +double eS_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eS(i,j); +} + +double eH_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eH(i,j); +} + +double eL_new(int i, int j, int p, int q){ + if(PF_COUNT_MODE_) return 0; + return eL(i,j,p,q); +} + double ED3_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; //return Ed3(i,j,k); return Ed5(j,i,k); + //return Ed5(i,j,k); + //return Ed3(j,i,k); } double ED5_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; //return Ed5(i,j,k); return Ed3(j,i,k); + //return Ed3(i,j,k); + //return Ed5(j,i,k); +} + +double EA_new(){ + if(PF_COUNT_MODE_) return 0; + return Ea; +} + +double EB_new(){ + if(PF_COUNT_MODE_) return 0; + return Eb; +} + +double EC_new(){ + if(PF_COUNT_MODE_) return 0; + return Ec; +} + +double auPenalty_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return auPenalty(i,j); } double f(int j, int h, int l){ if(j - 1 == l) return 1; else - return exp(-ED3_new(h,l,l+1)/RT); + return myExp(-ED3_new(h,l,l+1)/RT); } void printMatrix(double** u, int part_len){ @@ -162,8 +186,9 @@ printf("\n\nAfter calculation, s3 matrix:\n\n"); } -void calculate_partition(int len) -{ +void calculate_partition(int len, int pf_count_mode) +{printf("RT=%f\n",RT);//RT=RT/100; + PF_COUNT_MODE_ = pf_count_mode; int i, j; part_len = len; create_partition_arrays(); @@ -398,9 +423,9 @@ void fill_partition_arrays() int l; for (l = h; l < j; ++l) { - s1[h][j] = up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* - (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+ - up[l+1][j]*exp(-(auPenalty(l+1,j)/RT)))); + s1[h][j] = up[h][l]*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* + (myExp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]+(ud[l+1][j]+ + up[l+1][j]*myExp(-(auPenalty_new(l+1,j)/RT)))); } }*/ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of += @@ -409,12 +434,12 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of += double s1_val = 0.0; for (l = h+1; l < j; ++l)//ERROR { - double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); - double v2 = (exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)); + double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); + double v2 = (myExp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)); double v3 = get_ud(l+1,j); - double v4 = (get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT))); + double v4 = (get_up(l+1,j)*myExp(-(auPenalty_new(l+1,j)/RT))); double val = v1*(v2+v3+v4); - //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(exp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*exp(-(auPenalty(l+1,j)/RT)))); + //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(myExp(-ED3_new(h,l,l+1)/RT)*get_u(l+2,j)+(get_ud(l+1,j)+get_up(l+1,j)*myExp(-(auPenalty_new(l+1,j)/RT)))); s1_val += val; } set_s1(h,j,s1_val);//s1[h][j] = s1_val; @@ -427,12 +452,12 @@ void calc_s2(int h, int j) int l; double s2_val = 0.0; for (l = h+1; l < j; ++l)//ERROR - {//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)),(exp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1))); - double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); - double v2 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)); + {//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)),(myExp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1))); + double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); + double v2 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j-1)); double v3 = get_u1d(l+1,j-1); double val = v1*(v2+v3); - //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)) * (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)); + //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)) * (myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)); s2_val += val;//Error: Eb is added } set_s2(h, j, s2_val);//s2[h][j] = s2_val; @@ -445,12 +470,12 @@ void calc_s3(int h, int j) double s3_val = 0.0; for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l { - double v1 = (get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))); - double v2 = (f(j+1,h,l)*exp(-((j-l)*Eb)/RT)); - double v3 = (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j)); + double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); + double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT)); + double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j)); double v4 = get_u1d(l+1,j); double val = v1*(v2+v3+v4); - //double val = get_up(h,l)*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))*(f(j+1,h,l)*exp(-((j-l)*Eb)/RT) + exp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)); + //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(f(j+1,h,l)*myExp(-((j-l)*Eb)/RT) + myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)); s3_val += val; } set_s3(h, j, s3_val);//s3[h][j] = s3_val; @@ -494,19 +519,19 @@ void free_partition_arrays() if (canPair(RNA[i],RNA[j]) && j-i > TURN) { for(l=i+2; l maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;} + } + } + + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j]; + double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j]; + double upmProb = get_upm(i,j)/up[i][j]; + + if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT "); + else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL "); + else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK "); + else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM "); + +printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f, sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max); + +} + void calc_up(int i, int j) {//printf("Entering calc_up: i=%d, j =%d\n",i,j); double up_val = 0.0; @@ -744,7 +804,7 @@ void calc_up(int i, int j) for (q = minq; q <= maxq; q++) { if (canPair(p,q)==0) continue; - up_val += (get_up(p,q) * exp(-eL(i,j,p,q)/RT)); + up_val += (get_up(p,q) * myExp(-eL_new(i,j,p,q)/RT)); } }*/ int h,l; @@ -753,17 +813,18 @@ void calc_up(int i, int j) if (canPair(RNA[h],RNA[l])==0) continue; if(h==(i+1) && l==(j-1)) continue; //if((l-h)<=TURN) continue; - up_val += (get_up(h,l) * exp(-eL(i,j,h,l)/RT)); + up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT)); } } //ERROR below line should not be there - //up_val = up_val * exp(-ED3_new(i,j,i+1)/RT); - up_val = up_val + exp(-eH(i,j)/RT ); - up_val = up_val + (exp(-eS(i,j)/RT ) * get_up(i+1,j-1)); + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + up_val = up_val + myExp(-((double)eH_new(i,j))/RT ); + up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1)); up_val = up_val + get_upm(i,j); set_up(i, j, up_val);//up[i][j] = up_val; + //printUPprobabilities(i,j); } else { set_up(i, j, 0.0);//up[i][j] = 0; From f587da4138bfa2dd6fde09bd51cbb79875c13437 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 14 Oct 2011 19:45:55 -0400 Subject: [PATCH 168/187] Constraint Verification Tests - The tests generate random constraints and verifies that they are not violated in the generated structure. --- gtfold-mfe/src/algorithms.c | 2 +- gtfold-mfe/tests/config/test-list.conf | 3 +- gtfold-mfe/tests/config/test-params.conf | 7 + .../data/constraints_sequences/combseq3.seq | 1 + .../tests/scripts/ConstraintsVerification.pm | 162 ++++++++++++++++++ 5 files changed, 173 insertions(+), 2 deletions(-) create mode 100644 gtfold-mfe/tests/data/constraints_sequences/combseq3.seq create mode 100755 gtfold-mfe/tests/scripts/ConstraintsVerification.pm diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 0bbdceb..7d81bfe 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -229,7 +229,7 @@ int calculate(int len) { W[0] = 0; for (j = 1; j <= len; j++) { int i, Wj, Widjd, Wijd, Widj, Wij, Wim1; - Wj = INFINITY_; + Wj = 0; for (i = 1; i < j-TURN; i++) { Wij = Widjd = Wijd = Widj = INFINITY_; Wim1 = MIN(0, W[i-1]); diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf index fbc5593..bff0017 100644 --- a/gtfold-mfe/tests/config/test-list.conf +++ b/gtfold-mfe/tests/config/test-list.conf @@ -1,4 +1,5 @@ #Scoregtwithunafold #ExitCodes #CompareGTCTwithUNACT -SuboptMatchStructures +#SuboptMatchStructures +ConstraintsVerification diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf index 98f99cc..81ad292 100644 --- a/gtfold-mfe/tests/config/test-params.conf +++ b/gtfold-mfe/tests/config/test-params.conf @@ -26,4 +26,11 @@ G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test- # Directory containing sequences for testing pseudoknot detection logic L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/ +L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY=0 +L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY=1 +L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE=1 +L_SUBOPTMATCHSTRUCTURES_INCLUDE_SEQUENCES=d.5.a.H.* +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ diff --git a/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/scripts/ConstraintsVerification.pm b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm new file mode 100755 index 0000000..22617bb --- /dev/null +++ b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm @@ -0,0 +1,162 @@ +#!/usr/bin/perl +package ConstraintsVerification; +use strict; +use warnings; +use File::Basename; + +require 'test_utils.pl'; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$workdir/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd; + $gtcmd = "$gtdir/gtfold $seqfile -o $gtout > /dev/null 2>&1"; + system("$gtcmd"); + my $len = get_seq_len_from_ctfile($gtoutfilename); + my $CONSFILE; + open($CONSFILE, '>', $constraint_file) or die "Couldn't open $_"; + generate_constraints(1, $len, $CONSFILE); + close $CONSFILE; + + my $gtout_constraints = $gtout."_constraints"; + my $gtout_constraints_filename = "$gtout_constraints.ct"; + $gtcmd = "$gtdir/gtfold -c $constraint_file $seqfile -o $gtout_constraints > /dev/null 2>&1"; + my $exitcode = system("$gtcmd") >> 8; + + if ($exitcode != 0) { + $logger->error("TEST FAILED: $seqname : Assertion Failed, Exit Code incorrect: $exitcode. Constraint File: $constraint_file"); + next; + } + + my @violated_constraints = verify_constraints($gtout_constraints_filename, $constraint_file); + if (@violated_constraints) { + my @vc = join(',', @violated_constraints); + print scalar(@violated_constraints); + $logger->error("TEST FAILED: $seqname : Constraints Violated: Input Constraint File $constraint_file. Violated Constraints:\n @vc"); + } + else { + $logger->info("TEST PASSED: $seqname : Input Constraint File $constraint_file"); + } + } +} + +sub generate_constraints +{ + my $i = shift; + my $j = shift; + my $CONSFILE = shift; + + return if ($j-$i< 4); + + my $r = rand(); + print $CONSFILE "F $i $j 1\n" if $r <0.4; + print $CONSFILE "P $i $j 1\n" if $r >0.4 && $r<0.8; + print $CONSFILE "P $i 0 1\n" if $r >0.8; + + my $range = $j-$i; + my $ii = int(rand($range)) + $i; + $range = $j-$ii; + my $jj = int(rand($range)) + $ii; + + generate_constraints($i+1,$ii-1, $CONSFILE); + generate_constraints($jj+1,$j-1, $CONSFILE); +} + +sub get_seq_len_from_ctfile +{ + my $filename = shift; + open(IN, "<$filename"); + my $header = ; # ignore first line + close IN; + my ($len, $dG) = split(' ', $header); + return $len; +} + +sub verify_constraints { + + my $ctfilename = shift; + my $cffilename = shift; + + open CT, $ctfilename; + open CF, $cffilename; + + my %ct_hash = (); + my @rna; + my $count=1; + + my $header = ; # ignore first line + while () + { + my @ff = split(' ', $_); + $ct_hash{$ff[0]} = $ff[4]; + $rna[$count] = $ff[1]; + ++$count; + } + + my @violated_constraints = (); + while() + { + chomp; + my @ff = split(' ', $_); + if ($ff[0] eq 'P' && $ff[2] == 0) { # case SS + if ($ct_hash{$ff[1]} != 0) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + elsif ($ff[0] eq 'P' && $ct_hash{$ff[1]} == $ff[2] && $ct_hash{$ff[2]} == $ff[1]) { # case P + print $_."\n"; + print "$ct_hash{$ff[1]} $ct_hash{$ff[2]}\n"; + push(@violated_constraints, $_); + } + elsif ($ff[0] eq 'F' && $ff[2] == 0) { + my $b = canPair($rna[$ff[1]], $rna[$ff[2]]); + if ($b == 1) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + } + + close CT; + close CF; + + return @violated_constraints; +} + +sub canPair { + my ( $i, $j) = @_; + # (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). + return 1 if ($i eq 'A' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'A') ; + return 1 if ($i eq 'C' && $j eq 'G') ; + return 1 if ($i eq 'G' && $j eq 'C') ; + return 1 if ($i eq 'G' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'G') ; + return 0; +} +1; From c9ea34380121988d1084b54f089a97fa7cf47d18 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Sun, 16 Oct 2011 10:48:53 -0400 Subject: [PATCH 169/187] adding changes to sampling --- gtfold-mfe/include/stochastic-sampling.h | 6 +- gtfold-mfe/src/main.cc | 8 +- gtfold-mfe/src/stochastic-sampling.cc | 131 ++++++++++++++++------- 3 files changed, 99 insertions(+), 46 deletions(-) diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h index e318296..68fea91 100644 --- a/gtfold-mfe/include/stochastic-sampling.h +++ b/gtfold-mfe/include/stochastic-sampling.h @@ -67,7 +67,7 @@ struct base_pair friend std::ostream& operator << (std::ostream& out, const base_pair& bp) { - out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.isPaired() << std::endl; + out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.t << std::endl; return out; } }; @@ -76,12 +76,12 @@ void set_single_stranded(int i, int j, int* structure); void set_base_pair(int i, int j, int* structure); void rnd_upm(int i, int j, int* structure); -void rnd_u1d(int i, int j, int* structure); +void rnd_u1d(int i, int j, int* structure) ; void rnd_u1(int i, int j, int* structure); void rnd_up(int i, int j, int* structure); void rnd_ud(int i, int j, int* structure); void rnd_u(int i, int j, int* structure); -void rnd_structure(int* structure, int len); +double rnd_structure(int* structure, int len); #endif diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 07f6b19..1d5e1e3 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -297,8 +297,8 @@ int main(int argc, char** argv) { if (RND_SAMPLE == true) { printf("\nComputing partition function...\n"); - int pf_count_mode = 1; - //if(PF_COUNT_MODE) pf_count_mode=1; + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; calculate_partition(seq.length(),pf_count_mode); int* structure = new int[seq.length()+1]; @@ -309,7 +309,7 @@ int main(int argc, char** argv) { for (int count = 1; count <= num_rnd; ++count) { memset(structure, 0, (seq.length()+1)*sizeof(int)); - rnd_structure(structure, seq.length()); + double energy = rnd_structure(structure, seq.length()); std::string ensemble(seq.length()+1,'.'); for (int i = 1; i <= (int)seq.length(); ++ i) { @@ -320,7 +320,7 @@ int main(int argc, char** argv) { ensemble[structure[i]] = ')'; } } - std::cout << ensemble.substr(1) << std::endl; + std::cout << ensemble.substr(1) << ' ' << energy << std::endl; } } diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index 8ece94b..a311e10 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -6,7 +6,7 @@ #include std::stack g_stack; - +int energy = 0; double randdouble() { @@ -25,12 +25,12 @@ double U_0(int i, int j) double U_ij(int i, int j) { - return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty(i,j)/RT)/u[i][j]:0; + return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty_new(i,j)/RT)/u[i][j]:0; } double U_hj(int i, int h, int j) { - return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty(h,j))/RT)/u[i][j]:0; + return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty_new(h,j))/RT)/u[i][j]:0; } double U_il(int i, int j) @@ -45,42 +45,42 @@ double U_s1h(int i, int h, int j) double U_ihlj_case1(int i, int h, int l, int j) { - return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0; + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0; } double U_ihlj_case2(int i, int h, int l, int j) { - return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0; + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0; } double U_ihlj_case3(int i, int h, int l, int j) { - return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty(l+1,j)/RT))) /s1[h][j]:0; + return (feasible(h,l)&&feasible(l+1,j))?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty_new(l+1,j)/RT))) /s1[h][j]:0; } double UD_il_case1(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0; } double UD_il_case2(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp(-1*auPenalty(i,l)/RT)*ud[l+1][j])/ud[i][j]:0; + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*ud[l+1][j])/ud[i][j]:0; } double UD_il_case3(int i, int l, int j) { - return feasible(i,l)?up[i][l]*exp(-1*auPenalty(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty(l+1,j))/ud[i][j]:0; + return (feasible(i,l)&&feasible(l+1,j))?up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty_new(l+1,j))/ud[i][j]:0; } double Q_ijH(int i, int j) { - return exp(-eH(i,j)/RT)/up[i][j]; + return exp(-eH_new(i,j)/RT)/up[i][j]; } double Q_ijS(int i, int j) { - return exp(-eS(i,j)/RT)*up[i+1][j-1]/up[i][j]; + return exp(-eS_new(i,j)/RT)*up[i+1][j-1]/up[i][j]; } double Q_ijM(int i, int j) @@ -88,64 +88,77 @@ double Q_ijM(int i, int j) return upm[i][j]/up[i][j]; } +/* +double Q_ijBI(int i, int j) +{ + double sum = 0; + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + sum += feasible(h,l)?(exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]):0; + } + return sum/up[i][j]; +}*/ + double Q_ijhlBI(int i, int j, int h, int l) { - return feasible(h,l)?exp(-1*eL(i,j,h,l)/RT)*up[h][l]/up[i][j]:0; + return feasible(h,l)?exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]/up[i][j]:0; } double UPM_ip1l_case1(int i, int l, int j) { - return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+Eb)/RT) * u1[l+2][j-1])/upm[i][j]:0; + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+EB_new())/RT) * u1[l+2][j-1])/upm[i][j]:0; } double UPM_ip1l_case2(int i, int l, int j) { - return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(Ea+2*Ec+auPenalty(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; } double UPM_ip2l_case1(int i, int l , int j) { - return feasible(i+2,l)?up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+Eb)/RT)*u1[l+2][j-1])/upm[i][j]:0; + return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0; } double UPM_ip2l_case2(int i, int l , int j) { - return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(Ea+2*Ec+Eb+ED3_new(i,j,i+1)+auPenalty(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; + return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; } double UPM_ijs2h(int i, int h , int j) { - return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(Ea+2*Ec+(h-i-1)*Eb)/RT))/upm[i][j]; + return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j]; } double UPM_ijhl_case1(int i, int h, int l, int j) { - return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0; + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0; } double UPM_ijhl_case2(int i, int h, int l, int j) { - return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0; + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0; } // u1d : case 1 double U1D_ij_il_case1(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*Eb/RT)))/u1d[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*EB_new()/RT)))/u1d[i][j]:0; } // u1d : case 2 double U1D_ij_il_case2(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+Eb)/RT)*u1[l+2][j]))/u1d[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+EB_new())/RT)*u1[l+2][j]))/u1d[i][j]:0; } // u1d : case 3 double U1D_ij_il_case3(int i, int l, int j) { - return feasible(i,l)?(up[i][l]*exp((-1)*(Ec+auPenalty(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0; + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0; } // u1 @@ -157,40 +170,43 @@ double U1_ij(int i, int j) // u1 : sample h double U1_ij_s3h(int i, int h, int j) { - return (s3[h][j] * exp((-1)*(Ec+(h-i)*Eb)/RT))/u1[i][j]; + return (s3[h][j] * exp((-1)*(EC_new()+(h-i)*EB_new())/RT))/u1[i][j]; } // u1 : sample l double U1_j_hl_case1(int h, int l, int j) { - return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*Eb)/RT))) /s3[h][j]:0; + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*EB_new())/RT))) /s3[h][j]:0; } double U1_j_hl_case2(int h, int l, int j) { - return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+Eb)/RT)*u1[l+2][j])) /s3[h][j]:0; + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+EB_new())/RT)*u1[l+2][j])) /s3[h][j]:0; } double U1_j_hl_case3(int h, int l, int j) { - return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0; + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0; } void rnd_u(int i, int j, int* structure) { double rnd = randdouble(); double cum_prob = 0.0; + cum_prob += U_0(i,j); if (rnd < cum_prob) { //set_single_stranded(i,j, structure); + //energy += 0; return; } cum_prob += U_ij(i, j); if (rnd < cum_prob) { + energy += auPenalty_new(i,j); base_pair bp(i,j,UP); g_stack.push(bp); return; @@ -201,6 +217,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_hj(i,h,j); if (rnd < cum_prob) { + energy += ED5_new(h,j,h-1)+auPenalty_new(h,j); base_pair bp(h,j,UP); //set_single_stranded(i,h-1,structure); g_stack.push(bp); @@ -226,6 +243,7 @@ void rnd_u(int i, int j, int* structure) break; } } + assert (h1 != -1) ; rnd = randdouble(); @@ -236,6 +254,7 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { //set_single_stranded(i,h1-1,structure); + energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U); g_stack.push(bp1); @@ -246,6 +265,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case2(i,h1,l,j); if (rnd < cum_prob) { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UD); @@ -257,6 +277,7 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case3(i,h1,l,j); if (rnd < cum_prob) { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j)); //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UP); @@ -264,6 +285,7 @@ void rnd_u(int i, int j, int* structure) g_stack.push(bp2); return ; } + } assert(0); } @@ -277,6 +299,7 @@ void rnd_ud(int i, int j, int* structure) cum_prob += UD_il_case1(i,l,j); if (rnd < cum_prob) { + energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1)); base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U); g_stack.push(bp1); @@ -287,6 +310,7 @@ void rnd_ud(int i, int j, int* structure) cum_prob += UD_il_case2(i,l,j); if (rnd < cum_prob) { + energy += auPenalty_new(i,l); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UD); g_stack.push(bp1); @@ -297,6 +321,7 @@ void rnd_ud(int i, int j, int* structure) cum_prob += UD_il_case3(i,l,j); if (rnd < cum_prob) { + energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j)); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UP); g_stack.push(bp1); @@ -310,28 +335,32 @@ void rnd_ud(int i, int j, int* structure) void rnd_up(int i, int j, int* structure) { double rnd = randdouble(); + double cum_prob = 0; + //printf("%d %d %1.6lf %1.6lf %1.6lf %1.6lf\n",i,j,rnd,Q_ijH(i,j),Q_ijS(i,j), Q_ijM(i,j)); assert(structure[i] == 0); assert(structure[j] == 0); set_base_pair(i,j,structure); - rnd -= Q_ijH(i,j); - if (rnd < 0) + cum_prob += Q_ijH(i,j); + if (rnd < cum_prob) { + energy += eH_new(i,j); //set_single_stranded(i+1,j-1,structure); return ; } - rnd -= Q_ijS(i,j); - if (rnd < 0) + cum_prob += Q_ijS(i,j); + if (rnd < cum_prob) { + energy += eS_new(i,j); base_pair bp(i+1,j-1,UP); g_stack.push(bp); return ; } - rnd -= Q_ijM(i,j); - if (rnd < 0) + cum_prob += Q_ijM(i,j); + if (rnd < cum_prob) { rnd_upm(i,j,structure); return; @@ -341,14 +370,17 @@ void rnd_up(int i, int j, int* structure) for (int l = h+1; l < j; ++l) { if (h == i+1 && l == j-1) continue; - rnd -= Q_ijhlBI(i,j,h,l); - if (rnd < 0) + cum_prob += Q_ijhlBI(i,j,h,l); + if (rnd < cum_prob) { + energy += eL_new(i,j,h,l); base_pair bp(h,l,UP); g_stack.push(bp); return; } } + + assert(0); } void rnd_u1(int i, int j, int* structure) @@ -370,6 +402,7 @@ void rnd_u1(int i, int j, int* structure) cum_prob += U1_ij_s3h(i,h,j); if (rnd < cum_prob) { + energy += (EC_new()+(h-i)*EB_new()); h1 = h; break; } @@ -384,6 +417,8 @@ void rnd_u1(int i, int j, int* structure) cum_prob += U1_j_hl_case1(h1,l,j); if (rnd < cum_prob) { + int tt = (j == l)?0:ED3_new(h1,l,l+1); + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new()); base_pair bp(h1,l,UP); g_stack.push(bp); return; @@ -392,6 +427,7 @@ void rnd_u1(int i, int j, int* structure) cum_prob += U1_j_hl_case2(h1,l,j); if (rnd < cum_prob) { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new()); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -402,6 +438,7 @@ void rnd_u1(int i, int j, int* structure) cum_prob += U1_j_hl_case3(h1,l,j); if (rnd < cum_prob) { + energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -409,6 +446,8 @@ void rnd_u1(int i, int j, int* structure) return; } } + + assert(0); } void rnd_u1d(int i, int j, int* structure) @@ -421,6 +460,8 @@ void rnd_u1d(int i, int j, int* structure) cum_prob += U1D_ij_il_case1(i,l,j); if (rnd < cum_prob) { + int tt = (j==l)?(0):(ED5_new(i,l,l+1)); + energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new()); base_pair bp1(i,l,UP); //set_single_stranded(l+1,j,structure); g_stack.push(bp1); @@ -430,6 +471,7 @@ void rnd_u1d(int i, int j, int* structure) cum_prob += U1D_ij_il_case2(i,l,j); if (rnd < cum_prob) { + energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new()); base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -440,6 +482,7 @@ void rnd_u1d(int i, int j, int* structure) cum_prob += U1D_ij_il_case3(i,l,j); if (rnd < cum_prob) { + energy += (EC_new()+auPenalty_new(i,l)); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -447,6 +490,8 @@ void rnd_u1d(int i, int j, int* structure) return; } } + + assert(0); } void rnd_upm(int i, int j, int* structure) @@ -459,6 +504,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip1l_case1(i,l,j); if (rnd < cum_prob) { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ; base_pair bp1(i+1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp2); @@ -469,6 +515,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip1l_case2(i,l,j); if (rnd < cum_prob) { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l)); base_pair bp1(i+1,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp2); @@ -482,6 +529,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip2l_case1(i,l,j); if (rnd < cum_prob) { + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new()); base_pair bp1(i+2,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp2); @@ -492,6 +540,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip2l_case2(i,l,j); if (rnd < cum_prob) { + energy += EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l); base_pair bp1(i+2,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp1); @@ -499,17 +548,18 @@ void rnd_upm(int i, int j, int* structure) return ; } } - int h1 = -1; for (int h = i+3; h < j-1; ++h) { cum_prob += UPM_ijs2h(i,h,j); - if (rnd < cum_prob) + if (rnd < cum_prob ) { + energy += (ED3_new(i,j,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); h1 = h; break; } } + assert(h1!=-1); rnd = randdouble(); cum_prob = 0; @@ -518,6 +568,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ijhl_case1(i,h1,l,j); if (rnd < cum_prob) { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp1); @@ -528,6 +579,7 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ijhl_case2(i,h1,l,j); if (rnd < cum_prob) { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp1); @@ -535,13 +587,15 @@ void rnd_upm(int i, int j, int* structure) return; } } + assert(0); } -void rnd_structure(int* structure, int len) +double rnd_structure(int* structure, int len) { srand(rand()); base_pair first(1,len,U); g_stack.push(first); + energy = 0; while (!g_stack.empty()) { @@ -561,6 +615,7 @@ void rnd_structure(int* structure, int len) rnd_u1d(bp.i,bp.j,structure); } + return (double)energy/100.0; } void set_single_stranded(int i, int j, int* structure) @@ -572,9 +627,7 @@ void set_single_stranded(int i, int j, int* structure) void set_base_pair(int i, int j, int* structure) { bool cond = j-i > TURN && canPair(RNA[i],RNA[j]); - //if (cond == false) printf("UP(%d %d) = %lf \n",i,j,up[i][j]); assert(cond); - // printf("PAIRING %d %d\n",i,j); structure[i] = j; structure[j] = i; } From c008412a78ff920cd5c33f23097edea4931918b5 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 19 Oct 2011 23:41:30 -0400 Subject: [PATCH 170/187] fixes to sampling algorithm --- gtfold-mfe/src/main.cc | 33 ++++++++++++- gtfold-mfe/src/stochastic-sampling.cc | 71 ++++++++++++++++++++++++--- 2 files changed, 95 insertions(+), 9 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 1d5e1e3..0ecb57e 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -303,6 +303,7 @@ int main(int argc, char** argv) { int* structure = new int[seq.length()+1]; srand(time(NULL)); + std::map > uniq_structs; if (num_rnd > 0 ) { printf("\nSampling structures...\n"); @@ -320,9 +321,39 @@ int main(int argc, char** argv) { ensemble[structure[i]] = ')'; } } - std::cout << ensemble.substr(1) << ' ' << energy << std::endl; + std::map >::iterator iter ; + if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) + { + std::pair& pp = iter->second; + pp.first++; + } + else { + uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); + } + //std::cout << ensemble.substr(1) << ' ' << energy << std::endl; } } + + int pcount = 0; + int maxCount = 0; std::string bestStruct; + double bestE = INFINITY; + + std::map >::iterator iter ; + for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) + { + const std::string& ss = iter->first; + const std::pair& pp = iter->second; + // printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); + pcount += pp.first; + if (pp.first > maxCount) + { + maxCount = pp.first; + bestStruct = ss; + bestE = pp.second; + } + } + assert(num_rnd == pcount); + printf("Most favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); free_partition(); free_fold(seq.length()); diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index a311e10..a9b962f 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -5,8 +5,11 @@ #include #include +int ss_verbose = 0; + std::stack g_stack; -int energy = 0; + +double energy = 0; double randdouble() { @@ -118,18 +121,18 @@ double UPM_ip1l_case2(int i, int l, int j) double UPM_ip2l_case1(int i, int l , int j) { - return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0; + return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0; } double UPM_ip2l_case2(int i, int l , int j) { - return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; + return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; } double UPM_ijs2h(int i, int h , int j) { - return exp((-1)*ED3_new(i,j,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j]; + return exp((-1)*ED3_new(j,i,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j]; } @@ -207,6 +210,8 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { energy += auPenalty_new(i,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,auPenalty_new(i,j)/100.0); base_pair bp(i,j,UP); g_stack.push(bp); return; @@ -218,6 +223,8 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { energy += ED5_new(h,j,h-1)+auPenalty_new(h,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h,j,h-1)+auPenalty_new(h,j)) /100.0); base_pair bp(h,j,UP); //set_single_stranded(i,h-1,structure); g_stack.push(bp); @@ -255,6 +262,8 @@ void rnd_u(int i, int j, int* structure) { //set_single_stranded(i,h1-1,structure); energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U); g_stack.push(bp1); @@ -266,6 +275,8 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UD); @@ -278,6 +289,8 @@ void rnd_u(int i, int j, int* structure) if (rnd < cum_prob) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j))/100.0); //set_single_stranded(i,h1-1,structure); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UP); @@ -300,6 +313,8 @@ void rnd_ud(int i, int j, int* structure) if (rnd < cum_prob) { energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + ED3_new(i,l,l+1))/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U); g_stack.push(bp1); @@ -311,6 +326,8 @@ void rnd_ud(int i, int j, int* structure) if (rnd < cum_prob) { energy += auPenalty_new(i,l); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l))/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UD); g_stack.push(bp1); @@ -322,6 +339,8 @@ void rnd_ud(int i, int j, int* structure) if (rnd < cum_prob) { energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + auPenalty_new(l+1,j))/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,UP); g_stack.push(bp1); @@ -336,7 +355,6 @@ void rnd_up(int i, int j, int* structure) { double rnd = randdouble(); double cum_prob = 0; - //printf("%d %d %1.6lf %1.6lf %1.6lf %1.6lf\n",i,j,rnd,Q_ijH(i,j),Q_ijS(i,j), Q_ijM(i,j)); assert(structure[i] == 0); assert(structure[j] == 0); @@ -346,6 +364,8 @@ void rnd_up(int i, int j, int* structure) if (rnd < cum_prob) { energy += eH_new(i,j); + if (ss_verbose == 1) + printf("Hairpin(%d %d) %lf\n",i,j, (eH_new(i,j))/100.0); //set_single_stranded(i+1,j-1,structure); return ; } @@ -354,6 +374,8 @@ void rnd_up(int i, int j, int* structure) if (rnd < cum_prob) { energy += eS_new(i,j); + if (ss_verbose == 1) + printf("Stack(%d %d) %lf\n",i,j, (eS_new(i,j))/100.0); base_pair bp(i+1,j-1,UP); g_stack.push(bp); return ; @@ -374,6 +396,8 @@ void rnd_up(int i, int j, int* structure) if (rnd < cum_prob) { energy += eL_new(i,j,h,l); + if (ss_verbose == 1) + printf("IntLoop(%d %d) %lf\n",i,j, (eL_new(i,j,h,l))/100.0); base_pair bp(h,l,UP); g_stack.push(bp); return; @@ -403,6 +427,8 @@ void rnd_u1(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EC_new()+(h-i)*EB_new()); + if (ss_verbose == 1) + printf("U1_ij_s3h(%d %d) %lf\n",i,j, (EC_new()+(h-i)*EB_new())/100.0); h1 = h; break; } @@ -419,6 +445,8 @@ void rnd_u1(int i, int j, int* structure) { int tt = (j == l)?0:ED3_new(h1,l,l+1); energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case1(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0); base_pair bp(h1,l,UP); g_stack.push(bp); return; @@ -428,6 +456,8 @@ void rnd_u1(int i, int j, int* structure) if (rnd < cum_prob) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case2(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -439,6 +469,8 @@ void rnd_u1(int i, int j, int* structure) if (rnd < cum_prob) { energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l); + if (ss_verbose == 1) + printf("U1_j_hl_case3(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -462,6 +494,8 @@ void rnd_u1d(int i, int j, int* structure) { int tt = (j==l)?(0):(ED5_new(i,l,l+1)); energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) + printf("U1D_ij_il_case1(%d %d) %lf\n",i,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0); base_pair bp1(i,l,UP); //set_single_stranded(l+1,j,structure); g_stack.push(bp1); @@ -472,6 +506,8 @@ void rnd_u1d(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1D_ij_il_case2(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -483,6 +519,8 @@ void rnd_u1d(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EC_new()+auPenalty_new(i,l)); + if (ss_verbose == 1) + printf("U1D_ij_il_case3(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l))/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -498,6 +536,8 @@ void rnd_upm(int i, int j, int* structure) { double rnd = randdouble(); double cum_prob = 0; + if (ss_verbose == 1) + printf("Multiloop(%d %d)\n",i,j); for (int l = i+2; l < j; ++l) { @@ -505,6 +545,8 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ; + if (ss_verbose == 1) + printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0); base_pair bp1(i+1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp2); @@ -516,6 +558,8 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l)); + if (ss_verbose == 1) + printf("(%d %d) %s %lf\n",i,j,"UPM_ip1l_case2", (EA_new()+2*EC_new()+auPenalty_new(i+1,l))/100.0); base_pair bp1(i+1,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp2); @@ -529,7 +573,9 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip2l_case1(i,l,j); if (rnd < cum_prob) { - energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new()); + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case1", i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new())/100.0); base_pair bp1(i+2,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp2); @@ -540,7 +586,9 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ip2l_case2(i,l,j); if (rnd < cum_prob) { - energy += EA_new()+2*EC_new()+EB_new()+ED3_new(i,j,i+1)+auPenalty_new(i+2,l); + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case2",i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/100.0); base_pair bp1(i+2,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp1); @@ -554,7 +602,9 @@ void rnd_upm(int i, int j, int* structure) cum_prob += UPM_ijs2h(i,h,j); if (rnd < cum_prob ) { - energy += (ED3_new(i,j,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); + energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ijs2h",i,j,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0); h1 = h; break; } @@ -569,6 +619,8 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n","UPM_ijhl_case1",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp1); @@ -580,6 +632,8 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ijhl_case2",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp1); @@ -592,6 +646,7 @@ void rnd_upm(int i, int j, int* structure) double rnd_structure(int* structure, int len) { + //printf("%lf %lf %lf\n", EA_new(), EB_new(), EC_new()); srand(rand()); base_pair first(1,len,U); g_stack.push(first); From a1f5d30a839aea6c5a0baa2c791092e88b074ad5 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 19 Oct 2011 23:58:41 -0400 Subject: [PATCH 171/187] adding fix of Eb and Ec --- gtfold-mfe/src/partition-func.c | 163 ++++++++++++++------------------ 1 file changed, 73 insertions(+), 90 deletions(-) diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index fcd1b1d..da7649a 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -6,6 +6,7 @@ #include "algorithms-partition.h" #include "global.h" #include "utils.h" +#include //#include "options.h" double ** u; @@ -60,9 +61,9 @@ static void set_s3(int i, int j, double val); void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){ - printf(msg); + printf("%s", msg); printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal); - printf("\nprogram is exiting now due to above error\n"); + printf("%s","\nprogram is exiting now due to above error\n"); exit(-1); } @@ -112,19 +113,21 @@ double eL_new(int i, int j, int p, int q){ } double ED3_new(int i, int j, int k){ - if(PF_COUNT_MODE_) return 0; - //return Ed3(i,j,k); - return Ed5(j,i,k); - //return Ed5(i,j,k); - //return Ed3(j,i,k); + if(PF_COUNT_MODE_) return 0; + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed5(j,i,k)<0.1); + //} + return Ed5(j,i,k); } double ED5_new(int i, int j, int k){ - if(PF_COUNT_MODE_) return 0; - //return Ed5(i,j,k); + if(PF_COUNT_MODE_) return 0; + if (k<1) return 0; + + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed3(j,i,k)<0.1); + //} return Ed3(j,i,k); - //return Ed3(i,j,k); - //return Ed5(j,i,k); } double EA_new(){ @@ -134,12 +137,12 @@ double EA_new(){ double EB_new(){ if(PF_COUNT_MODE_) return 0; - return Eb; + return Ec; } double EC_new(){ if(PF_COUNT_MODE_) return 0; - return Ec; + return Eb; } double auPenalty_new(int i, int j){ @@ -189,7 +192,7 @@ printf("\n\nAfter calculation, s3 matrix:\n\n"); void calculate_partition(int len, int pf_count_mode) {printf("RT=%f\n",RT);//RT=RT/100; PF_COUNT_MODE_ = pf_count_mode; - int i, j; + //int i, j; part_len = len; create_partition_arrays(); init_partition_arrays(); @@ -448,38 +451,34 @@ void calc_s1(int h, int j)//ERROR_FOUND s1[h][j]= instead of += void calc_s2(int h, int j) -{//printf("Entering calc_s2: h=%d, j =%d\n",h,j); +{ int l; double s2_val = 0.0; for (l = h+1; l < j; ++l)//ERROR - {//printf("In calc_s2 loop: get_up(h,l)=%.3f second term=%.3f third term=%.3f\n",get_up(h,l),(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)),(myExp(-ED3_new(h,l,l+1)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1))); + { double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); double v2 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j-1)); double v3 = get_u1d(l+1,j-1); double val = v1*(v2+v3); - //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)) * (myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j-1)+get_u1d(l+1,j-1)); - s2_val += val;//Error: Eb is added + s2_val += val;//Error: Eb is added } - set_s2(h, j, s2_val);//s2[h][j] = s2_val; -//printf("Exiting calc_s2: h=%d, j =%d, val=%.3f\n",h,j,s2[h][j]); + set_s2(h, j, s2_val); } void calc_s3(int h, int j) -{//printf("Entering calc_s3: h=%d, j =%d\n",h,j); +{ int l; double s3_val = 0.0; for (l = h+1; l <= j && l+2<=part_len; ++l)//ERROR in for loop variable l { - double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); - double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT)); - double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j)); - double v4 = get_u1d(l+1,j); - double val = v1*(v2+v3+v4); - //double val = get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))*(f(j+1,h,l)*myExp(-((j-l)*Eb)/RT) + myExp(-(ED3_new(h,l,l+1)+Eb)/RT)*get_u1(l+2,j) + get_u1d(l+1,j)); - s3_val += val; + double v1 = (get_up(h,l)*(myExp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))); + double v2 = (f(j+1,h,l)*myExp(-((j-l)*EB_new())/RT)); + double v3 = (myExp(-(ED3_new(h,l,l+1)+EB_new())/RT)*get_u1(l+2,j)); + double v4 = get_u1d(l+1,j); + double val = v1*(v2+v3+v4); + s3_val += val; } set_s3(h, j, s3_val);//s3[h][j] = s3_val; -//printf("Exiting calc_s3: h=%d, j =%d, val=%.3f\n",h,j,s3[h][j]); } void create_partition_arrays() @@ -542,35 +541,33 @@ void free_partition_arrays() }*/ void calc_upm(int i, int j){//printf("Entering calc_upm: i=%d, j =%d\n",i,j); - double a = EA_new(); - double b = EB_new(); - double c = EC_new(); - double p_val = 0; - int l,h; - double quadraticSum = 0; + double a = EA_new(); + double b = EB_new(); + double c = EC_new(); + double p_val = 0; + int l,h; + double quadraticSum = 0; if (canPair(RNA[i],RNA[j])) { - for(l=i+2; l maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;} - } + int h,l; + double maxIntLoopProb = 0.0; + int h_max=-1, l_max=-1; + double sum=0.0; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + //if((l-h)<=TURN) continue; + double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j]; + sum+=intLoopProb; + if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;} } + } - //ERROR below line should not be there - //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); - double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j]; - double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j]; - double upmProb = get_upm(i,j)/up[i][j]; + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j]; + double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j]; + double upmProb = get_upm(i,j)/up[i][j]; - if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT "); - else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL "); - else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK "); - else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM "); + if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT "); + else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL "); + else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK "); + else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM "); -printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f, sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max); + printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f, sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max); } void calc_up(int i, int j) {//printf("Entering calc_up: i=%d, j =%d\n",i,j); double up_val = 0.0; - int p,q; + //int p,q; if (canPair(RNA[i],RNA[j]))// if(j-i>TURN) { - /*for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - int maxq = (p==(i+1))?(j-2):(j-1); - - for (q = minq; q <= maxq; q++) { - if (canPair(p,q)==0) continue; - up_val += (get_up(p,q) * myExp(-eL_new(i,j,p,q)/RT)); - } - }*/ - int h,l; + int h,l; for (h = i+1; h < j ; h++) { for (l = h+1; l < j; l++) { if (canPair(RNA[h],RNA[l])==0) continue; - if(h==(i+1) && l==(j-1)) continue; - //if((l-h)<=TURN) continue; + if(h==(i+1) && l==(j-1)) continue; up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT)); } } - //ERROR below line should not be there + //ERROR below line should not be there //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); up_val = up_val + myExp(-((double)eH_new(i,j))/RT ); up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1)); up_val = up_val + get_upm(i,j); set_up(i, j, up_val);//up[i][j] = up_val; - //printUPprobabilities(i,j); + } else { set_up(i, j, 0.0);//up[i][j] = 0; } -//printf("Exiting calc_up: i=%d, j =%d, val=%.3f\n",i,j,up[i][j]); } - - From ea006938011a19b85853794ea86debc90c2f3ec2 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 21 Oct 2011 18:16:40 -0400 Subject: [PATCH 172/187] fix RT scaling factor --- gtfold-mfe/src/energy.c | 2 +- gtfold-mfe/src/main.cc | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 314d35a..7ac6fbe 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -18,7 +18,7 @@ int *indx; int **PP; int alloc_flag = 0; -const float RT = ((0.00198721 * 310.15)*10000); //* 100.00); +const float RT = ((0.00198721 * 310.15)*100); //* 100.00); void create_tables(int len) { V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 0ecb57e..30e1eab 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -343,7 +343,7 @@ int main(int argc, char** argv) { { const std::string& ss = iter->first; const std::pair& pp = iter->second; - // printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); + // printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); pcount += pp.first; if (pp.first > maxCount) { From 2d8a3299320cda0a0108e3062261c74c76dba350 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 21 Oct 2011 18:25:17 -0400 Subject: [PATCH 173/187] print sampling probablities --- gtfold-mfe/src/main.cc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 30e1eab..99a8f91 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -343,7 +343,7 @@ int main(int argc, char** argv) { { const std::string& ss = iter->first; const std::pair& pp = iter->second; - // printf("%s\tp=%lf, e=%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); + printf("%s\t%lf\t%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); pcount += pp.first; if (pp.first > maxCount) { @@ -353,7 +353,7 @@ int main(int argc, char** argv) { } } assert(num_rnd == pcount); - printf("Most favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); free_partition(); free_fold(seq.length()); From c8b8ccd2386987d5884f39b18c7fa8fcd327c71f Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 26 Oct 2011 10:46:06 -0400 Subject: [PATCH 174/187] added boltzmann prob calculation --- gtfold-mfe/src/energy.c | 1 + gtfold-mfe/src/main.cc | 26 ++++++++++++++++++++++++-- gtfold-mfe/src/partition-func.c | 4 +++- 3 files changed, 28 insertions(+), 3 deletions(-) diff --git a/gtfold-mfe/src/energy.c b/gtfold-mfe/src/energy.c index 7ac6fbe..a4259bd 100644 --- a/gtfold-mfe/src/energy.c +++ b/gtfold-mfe/src/energy.c @@ -19,6 +19,7 @@ int **PP; int alloc_flag = 0; const float RT = ((0.00198721 * 310.15)*100); //* 100.00); +const float RT_ = (0.00198721 * 310.15); void create_tables(int len) { V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 99a8f91..014ce16 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -299,11 +299,12 @@ int main(int argc, char** argv) { printf("\nComputing partition function...\n"); int pf_count_mode = 0; if(PF_COUNT_MODE) pf_count_mode=1; - calculate_partition(seq.length(),pf_count_mode); + double U = calculate_partition(seq.length(),pf_count_mode); int* structure = new int[seq.length()+1]; srand(time(NULL)); std::map > uniq_structs; + std::map energy_freq;; if (num_rnd > 0 ) { printf("\nSampling structures...\n"); @@ -330,6 +331,15 @@ int main(int argc, char** argv) { else { uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); } + + std::map::iterator iter1 ; + if ((iter1 = energy_freq.find(energy)) != energy_freq.end()) { + int& freq = iter1->second; + ++freq; + } + else { + energy_freq.insert(make_pair(energy,1)); + } //std::cout << ensemble.substr(1) << ' ' << energy << std::endl; } } @@ -343,7 +353,11 @@ int main(int argc, char** argv) { { const std::string& ss = iter->first; const std::pair& pp = iter->second; - printf("%s\t%lf\t%lf\n",ss.c_str(),(double)pp.first/(double)num_rnd,pp.second); + const double& estimated_p = (double)pp.first/(double)num_rnd; + const double& energy = pp.second; + double actual_p = pow(2.718281,-1.0*energy/RT_)/U; + + printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p); pcount += pp.first; if (pp.first > maxCount) { @@ -355,6 +369,14 @@ int main(int argc, char** argv) { assert(num_rnd == pcount); printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + std::map::iterator iter1 ; + int eCount = 0; + for (iter1 = energy_freq.begin(); iter1 != energy_freq.end(); ++iter1) { + eCount += iter1->second; + //printf("%4.6f\t%0.6f\t%d\n",iter1->first,(double)iter1->second/(double)num_rnd,iter1->second); + } + assert(num_rnd == eCount); + free_partition(); free_fold(seq.length()); delete [] structure; diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c index da7649a..4547364 100644 --- a/gtfold-mfe/src/partition-func.c +++ b/gtfold-mfe/src/partition-func.c @@ -189,7 +189,7 @@ printf("\n\nAfter calculation, s3 matrix:\n\n"); } -void calculate_partition(int len, int pf_count_mode) +double calculate_partition(int len, int pf_count_mode) {printf("RT=%f\n",RT);//RT=RT/100; PF_COUNT_MODE_ = pf_count_mode; //int i, j; @@ -212,6 +212,8 @@ void calculate_partition(int len, int pf_count_mode) //printAllMatrixes(); printf("%4.4f\n",u[1][part_len]); + + return u[1][part_len]; } void free_partition() From ded86f0ebc7a8952d22bee98f523462e2e595ed3 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Wed, 26 Oct 2011 11:03:11 -0400 Subject: [PATCH 175/187] changed part func to return U --- gtfold-mfe/include/energy.h | 1 + gtfold-mfe/include/partition-func.h | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index b4beeb3..30d3fd3 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -21,6 +21,7 @@ extern int **PP; #define VBI(i,j) VBI[indx[j]+i] //#define RT ((0.00198721 * 310.15) * 100.00) extern const float RT; +extern const float RT_; #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h index b2e8c80..e9bdffa 100644 --- a/gtfold-mfe/include/partition-func.h +++ b/gtfold-mfe/include/partition-func.h @@ -30,7 +30,7 @@ double eL_new(int i, int j, int p, int q); double eH_new(int i, int j); double auPenalty_new(int i, int j); double f(int j, int h, int l); -void calculate_partition(int len, int pf_count_mode); +double calculate_partition(int len, int pf_count_mode); void free_partition(); #ifdef __cplusplus From 3f7c982e637742f713fef4d8146edb70c31a459e Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Tue, 1 Nov 2011 23:23:36 -0400 Subject: [PATCH 176/187] fixed energy traceback --- gtfold-mfe/src/main.cc | 106 +++++++++++--------------- gtfold-mfe/src/stochastic-sampling.cc | 42 +++++----- 2 files changed, 64 insertions(+), 84 deletions(-) diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 014ce16..f5dbc21 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -304,24 +304,24 @@ int main(int argc, char** argv) { int* structure = new int[seq.length()+1]; srand(time(NULL)); std::map > uniq_structs; - std::map energy_freq;; - - if (num_rnd > 0 ) { - printf("\nSampling structures...\n"); - for (int count = 1; count <= num_rnd; ++count) - { - memset(structure, 0, (seq.length()+1)*sizeof(int)); - double energy = rnd_structure(structure, seq.length()); - - std::string ensemble(seq.length()+1,'.'); - for (int i = 1; i <= (int)seq.length(); ++ i) { - // printf("%d %d\n",i,structure[i]); - if (structure[i] > 0 && ensemble[i] == '.') - { - ensemble[i] = '('; - ensemble[structure[i]] = ')'; - } - } + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + + for (int count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (seq.length()+1)*sizeof(int)); + double energy = rnd_structure(structure, seq.length()); + + std::string ensemble(seq.length()+1,'.'); + for (int i = 1; i <= (int)seq.length(); ++ i) { + // printf("%d %d\n",i,structure[i]); + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } std::map >::iterator iter ; if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) { @@ -331,53 +331,35 @@ int main(int argc, char** argv) { else { uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); } + // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; + } - std::map::iterator iter1 ; - if ((iter1 = energy_freq.find(energy)) != energy_freq.end()) { - int& freq = iter1->second; - ++freq; - } - else { - energy_freq.insert(make_pair(energy,1)); - } - //std::cout << ensemble.substr(1) << ' ' << energy << std::endl; - } - } - - int pcount = 0; - int maxCount = 0; std::string bestStruct; - double bestE = INFINITY; - - std::map >::iterator iter ; - for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) - { - const std::string& ss = iter->first; - const std::pair& pp = iter->second; - const double& estimated_p = (double)pp.first/(double)num_rnd; - const double& energy = pp.second; - double actual_p = pow(2.718281,-1.0*energy/RT_)/U; - - printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p); - pcount += pp.first; - if (pp.first > maxCount) + int pcount = 0; + int maxCount = 0; std::string bestStruct; + double bestE = INFINITY; + + std::map >::iterator iter ; + for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) { - maxCount = pp.first; - bestStruct = ss; - bestE = pp.second; + const std::string& ss = iter->first; + const std::pair& pp = iter->second; + const double& estimated_p = (double)pp.first/(double)num_rnd; + const double& energy = pp.second; + double actual_p = pow(2.718281,-1.0*energy/RT_)/U; + + printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p); + pcount += pp.first; + if (pp.first > maxCount) + { + maxCount = pp.first; + bestStruct = ss; + bestE = pp.second; + } } - } - assert(num_rnd == pcount); - printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); - - std::map::iterator iter1 ; - int eCount = 0; - for (iter1 = energy_freq.begin(); iter1 != energy_freq.end(); ++iter1) { - eCount += iter1->second; - //printf("%4.6f\t%0.6f\t%d\n",iter1->first,(double)iter1->second/(double)num_rnd,iter1->second); - } - assert(num_rnd == eCount); - - free_partition(); + assert(num_rnd == pcount); + printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + } + free_partition(); free_fold(seq.length()); delete [] structure; exit(0); diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index a9b962f..bdc9ee9 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -201,8 +201,6 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_0(i,j); if (rnd < cum_prob) { - //set_single_stranded(i,j, structure); - //energy += 0; return; } @@ -260,7 +258,6 @@ void rnd_u(int i, int j, int* structure) cum_prob += U_ihlj_case1(i,h1,l,j); if (rnd < cum_prob) { - //set_single_stranded(i,h1-1,structure); energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); if (ss_verbose == 1) printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0); @@ -277,7 +274,7 @@ void rnd_u(int i, int j, int* structure) energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); if (ss_verbose == 1) printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); - //set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,UD); g_stack.push(bp1); @@ -428,7 +425,7 @@ void rnd_u1(int i, int j, int* structure) { energy += (EC_new()+(h-i)*EB_new()); if (ss_verbose == 1) - printf("U1_ij_s3h(%d %d) %lf\n",i,j, (EC_new()+(h-i)*EB_new())/100.0); + printf("U1_ij_s3h(%d) %lf\n",h, (EC_new()+(h-i)*EB_new())/100.0); h1 = h; break; } @@ -446,7 +443,7 @@ void rnd_u1(int i, int j, int* structure) int tt = (j == l)?0:ED3_new(h1,l,l+1); energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new()); if (ss_verbose == 1) - printf("U1_j_hl_case1(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0); + printf("U1_j_hl_case1(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0); base_pair bp(h1,l,UP); g_stack.push(bp); return; @@ -457,7 +454,7 @@ void rnd_u1(int i, int j, int* structure) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new()); if (ss_verbose == 1) - printf("U1_j_hl_case2(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0); + printf("U1_j_hl_case2(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -470,7 +467,7 @@ void rnd_u1(int i, int j, int* structure) { energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l); if (ss_verbose == 1) - printf("U1_j_hl_case3(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + printf("U1_j_hl_case3(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -492,12 +489,12 @@ void rnd_u1d(int i, int j, int* structure) cum_prob += U1D_ij_il_case1(i,l,j); if (rnd < cum_prob) { - int tt = (j==l)?(0):(ED5_new(i,l,l+1)); + int tt = (j==l)?(0):(ED3_new(i,l,l+1)); energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new()); - if (ss_verbose == 1) - printf("U1D_ij_il_case1(%d %d) %lf\n",i,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0); + if (ss_verbose == 1) { + printf("U1D_ij_il_case1(%d %d %d) %lf\n",i,l,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0); + } base_pair bp1(i,l,UP); - //set_single_stranded(l+1,j,structure); g_stack.push(bp1); return; } @@ -507,7 +504,7 @@ void rnd_u1d(int i, int j, int* structure) { energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new()); if (ss_verbose == 1) - printf("U1D_ij_il_case2(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0); + printf("U1D_ij_il_case2(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+2,j,U1); g_stack.push(bp1); @@ -520,7 +517,7 @@ void rnd_u1d(int i, int j, int* structure) { energy += (EC_new()+auPenalty_new(i,l)); if (ss_verbose == 1) - printf("U1D_ij_il_case3(%d %d) %lf\n",i,j, (EC_new()+auPenalty_new(i,l))/100.0); + printf("U1D_ij_il_case3(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l))/100.0); base_pair bp1(i,l,UP); base_pair bp2(l+1,j,U1D); g_stack.push(bp1); @@ -528,7 +525,6 @@ void rnd_u1d(int i, int j, int* structure) return; } } - assert(0); } @@ -537,7 +533,7 @@ void rnd_upm(int i, int j, int* structure) double rnd = randdouble(); double cum_prob = 0; if (ss_verbose == 1) - printf("Multiloop(%d %d)\n",i,j); + printf("Multiloop (%d %d)\n",i,j); for (int l = i+2; l < j; ++l) { @@ -545,8 +541,9 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob) { energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ; - if (ss_verbose == 1) + if (ss_verbose == 1) { printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0); + } base_pair bp1(i+1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp2); @@ -603,9 +600,10 @@ void rnd_upm(int i, int j, int* structure) if (rnd < cum_prob ) { energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); - if (ss_verbose == 1) - printf("%s(%d %d) %lf\n", "UPM_ijs2h",i,j,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0); h1 = h; + if (ss_verbose == 1) { + printf("%s(%d) %lf\n", "UPM_ijs2h",h1,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0); + } break; } } @@ -620,7 +618,7 @@ void rnd_upm(int i, int j, int* structure) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); if (ss_verbose == 1) - printf("%s(%d %d) %lf\n","UPM_ijhl_case1",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0); + printf("%s(%d %d) %lf\n","UPM_ijhl_case1",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+2,j-1,U1); g_stack.push(bp1); @@ -633,7 +631,7 @@ void rnd_upm(int i, int j, int* structure) { energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); if (ss_verbose == 1) - printf("%s(%d %d) %lf\n", "UPM_ijhl_case2",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + printf("%s(%d %d) %lf\n", "UPM_ijhl_case2",h1,l,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); base_pair bp1(h1,l,UP); base_pair bp2(l+1,j-1,U1D); g_stack.push(bp1); @@ -650,7 +648,7 @@ double rnd_structure(int* structure, int len) srand(rand()); base_pair first(1,len,U); g_stack.push(first); - energy = 0; + energy = 0.0; while (!g_stack.empty()) { From 29cc8073c91c784f23532a932b63d37fe0e08644 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 4 Nov 2011 11:52:41 -0700 Subject: [PATCH 177/187] Implementation of Unique Multiloop Decomposition --- gtfold-mfe/include/subopt_traceback.h | 11 +- gtfold-mfe/src/main.cc | 2 +- gtfold-mfe/src/subopt_traceback.cc | 262 +++++++++++++++++++++++++- 3 files changed, 267 insertions(+), 8 deletions(-) diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h index fd819b6..2ab2241 100644 --- a/gtfold-mfe/include/subopt_traceback.h +++ b/gtfold-mfe/include/subopt_traceback.h @@ -30,7 +30,9 @@ #include #include -enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime}; +#define UNIQUE_MULTILOOP_DECOMPOSITION + +enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime, lM, lM1}; extern const char* lstr[]; struct segment @@ -177,7 +179,7 @@ struct pstruct return st_v.empty(); } - void print() + void print() const { SEGSTACK st = st_segment; std::cout <<'[' << ' ' ; @@ -225,4 +227,9 @@ void traceWM(int i, int j, ps_t & ps, ps_stack_t & gs); void traceWMPrime(int i, int j, ps_t & ps, ps_stack_t & gs); //void traceWM(ps_t& ps, ps_map_t& filter); +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION +void traceM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceM1(int i, int j, ps_t & ps, ps_stack_t & gs); +#endif + #endif diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 89ba476..67e8a1b 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -225,7 +225,7 @@ void save_subopt_file(string outputFile, ss_map_t& ss_data, { ofstream outfile; outfile.open(outputFile.c_str()); - char buff[1024]; + char buff[4096]; sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0); outfile << buff << std::endl; diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index b27b059..150d6bc 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -28,18 +28,102 @@ along with this program. If not, see . #include "global.h" #include "subopt_traceback.h" +#include +#include +#include + //#define DEBUG 1 -const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime"}; +using std::pair; +using std::cout; +using std::endl; + +const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime", "fm", "fm1"}; -void (*trace_func[6]) (int i, int j, ps_t& ps, ps_stack_t& gs); +void (*trace_func[8]) (int i, int j, ps_t& ps, ps_stack_t& gs); static int delta = 0; static int mfe = INFINITY_; static int length = -1; static int gflag = 0; +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + +static int FM1[1500][1500] = {{0}}; +static int FM[1500][1500] = {{0}}; + +static inline int Ed5_new(int i, int j, int k) { + return (k!=0) ? Ed3(j, i, k) : Ed3(j,i,length); +} + +static inline int Ed3_new(int i, int j, int k) { + return (k!=length+1)?Ed5(j, i, k) : Ed5(j, i, 1); +} + +void calculate_fm1() { + + //printf("length %d\n", length); + //printf("Ea: %d , Eb: %d , Ec: %d\n", Ea, Eb, Ec); + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length; ++j) { + //printf("\nFinding FM1[%d][%d]\n", i, j); + int min = INFINITY_; + for (int l = i+TURN+1; l <= j; ++l) { + int d5 = Ed5_new(i,l,i-1); + int d3 = Ed3_new(i,l,l+1); + + int fm1 = V(i,l) + auPenalty(i,l) + d5 + d3 + Ec*(j-l) + Eb; + + //printf("l: %d\n", l); + //printf("V(%d, %d): %d, auPenalty: %d, Ed3(%d, %d, %d): %d, Ed5(%d, %d, %d): %d\n", + // i, l, V(i,l), + // auPenalty(i,l), + // i, l, i-1, d5, + // i, l, l+1, d3 + // ); + //printf("min: %d, fm1: %d, final_min: %d\n", min, fm1, MIN(min,fm1)); + min = MIN(min, fm1); + } + FM1[i][j] = min; + //printf("Value: %d ", FM1[i][j]); + } + //printf("\n"); + } + +} + +void calculate_fm() { + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length;++j) { + int min1 = INFINITY_; + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + int x = FM[i][k-1] + FM1[k][j]; + min1 = MIN(min1, x); + } + int min2 = INFINITY_; + for (int k = i; k <= j-TURN-1; ++k) { + int x = FM1[k][j] + Ec*(k-i); + min2 = MIN(min2, x); + } + FM[i][j] = MIN(min1, min2); + //printf("%d %d %d ", i, j, FM[i][j]); + } + //printf("\n"); + } +} + +#endif + void process(ss_map_t& subopt_data, int len) { int count = 0; + length = len; + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + calculate_fm1(); + calculate_fm(); +#endif + ps_stack_t gstack; @@ -55,7 +139,13 @@ void process(ss_map_t& subopt_data, int len) { if (ps.empty()) { count++; - subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + //pair ins_result; + // ins_result = subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + //if (ins_result.second == false) { + //printf("Duplicate Structure!!!"); + // exit(1); + //} + cout << ps.str << endl; continue; } else { @@ -76,7 +166,7 @@ void process(ss_map_t& subopt_data, int len) { } #ifdef DEBUG - printf("# SS = %d\n", count); + //printf("# SS = %d\n", count); #endif } @@ -87,6 +177,10 @@ ss_map_t subopt_traceback(int len, int _delta) { trace_func[3] = traceVM; trace_func[4] = traceWM; trace_func[5] = traceWMPrime; +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + trace_func[6] = traceM; + trace_func[7] = traceM1; +#endif mfe = W[len]; delta = _delta; @@ -99,8 +193,11 @@ ss_map_t subopt_traceback(int len, int _delta) { } void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("V %d %d\n", i, j); // Hairpin Loop if (eH(i,j) + ps.total() <= mfe + delta) { + //printf("hairpin\n"); ps_t ps1(ps); ps1.accumulate(eH(i,j)); ps1.update(i, j, '(', ')'); @@ -109,6 +206,7 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { // Stack if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { + //printf("stack %d %d %d %d\n", i, j, eS(i,j), V(i+1,j-1)); ps_t ps1(ps); ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); ps1.accumulate(eS(i,j)); @@ -118,16 +216,56 @@ void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { // Internal Loop if (VBI(i,j) + ps.total() <= mfe + delta) { + //printf("internal loop\n"); traceVBI(i,j,ps,gstack); } +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + int k; + + for (k = i+2; k <= j-TURN-1; ++k) { + + int kenergy1 = FM[i+1][k] + FM1[k+1][j-1]; + int d5 = Ed5(i, j, i+1); + int d3 = Ed3(i, j, j-1); + int aup = auPenalty(i,j); + int kenergy2 = d5 + d3 + aup + Ea + Eb; + int kenergy_total = kenergy1 + kenergy2; + if (i == 4 && j == 41) { + //printf("ps: "); + ps.print(); + //printf("\n"); + } + //printf("FM[%d][%d]: %d FM1[%d][%d]: %d\n", i+1, k, FM[i+1][k], k+1, j-1, FM1[k+1][j-1]); + //printf("Ed3(%d, %d, %d): %d Ed5(%d, %d, %d): %d Ea: %d\n", + // i,j,i+1, Ed5_new(i,j,i+1), i, j, j-1, Ed3_new(i,j,j-1), Ea); + //printf("Ed5(%d, %d, %d): %d Ed3(%d, %d, %d): %d Ea: %d %d %d\n", + // i,j,i+1, Ed5(i,j,i+1), i, j, i+1, Ed3(i,j,j-1), Ea, auPenalty(i,j), Eb); + //printf("kenergy_total: %d ps.total(): %d mfe+delta: %d i: %d j: %d k: %d\n", kenergy_total, + // ps.total(), mfe+delta, i, j, k); + if (kenergy_total + ps.total() <= mfe + delta) { + //printf("multiloop\n"); + ps_t ps1(ps); + ps1.push(segment(i+1,k, lM, FM[i+1][k])); + ps1.push(segment(k+1,j-1, lM1, FM1[k+1][j-1])); + ps1.accumulate(kenergy2); + ps1.update(i,j,'(',')'); + //printf("auPenalty: %d\n", auPenalty(i,j)); + push_to_gstack(gstack, ps1); + } + } +#else + // Multiloop - if ( VM(i,j) + ps.total() <= mfe + delta) { + if (VM(i,j) + ps.total() <= mfe + delta) { ps_t ps1(ps); ps1.push(segment(i, j, lVM, VM(i,j))); ps1.update(i, j, '(', ')'); push_to_gstack(gstack, ps1); } + +#endif + } void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { @@ -151,6 +289,7 @@ void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) { + //printf("W %d %d\n", i, j); for (int l = i; l < j-TURN; ++l) { int wim1 = MIN(0, W[l-1]); int d3 = (l>i)?Ed3(j,l,l-1):0; @@ -173,10 +312,118 @@ void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) { } } +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION +void traceM1(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("M1 %d %d\n", i, j); + //if (i == 14) + //printf("%d %d\n", FM1[i][j-1], FM1[i][j-1] + Ec + ps.total()); + + if (FM1[i][j-1] + Ec + ps.total() <= mfe + delta) { + //printf("here1\n"); + ps_t ps1(ps); + ps1.push(segment(i, j-1, lM1, FM1[i][j-1])); + ps1.accumulate(Ec); + push_to_gstack(gstack, ps1); + } + + //printf("V(i,j):%d Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1)); + int d5; + int d3; + int aup; + //d5 = (i != 1) ? Ed5(i,j,i-1) : Ed5(i,j,length); + //d3 = (j != length) ? Ed3(i,j,j+1) : Ed3(i,j,1); + d5 = Ed5_new(i, j, i-1); + d3 = Ed3_new(i, j, j+1); + aup = auPenalty(i,j); + + if (V(i,j) + d5 + d3 + aup + Eb + ps.total() <= mfe + delta) { + //printf("here2\n"); + ps_t ps1(ps); + ps1.push(segment(i, j, lV, V(i,j))); + ps1.accumulate(d5 + d3 + aup + Eb); + ps1.update(i,j,'(',')'); + //printf("auPenalty: %d\n", auPenalty(i,j)); + push_to_gstack(gstack, ps1); + } +} + +void traceM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("M %d %d\n", i, j); + int d5, d3; + int aup; + + if (FM[i][j-1] + Ec + ps.total() <= mfe + delta) { + //printf("here11\n"); + ps_t ps1(ps); + ps1.push(segment(i, j-1, lM, FM[i][j-1])); + ps1.accumulate(Ec); + push_to_gstack(gstack, ps1); + } + + //printf("V(i,j):%d Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1)); + //d5 = (i != 1) ? Ed3(i,j,i-1) : Ed3(i,j,length); + //d3 = (j != length) ? Ed5(i,j,j+1) : Ed5(i,j,1); + d5 = Ed5_new(i, j, i-1); + d3 = Ed3_new(i, j, j+1); + aup = auPenalty(i,j); + if (V(i,j) + d5 + d3 + Eb + aup + ps.total() <= mfe + delta) { + //printf("here12\n"); + ps_t ps1(ps); + ps1.push(segment(i, j, lV, V(i,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + ps1.update(i,j,'(',')'); + push_to_gstack(gstack, ps1); + } + + + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (FM[i][k] + V(k+1,j) + d5 + d3 + + Eb + aup + ps.total() <= mfe + delta) { + //printf("here3\n"); + ps_t ps1(ps); + ps1.push(segment(i, k, lM, FM[i][k])); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + //printf("auPenalty: %d\n", auPenalty(i,k)); + ps1.update(k+1,j,'(',')'); + push_to_gstack(gstack, ps1); + } + } + + for (int k = i; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (V(k+1,j) + d5 + d3 + + Eb + Ec*(k-i+1) + aup + ps.total() <= mfe+delta) { + //printf("here4\n"); + ps_t ps1(ps); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + Ec*(k-i+1) + aup); + ps1.update(k+1, j, '(', ')'); + //printf("auPenalty: %d\n", auPenalty(k+1,j)); + push_to_gstack(gstack, ps1); + } + } +} + +#endif + void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) { int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); int d5 = Ed5(j,i,j+1); + //printf("WM %d %d\n", i, j); + //printf("normal auPenalty: %d\n", auPenalty(i,j)); if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) { ps_t ps_new(ps); ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5); @@ -217,6 +464,8 @@ void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) { } void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("VM %d %d\n", i, j); int d3 = Ed3(i,j,j-1); int d5 = Ed5(i,j,i+1); @@ -231,4 +480,7 @@ void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { void push_to_gstack(ps_stack_t& gstack, const ps_t& v) { gflag = 1; gstack.push(v); + //printf("Pushing to gstack: \n"); +// v.print(); + //printf("\n"); } From 90b4481f7a3a74329483a468836af8cdac898481 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 11 Nov 2011 08:47:51 -0800 Subject: [PATCH 178/187] Added a Sample Test Module --- gtfold-mfe/tests/scripts/SampleTest.pm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100755 gtfold-mfe/tests/scripts/SampleTest.pm diff --git a/gtfold-mfe/tests/scripts/SampleTest.pm b/gtfold-mfe/tests/scripts/SampleTest.pm new file mode 100755 index 0000000..9686997 --- /dev/null +++ b/gtfold-mfe/tests/scripts/SampleTest.pm @@ -0,0 +1,26 @@ +#!/usr/bin/perl +package SampleTest; +use strict; +use warnings; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + } +} +1; From cdd5c97417e064260bd818a17ce1ff9cab35e260 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 11 Nov 2011 10:33:56 -0800 Subject: [PATCH 179/187] Pretty Output for Suboptimal Structures Match Test. Output sent to a separate file. --- .../tests/scripts/SuboptMatchStructures.pm | 80 ++++++++++++++++--- 1 file changed, 68 insertions(+), 12 deletions(-) diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm index 1697a46..fa9d7ed 100755 --- a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm +++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm @@ -1,5 +1,5 @@ #!/usr/bin/perl -package SuboptNumStructures; +package SuboptMatchStructures; use strict; use warnings; use File::Basename; @@ -14,12 +14,24 @@ sub test() my $gtdir = $Config{"G_GTFOLD_DIR"}; my $rnadir = $Config{"G_RNAFOLD_DIR"}; my $workdir = $Config{"G_WORK_DIR"}; + my $min_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY"}; + my $max_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY"}; + my $energy_stride = $Config{"L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE"}; + + if (not(defined($min_energy))) { + $min_energy = 0; + } + if (not(defined($max_energy))) { + $max_energy = 3; + } + if (not(defined($energy_stride))) { + $energy_stride = 1; + } my $key; my $value; my %new_hash = (%local_sequences); - # For testing pseudoknot detection logic - # we may only test the sequences specified in local_sequences + while (($key, $value) = each(%new_hash)) { my $seqname=$key; @@ -32,8 +44,11 @@ sub test() my $rnaout = "$workdir$seqname-rna"; my $gtoutfilename = $workdir."$seqname-gt.ct"; + my %gtstruct_hash; + my %rnastruct_hash; + my $energy; - for ($energy = 1; $energy <=10; ++$energy) { + for ($energy=$min_energy; $energy<=$max_energy; $energy=$energy+$energy_stride) { my $gtfile = $gtout.$energy; my $rnafile = $rnaout.$energy."_ss.txt"; @@ -50,19 +65,60 @@ sub test() my $gtsorted = $gtsubopt_file."_sorted"; my $rnasubopt_sorted = $rnafile."_sorted"; - `cat $gtsubopt_file | sed '/[A-Z]/d' | sort -o $gtsorted`; - `cat $rnasubopt_file | sed '/[A-Z]/d' | sort -o $rnasubopt_sorted`; - #`sort $gtsubopt_file -o $gtsorted`; - #`sort $rnasubopt_file -o $rnasubopt_sorted`; + my $gtstructs = `cat $gtsubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + my $rnastructs = `cat $rnasubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + + %gtstruct_hash = split('[ \n]',$gtstructs); + %rnastruct_hash = split('[ \n]',$rnastructs); + + my $diff_file_name = "$workdir$seqname\_$energy.diff"; + + open (DIFF_FILE, ">> $diff_file_name"); + + my $diff = 0; + foreach my $key ( keys %gtstruct_hash ) + { + my $change = $gtstruct_hash{$key} + unless ( (exists $rnastruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + if (exists $rnastruct_hash{$key}) { + print DIFF_FILE "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + } + else { + print DIFF_FILE "\nRNASubopt Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } + + foreach my $key ( keys %rnastruct_hash ) + { + my $change = $rnastruct_hash{$key} + unless ( (exists $gtstruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + if (exists $gtstruct_hash{$key}) { + print DIFF_FILE "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + } + else { + print DIFF_FILE "\nGTFOLD Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } - my $diff_str = `diff $gtsorted $rnasubopt_sorted`; - #print $diff_str; + close DIFF_FILE; - if ($diff_str eq "") { + if ($diff == 0) { $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched"); } else { - $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched\n $diff_str"); + $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched. Difference Written to file $diff_file_name"); } } } From 45111dc19f1b21cb9ec0a3bda5e5b14c267ac1a9 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 18 Nov 2011 11:57:02 -0500 Subject: [PATCH 180/187] adding stochastic smaplign changes --- gtfold-mfe/include/stochastic-sampling.h | 1 + gtfold-mfe/src/main.cc | 69 +++------------------- gtfold-mfe/src/stochastic-sampling.cc | 73 ++++++++++++++++++++++++ 3 files changed, 81 insertions(+), 62 deletions(-) diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h index 68fea91..38f037f 100644 --- a/gtfold-mfe/include/stochastic-sampling.h +++ b/gtfold-mfe/include/stochastic-sampling.h @@ -83,5 +83,6 @@ void rnd_ud(int i, int j, int* structure); void rnd_u(int i, int j, int* structure); double rnd_structure(int* structure, int len); +void batch_sample(int num_rnd, int length, double U); #endif diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index f5dbc21..d183fea 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -19,6 +19,7 @@ */ #include +#include #include #include #include @@ -278,9 +279,9 @@ int main(int argc, char** argv) { // Read in thermodynamic parameters. Always use Turner99 data (for now) if (SUBOPT_ENABLED) - readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH); else - readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); printRunConfiguration(seq); @@ -294,74 +295,18 @@ int main(int argc, char** argv) { free_fold(seq.length()); exit(0); } + if (RND_SAMPLE == true) { - printf("\nComputing partition function...\n"); + printf("\nComputing partition function...\n"); int pf_count_mode = 0; if(PF_COUNT_MODE) pf_count_mode=1; double U = calculate_partition(seq.length(),pf_count_mode); + + batch_sample(num_rnd, seq.length(), U); - int* structure = new int[seq.length()+1]; - srand(time(NULL)); - std::map > uniq_structs; - - if (num_rnd > 0 ) { - printf("\nSampling structures...\n"); - - for (int count = 1; count <= num_rnd; ++count) - { - memset(structure, 0, (seq.length()+1)*sizeof(int)); - double energy = rnd_structure(structure, seq.length()); - - std::string ensemble(seq.length()+1,'.'); - for (int i = 1; i <= (int)seq.length(); ++ i) { - // printf("%d %d\n",i,structure[i]); - if (structure[i] > 0 && ensemble[i] == '.') - { - ensemble[i] = '('; - ensemble[structure[i]] = ')'; - } - } - std::map >::iterator iter ; - if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) - { - std::pair& pp = iter->second; - pp.first++; - } - else { - uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); - } - // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; - } - - int pcount = 0; - int maxCount = 0; std::string bestStruct; - double bestE = INFINITY; - - std::map >::iterator iter ; - for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) - { - const std::string& ss = iter->first; - const std::pair& pp = iter->second; - const double& estimated_p = (double)pp.first/(double)num_rnd; - const double& energy = pp.second; - double actual_p = pow(2.718281,-1.0*energy/RT_)/U; - - printf("%s\t%lf\t%lf\t%lf\n",ss.c_str(),energy,actual_p,estimated_p); - pcount += pp.first; - if (pp.first > maxCount) - { - maxCount = pp.first; - bestStruct = ss; - bestE = pp.second; - } - } - assert(num_rnd == pcount); - printf("\nMost favourable structure is : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); - } free_partition(); free_fold(seq.length()); - delete [] structure; exit(0); } diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index bdc9ee9..53b2f3b 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -3,7 +3,10 @@ #include "global.h" #include #include +#include +#include #include +#include int ss_verbose = 0; @@ -671,6 +674,76 @@ double rnd_structure(int* structure, int len) return (double)energy/100.0; } +void batch_sample(int num_rnd, int length, double U) +{ + int* structure = new int[length+1]; + srand(time(NULL)); + std::map > uniq_structs; + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + int count,nsamples =0; + for (count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (length+1)*sizeof(int)); + double energy = rnd_structure(structure, length); + + std::string ensemble(length+1,'.'); + for (int i = 1; i <= (int)length; ++ i) { + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } + //double myEnegry = -88.4; + //++nsamples; + //if (fabs(energy-myEnegry)>0.0001) continue; //TODO: debug + //++count; + + std::map >::iterator iter ; + if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) + { + std::pair& pp = iter->second; + pp.first++; + } + else { + uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); + } + + // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; + } + std::cout << nsamples << std::endl; + int pcount = 0; + int maxCount = 0; std::string bestStruct; + double bestE = INFINITY; + + std::map >::iterator iter ; + for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) + { + const std::string& ss = iter->first; + const std::pair& pp = iter->second; + const double& estimated_p = (double)pp.first/(double)num_rnd; + const double& energy = pp.second; + double actual_p = pow(2.718281,-1.0*energy/RT_)/U; + + printf("%s %lf %lf %lf %d\n",ss.c_str(),energy,actual_p,estimated_p,pp.first); + pcount += pp.first; + if (pp.first > maxCount) + { + maxCount = pp.first; + bestStruct = ss; + bestE = pp.second; + } + } + assert(num_rnd == pcount); + printf("\nMax frequency structure : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + + } + + delete [] structure; +} + void set_single_stranded(int i, int j, int* structure) { for(;i<=j;++i) From 99e46c42c525ca86193c43e51c26885aee11d613 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 18 Nov 2011 10:50:58 -0800 Subject: [PATCH 181/187] Adding Paul Specials --- gtfold-mfe/tests/scripts/paul_specials.pm | 163 ++++++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100755 gtfold-mfe/tests/scripts/paul_specials.pm diff --git a/gtfold-mfe/tests/scripts/paul_specials.pm b/gtfold-mfe/tests/scripts/paul_specials.pm new file mode 100755 index 0000000..304260d --- /dev/null +++ b/gtfold-mfe/tests/scripts/paul_specials.pm @@ -0,0 +1,163 @@ +package paul_specials; + +use strict; +use warnings; + +require Exporter; +our @ISA = qw(Exporter); +our @EXPORT = qw( table_to_bracket table_to_bracket5 make_pair_table); + +#input is base-pair table, output is dot-bracket notation. NOte: $table[0]=seq_length. +#ADD PKNOTS SUPPORT! +sub table_to_bracket { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; # + my $len = $tbl[0]; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + #print "\n$dotb\n\n"; + + for (my $j = 1; $j < $len+1; $j++ ) { + + if ($tbl[$j]>$j) { + substr($dotb, $j-1, 1) = "\("; + $temp = $tbl[$j] - 1; + substr($dotb, $temp, 1) = "\)"; + } + + } + + return $dotb; +} + +sub table_to_bracket5 { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; + my $len = $tbl[0]+1; + + #print "table_to_bracket: len = $len\n"; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + + for (my $j = 0; $j < $len; $j++ ) { + + if ($tbl[$j+1]>$j+1) { + substr($dotb, $j, 1) = "\("; + $temp = $tbl[$j+1] - 2; + substr($dotb, $temp, 1) = "\)"; + } + #elsif ($tbl[$j+1]== 0) { + # substr($dotb, $j, 1) = "\."; + #} + } + + return $dotb; +} + + + +sub make_pair_table { + my $str = shift; + my $i; + my @bps = (); + my @bps_square = (); + my @bps_curly = (); + my @bps_angle = (); + my @pair_table; + my $prime5; + my $prime3; + my $count = 0; + + my $len = length($str); + + #print "make_pair_table: len = $len\n"; + + $pair_table[0] = $len; + + for (my $j = 0; $j < $len; $j++ ) { + $pair_table[$j+1] = 0; + if ( substr($str,$j,1) =~ '\(' ){ + push(@bps, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\)' ){ + $prime5 = pop(@bps); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + #print "base-pair: $pair_table[$i][$prime3] . $pair_table[$i][$prime5]\n" + } + elsif ( substr($str,$j,1) =~ '\[' ){ + push(@bps_square, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\]' ){ + $prime5 = pop(@bps_square); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\{' ){ + push(@bps_curly, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\}' ){ + $prime5 = pop(@bps_curly); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\<' ){ + push(@bps_angle, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\>' ){ + $prime5 = pop(@bps_angle); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + } + +#({[<.>]}) + +#print "pair table:\n"; +#for ($i = 1; $i < $len+1; $i++ ) { +# print "$pair_table[$i] "; +#} + +#print "\n"; +# +#print "pair_table = $#pair_table\n"; + +if ($count){ + print "Unbalanced brackets in: +$str\n"; + die; +} + + + return @pair_table; + +} + + + + +1; From 7fa3ab83096aedd2aaf92c7f65decf3d76cf6a30 Mon Sep 17 00:00:00 2001 From: Rohit Banga Date: Fri, 18 Nov 2011 14:36:10 -0500 Subject: [PATCH 182/187] Duplicate Structures should be reported if partial structure encountered again in suboptimal traceback. --- gtfold-mfe/src/subopt_traceback.cc | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 150d6bc..d67a852 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -139,13 +139,13 @@ void process(ss_map_t& subopt_data, int len) { if (ps.empty()) { count++; - //pair ins_result; - // ins_result = subopt_data.insert(std::make_pair(ps.str,ps.ae_)); - //if (ins_result.second == false) { - //printf("Duplicate Structure!!!"); - // exit(1); - //} - cout << ps.str << endl; + pair ins_result; + ins_result = subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + if (ins_result.second == false) { + printf("Duplicate Structure!!!"); + exit(1); + } + //cout << ps.str << endl; continue; } else { From fb6500bef4d684ce051bb0cf8575449405b4de97 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 15 Dec 2011 22:08:31 -0500 Subject: [PATCH 183/187] code cleanup --- gtfold-mfe/include/boltzmann_main.h | 6 + gtfold-mfe/include/constraints.h | 7 +- gtfold-mfe/include/main.h | 17 +- gtfold-mfe/include/mfe_main.h | 8 + gtfold-mfe/include/options.h | 13 +- gtfold-mfe/include/subopt_main.h | 6 + gtfold-mfe/include/utils.h | 7 +- gtfold-mfe/src/Makefile.am | 7 +- gtfold-mfe/src/Makefile.in | 36 ++- gtfold-mfe/src/algorithms.c | 2 +- gtfold-mfe/src/boltzmann_main.cc | 197 +++++++++++ gtfold-mfe/src/constraints.cc | 15 +- gtfold-mfe/src/global.cc | 227 +++++++++++++ gtfold-mfe/src/main.cc | 274 ++-------------- gtfold-mfe/src/mfe_main.cc | 448 ++++++++++++++++++++++++++ gtfold-mfe/src/options.cc | 8 +- gtfold-mfe/src/shapereader.cc | 6 + gtfold-mfe/src/stochastic-sampling.cc | 4 +- gtfold-mfe/src/subopt_main.cc | 158 +++++++++ gtfold-mfe/src/traceback.c | 8 +- gtfold-mfe/src/utils.cc | 17 +- 21 files changed, 1180 insertions(+), 291 deletions(-) create mode 100644 gtfold-mfe/include/boltzmann_main.h create mode 100644 gtfold-mfe/include/mfe_main.h create mode 100644 gtfold-mfe/include/subopt_main.h create mode 100644 gtfold-mfe/src/boltzmann_main.cc create mode 100644 gtfold-mfe/src/global.cc create mode 100644 gtfold-mfe/src/mfe_main.cc create mode 100644 gtfold-mfe/src/subopt_main.cc diff --git a/gtfold-mfe/include/boltzmann_main.h b/gtfold-mfe/include/boltzmann_main.h new file mode 100644 index 0000000..50841d4 --- /dev/null +++ b/gtfold-mfe/include/boltzmann_main.h @@ -0,0 +1,6 @@ +#ifndef _BPP_MAIN_H_ +#define _BPP_MAIN_H_ + +int boltzmann_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h index 9805dbd..f21e115 100644 --- a/gtfold-mfe/include/constraints.h +++ b/gtfold-mfe/include/constraints.h @@ -13,11 +13,11 @@ extern int nFBP; #define BP(i,j) BP[ind[j]+i] + int init_constraints(const char* constr_file, int length) ; void free_constraints(int length) ; void print_constraints(int length) ; - #ifdef __cplusplus extern "C" { #endif @@ -34,6 +34,11 @@ int forcePair(int i, int j); int withinCD(int i, int j); int verify_structure(); + +void enable_constraints(int b); +void enable_limit_distance(int b); +void set_contact_distance(int dist); + #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h index 7faf980..8fe342e 100644 --- a/gtfold-mfe/include/main.h +++ b/gtfold-mfe/include/main.h @@ -27,20 +27,13 @@ using namespace std; -void init_fold(string seq); -void free_fold(int len); +//void init_fold(string seq); +//void free_fold(int len); -bool encodeSequence(string seq); +//bool encodeSequence(string seq); void limit_contact_distance(int lCD, int length); -bool is_valid_base(char c) -{ - return ( (c-'A' == 0) || (c-'a' == 0) || - (c-'C' == 0) || (c-'c' == 0) || - (c-'G' == 0) || (c-'g' == 0) || - (c-'U' == 0) || (c-'u' == 0)); -} - +/* void trim_spaces(std::string& str) { // Trim Both leading and trailing spaces @@ -73,5 +66,5 @@ void tokenize(const std::string& str, std::vector& tokens, const st pos = str.find_first_of(delimiters, lastPos); } } - + */ #endif diff --git a/gtfold-mfe/include/mfe_main.h b/gtfold-mfe/include/mfe_main.h new file mode 100644 index 0000000..683be07 --- /dev/null +++ b/gtfold-mfe/include/mfe_main.h @@ -0,0 +1,8 @@ +#ifndef _MFE_MAIN_H_ +#define _MFE_MAIN_H_ + +int mfe_main(int argc, char** argv); +void init_fold(const char* seq); +void free_fold(int len); + +#endif diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 7965698..a1ecd7a 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -8,10 +8,11 @@ using namespace std; -extern bool ILSA; -extern bool NOISOLATE; +//extern bool ILSA; +//extern bool NOISOLATE; //extern bool USERDATA; //extern bool PARAMS; +/* extern bool LIMIT_DISTANCE; extern bool BPP_ENABLED; extern bool SUBOPT_ENABLED; @@ -45,11 +46,11 @@ extern int num_rnd; extern bool LIMIT_DISTANCE; extern int contactDistance; +*/ - -void help(); -void parse_options(int argc, char** argv); -void printRunConfiguration(string seq); +//void help(); +//void parse_options(int argc, char** argv); +//void printRunConfiguration(string seq); #endif diff --git a/gtfold-mfe/include/subopt_main.h b/gtfold-mfe/include/subopt_main.h new file mode 100644 index 0000000..1f26e43 --- /dev/null +++ b/gtfold-mfe/include/subopt_main.h @@ -0,0 +1,6 @@ +#ifndef _SUBOPT_MAIN_H_ +#define _SUBOPT_MAIN_H_ + +int subopt_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h index 8b33655..a8e5c28 100644 --- a/gtfold-mfe/include/utils.h +++ b/gtfold-mfe/include/utils.h @@ -3,7 +3,6 @@ #include "constants.h" - #define MIN(X,Y) ((X) < (Y) ? (X) : (Y)) #define MAX(X,Y) ((X) > (Y) ? (X) : (Y)) #define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z)) @@ -12,5 +11,11 @@ char baseToDigit(const char* base) ; unsigned char encode(char base); int isWatsonCrickBase(char base); +double get_seconds(); + +#ifdef __cplusplus +extern "C" +#endif +int is_valid_base(char c); #endif diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 62cedca..8a1ba22 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -7,17 +7,20 @@ bin_PROGRAMS = gtfold gtfold_SOURCES = \ main.cc\ - loader.cc\ + mfe_main.cc\ + loader.cc\ utils.cc\ options.cc\ constraints.cc\ - global.c\ + global.cc\ energy.c\ algorithms.c\ traceback.c\ + subopt_main.cc\ subopt_traceback.cc\ stochastic-sampling.cc\ algorithms-partition.c\ + boltzmann_main.cc\ partition-dangle.c\ partition-func.c\ shapereader.cc diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index d36b292..86a7787 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -31,7 +31,7 @@ PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : -POST_UNINSTALL = : +POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ target_triplet = @target@ @@ -48,12 +48,13 @@ CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" PROGRAMS = $(bin_PROGRAMS) -am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ - options.$(OBJEXT) constraints.$(OBJEXT) global.$(OBJEXT) \ - energy.$(OBJEXT) algorithms.$(OBJEXT) traceback.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) algorithms-partition.$(OBJEXT) \ - partition-dangle.$(OBJEXT) partition-func.$(OBJEXT) \ - shapereader.$(OBJEXT) stochastic-sampling.$(OBJEXT) +am_gtfold_OBJECTS = main.$(OBJEXT) mfe_main.$(OBJEXT) loader.$(OBJEXT) \ + utils.$(OBJEXT) options.$(OBJEXT) constraints.$(OBJEXT) \ + global.$(OBJEXT) energy.$(OBJEXT) algorithms.$(OBJEXT) \ + traceback.$(OBJEXT) subopt_main.$(OBJEXT) \ + subopt_traceback.$(OBJEXT) stochastic-sampling.$(OBJEXT) \ + algorithms-partition.$(OBJEXT) boltzmann_main.$(OBJEXT) partition-dangle.$(OBJEXT) \ + partition-func.$(OBJEXT) shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -183,18 +184,21 @@ AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/@PACKAGE@' AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@' gtfold_SOURCES = \ main.cc\ - loader.cc\ + mfe_main.cc\ + loader.cc\ utils.cc\ options.cc\ constraints.cc\ - global.c\ + global.cc\ energy.c\ algorithms.c\ traceback.c\ + subopt_main.cc\ subopt_traceback.cc\ - algorithms-partition.c\ stochastic-sampling.cc\ - partition-dangle.c\ + algorithms-partition.c\ + boltzmann_main.cc\ + partition-dangle.c\ partition-func.c\ shapereader.cc @@ -255,8 +259,11 @@ install-binPROGRAMS: $(bin_PROGRAMS) while read type dir files; do \ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ test -z "$$files" || { \ - echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + echo "$(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtmfe || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtsubopt || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtboltzmann || exit $$?;\ } \ ; done @@ -283,17 +290,20 @@ distclean-compile: -rm -f *.tab.c @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@ -@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/boltzmann_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mfe_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@ diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 7d81bfe..07f987f 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -129,7 +129,7 @@ int calculate(int len) { #ifdef _OPENMP #pragma omp parallel #pragma omp master - fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); + if (g_verbose) fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif initializeMatrix(len); diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc new file mode 100644 index 0000000..f590dc6 --- /dev/null +++ b/gtfold-mfe/src/boltzmann_main.cc @@ -0,0 +1,197 @@ +#include +#include +#include +#include +#include + +#include "global.h" +#include "loader.h" +#include "algorithms-partition.h" +#include "boltzmann_main.h" +#include "partition-func.h" +#include "mfe_main.h" +#include "stochastic-sampling.h" +#include "algorithms.h" +#include "traceback.h" + +using namespace std; + +static bool CALC_PART_FUNC = false; +static bool PF_COUNT_MODE = false; +static bool BPP_ENABLED = false; +static bool PARAM_DIR = false; +static bool RND_SAMPLE = false; + +static string seqfile = ""; +static string outputPrefix = ""; +static string outputDir = ""; +static string outputFile = ""; +static string paramDir; // default value +static string bppOutFile = ""; +static int num_rnd = 0; + +static void help() { + printf("Usage: gtboltzmann [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + + printf(" --partition Calculate the partition function.\n"); + printf(" --sample INT Sample number of structures equal to INT\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +static void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; +} + + +int boltzmann_main(int argc, char** argv) { + std::string seq; + + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0); + + calculate(seq.length()) ; + trace(seq.length()); + + if (CALC_PART_FUNC == true) + { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + + calculate_partition(seq.length(),pf_count_mode); + free_partition(); + } else if (RND_SAMPLE == true) { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + double U = calculate_partition(seq.length(),pf_count_mode); + + batch_sample(num_rnd, seq.length(), U); + + free_partition(); + } + else if(BPP_ENABLED){ + printf("\n"); + printf("Calculating partition function\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + fillBasePairProbabilities(seq.length(), Q, QB, QM, P); + printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str()); + printf("Saved BPP output in %s\n",bppOutFile.c_str()); + + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } else { + printf("No valid option specified !\n\n"); + help(); + } + + free_fold(seq.length()); + return EXIT_SUCCESS; +} diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index ce96636..b1f2a1b 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -41,12 +41,18 @@ int** FBP; int nPBP; int nFBP; +static bool CONS_ENABLED = false; +static bool LIMIT_DISTANCE = false; +static int contactDistance = -1; + +void enable_constraints(int b) {CONS_ENABLED = b;} +void enable_limit_distance(int b) {LIMIT_DISTANCE = b;} +void set_contact_distance(int dist) {contactDistance = dist;} + static int load_constraints(const char* constr_file, int seq_length, int verbose=0) { - fprintf(stdout, "- Running with constraints\n"); - std::ifstream cfcons; cfcons.open(constr_file, std::ios::in); if (cfcons == 0) { @@ -164,8 +170,9 @@ static int load_constraints(const char* constr_file, int seq_length, int verbose } int init_constraints(const char* constr_file,int length) { - load_constraints(constr_file, length); - + enable_constraints(true); + load_constraints(constr_file, length); + int i,j,it,k; ind = (int*) malloc((length+1) * sizeof(int)); diff --git a/gtfold-mfe/src/global.cc b/gtfold-mfe/src/global.cc new file mode 100644 index 0000000..eb91d90 --- /dev/null +++ b/gtfold-mfe/src/global.cc @@ -0,0 +1,227 @@ +#include +#include +#include + +#include "utils.h" +#include "global.h" +#include "constraints.h" + +unsigned char *RNA; +int *structure; +unsigned int chPairKey; + +int g_nthreads; +int g_dangles; +int g_unamode; +int g_mismatch; +int g_verbose; +int g_prefilter_mode; +int g_prefilter1; +int g_prefilter2; + +void init_global_params(int len) { + RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char)); + if (RNA == NULL) { + perror("Cannot allocate variable 'RNA'"); + exit(-1); + } + structure = (int *) malloc((len+1) * sizeof(int)); + if (structure == NULL) { + perror("Cannot allocate variable 'structure'"); + exit(-1); + } + + init_checkPair(); +} + +void free_global_params() { + free(structure); + free(RNA); +} + +void print_sequence(int len) { + int i; + for (i = 1; i <= len; i++) { + if (RNA[i] == BASE_A) + printf("A"); + else if (RNA[i] == BASE_C) + printf("C"); + else if (RNA[i] == BASE_G) + printf("G"); + else if (RNA[i] == BASE_U) + printf("U"); + else + printf("N"); + } + printf("\n"); +} + +void print_structure(int len) { + int i = 1; + for (i = 1; i <= len; i++) + { + if (structure[i] > 0 && structure[i] > i) + printf("("); + else if (structure[i] > 0 && structure[i] < i) + printf(")"); + else + printf("."); + } + printf("\n"); +} + +int read_sequence_file(const char* filename, std::string& seq) { + seq = ""; + + ifstream fs; + fs.open(filename, ios::in); + if (!fs.good()) return FAILURE; + + string line; + while(fs.good()) { + getline(fs, line); + // exclude lines starting with FASTA comment characters + if(line[0] != ';' && line[0] != '>' && line.length() > 0) + seq += line; + } + + fs.close(); + + size_t loc; + while((loc = seq.find(" ")) != string::npos) + seq.erase(loc, 1); + + return SUCCESS; +} + +bool encodeSequence(string seq) { + unsigned int unspecifiedBaseCount=0; + unsigned int unspecifiedBases[seq.length()]; + + for(unsigned int i=1; i<=seq.length(); i++) { + RNA[i] = encode(seq[i-1]); + + // die on non-IUPAC codes + if (RNA[i]=='X') { + fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]); + fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n"); + return false; + } + + // add non-canonical IUPAC codes to the warning list + if(!isWatsonCrickBase(seq[i-1])) + unspecifiedBases[unspecifiedBaseCount++]=i; + } + + // just print a warning for non-canonical IUPAC codes + if(unspecifiedBaseCount > 0) { + printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s"); + + // put [0] first for nice comma separation + printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1)); + for(unsigned int i=1; i= 0 && i <=3 )&&(j >=0 && j <=3))) + return r; + if (!(chPairKey & (1 << ((i << 2) + j)))) { + chPairKey += 1 << ((i << 2) + j); + r = 1; + } + return r; +} + +int canPair(int a, int b) { + return (chPairKey & (1 << (((a)<<2) + (b)))); +} + +/* +void help() { + printf("Usage: gtfold [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf("\nBETA OPTIONS\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} +*/ diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 13942f4..1689af9 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -24,258 +24,43 @@ #include #include #include -#include -#include #include #include #include #include #include "main.h" +#include "mfe_main.h" +#include "boltzmann_main.h" +#include "subopt_main.h" #include "utils.h" -#include "loader.h" -#include "options.h" #include "global.h" -#include "energy.h" -#include "algorithms.h" -#include "algorithms-partition.h" -#include "partition-func.h" -#include "constraints.h" -#include "traceback.h" -#include "subopt_traceback.h" -#include "shapereader.h" -#include "stochastic-sampling.h" -#define DEBUG 1 - -using namespace std; - -double get_seconds() { - struct timeval tv; - gettimeofday(&tv, NULL); - return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; -} - -void init_fold(string seq) { - int len = seq.length(); - - init_global_params(len); - - if (!encodeSequence(seq)) { - free_fold(seq.length()); - exit(0); - } - - create_tables(len); - - if (CONS_ENABLED) { - init_constraints(constraintsFile.c_str(), len); - } - - if (SHAPE_ENABLED) { - readSHAPEarray(shapeFile.c_str(),len); - } - - if (UNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --unafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --unafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - - if (RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); - if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); - if (dangles == 0 || dangles == 2) - printf("Ignoring -d option, using --rnafold\n"); - if (b_prefilter == 1) - printf("Ignoring --prefilter option, using --rnafold\n"); - T_MISMATCH = false; - PARAM_DIR = false; - dangles = -1; - b_prefilter = false; - } - - if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { - if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); - T_MISMATCH = false; - } else { - if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); - dangles = -1; - } - - g_nthreads = nThreads; - g_unamode = UNAMODE; - g_mismatch = T_MISMATCH; - g_verbose = VERBOSE; - g_prefilter_mode = b_prefilter; - g_prefilter1 = prefilter1; - g_prefilter2 = prefilter2; - g_dangles = dangles; - - #ifdef DEBUG - printf("g_nthreads = %d\n", g_nthreads); - printf("g_unamode = %d\n", g_unamode); - printf("g_mismatch = %d\n", g_mismatch); - printf("g_prefilter_mode = %d\n", g_prefilter_mode); - printf("g_dangles = %d\n", g_dangles); - -#endif - -} - -void free_fold(int len) { - if (CONS_ENABLED) - free_constraints(len); - if (SHAPE_ENABLED){ - free_shapeArray(len); - } - - free_tables(len); - free_global_params(); -} - -/** - * Read the sequence out of the given filename and store it in seq - * - * @param filename A c string with the file to open - * @param seq A C++ string object (passed by reference) to save to - * @return SUCCESS or FAILURE - */ -int read_sequence_file(const char* filename, std::string& seq) { - seq = ""; - - ifstream fs; - fs.open(filename, ios::in); - if (!fs.good()) return FAILURE; - - string line; - while(fs.good()) { - getline(fs, line); - // exclude lines starting with FASTA comment characters - if(line[0] != ';' && line[0] != '>' && line.length() > 0) - seq += line; - } - - fs.close(); - - size_t loc; - while((loc = seq.find(" ")) != string::npos) - seq.erase(loc, 1); - - return SUCCESS; -} - -/** - * Encode the given string of letters into an RNA sequence. - * - * This handles IUPAC codes and places the results into the array RNA. - * - * @param seq The string to encode - * @return A boolean representing success or failure of the encoding. Failure - * can occur when seeing unknown IUPAC codes. - */ -bool encodeSequence(string seq) { - unsigned int unspecifiedBaseCount=0; - unsigned int unspecifiedBases[seq.length()]; - - for(unsigned int i=1; i<=seq.length(); i++) { - RNA[i] = encode(seq[i-1]); - - // die on non-IUPAC codes - if (RNA[i]=='X') { - fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]); - fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n"); - return false; - } - - // add non-canonical IUPAC codes to the warning list - if(!isWatsonCrickBase(seq[i-1])) - unspecifiedBases[unspecifiedBaseCount++]=i; - } - - // just print a warning for non-canonical IUPAC codes - if(unspecifiedBaseCount > 0) { - printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s"); - - // put [0] first for nice comma separation - printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1)); - for(unsigned int i=1; ifirst).c_str(), it->second/100.0); - //outfile << it->first << '\t' << it->second/100.0 << std::endl; - outfile << buff << std::endl; - } - - outfile.close(); -} - -/** - * Save the output to a ct file - * - * @param outputFile The file to save to - * @param energy The MFE energy (multiplied by 100) - */ -void save_ct_file(string outputFile, string seq, int energy) { - - ofstream outfile; - outfile.open(outputFile.c_str()); - - outfile << seq.length() << "\t dG = " << energy/100.0 << endl; - //outfile << seq.length() << "\tdG = " << energy/100.0 << "\t" << seqfile << endl; - - unsigned int i = 1; - for(i=1; i <= seq.length(); i++) - outfile << i << "\t" << seq[i-1] << "\t" << i-1 << "\t" << (i+1)%(seq.length()+1) << "\t" << structure[i] << "\t" << i << endl; - - outfile.close(); -} int main(int argc, char** argv) { - std::string seq; - int energy; - double t1; - - print_header(); + print_header(); + + std::string cmd = argv[0]; + + if (cmd.find("gtmfe") != std::string::npos) { + mfe_main(argc, argv); + } else if (cmd.find("gtsubopt") != std::string::npos){ + subopt_main(argc,argv); + } else if (cmd.find("gtboltzmann") != std::string::npos) { + boltzmann_main(argc,argv); + } - parse_options(argc, argv); + return EXIT_SUCCESS; +} + /* if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); exit(-1); - } - init_fold(seq); + }*/ + + /* + //init_fold(seq); // Read in thermodynamic parameters. Always use Turner99 data (for now) if (SUBOPT_ENABLED) @@ -292,7 +77,7 @@ int main(int argc, char** argv) { if(PF_COUNT_MODE) pf_count_mode=1; calculate_partition(seq.length(),pf_count_mode); free_partition(); - free_fold(seq.length()); + //free_fold(seq.length()); exit(0); } @@ -306,7 +91,7 @@ int main(int argc, char** argv) { batch_sample(num_rnd, seq.length(), U); free_partition(); - free_fold(seq.length()); + //free_fold(seq.length()); exit(0); } @@ -335,7 +120,7 @@ int main(int argc, char** argv) { printf("Subopt structures saved in %s\n", suboptFile.c_str()); save_subopt_file(suboptFile, subopt_data, seq, energy); - free_fold(seq.length()); + //free_fold(seq.length()); exit(0); } @@ -368,7 +153,8 @@ int main(int argc, char** argv) { fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); } } - + */ +/* if(BPP_ENABLED){ printf("\n"); printf("Calculating partition function\n"); @@ -389,14 +175,14 @@ int main(int argc, char** argv) { freeTwoD(QB, seq.length() + 1, seq.length() + 1); freeTwoD(P, seq.length() + 1, seq.length() + 1); } - +*/ // release the malloc'd arrays - free_fold(seq.length()); + //free_fold(seq.length()); /* dangle_struct partition; partition = malloc_partition_arrays_d(seq.length()); fill_partition_arrays_d(partition); printf("Done with the partition functioni.\n"); */ - return EXIT_SUCCESS; -} + //return EXIT_SUCCESS; +//} diff --git a/gtfold-mfe/src/mfe_main.cc b/gtfold-mfe/src/mfe_main.cc new file mode 100644 index 0000000..0525ea2 --- /dev/null +++ b/gtfold-mfe/src/mfe_main.cc @@ -0,0 +1,448 @@ +/* + GTfold: compute minimum free energy of RNA secondary structure + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey + http://www.cc.gatech.edu/~bader + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "main.h" +#include "mfe_main.h" +#include "utils.h" +#include "loader.h" +//#include "options.h" +#include "global.h" +#include "energy.h" +#include "algorithms.h" +#include "constraints.h" +#include "traceback.h" +#include "shapereader.h" + +using namespace std; + +static bool PARAM_DIR = false; +//static bool LIMIT_DISTANCE; +static bool CONS_ENABLED = false; +static bool VERBOSE = false; +static bool SHAPE_ENABLED = false; +static bool T_MISMATCH = false; +static bool UNAMODE = false; +static bool RNAMODE = false; +static bool b_prefilter = false; + +static string seqfile = ""; +static string constraintsFile = ""; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string shapeFile = ""; +static string paramDir; // default value + +static int dangles=-1; +static int prefilter1=2; +static int prefilter2=2; + +static int nThreads = -1; +static int contactDistance = -1; + +static void help(); +void printRunConfiguration(string seq); +void parse_mfe_options(int argc, char** argv); + +void init_fold(const char* seq) { + assert(seq != NULL); + int len = strlen(seq); + + init_global_params(len); + + if (!encodeSequence(seq)) { + free_fold(len); + exit(0); + } + + create_tables(len); + + if (CONS_ENABLED) { + init_constraints(constraintsFile.c_str(), len); + } + + if (SHAPE_ENABLED) { + readSHAPEarray(shapeFile.c_str(),len); + } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + + g_nthreads = nThreads; + g_unamode = UNAMODE; + g_mismatch = T_MISMATCH; + g_verbose = VERBOSE; + g_prefilter_mode = b_prefilter; + g_prefilter1 = prefilter1; + g_prefilter2 = prefilter2; + g_dangles = dangles; + +#ifdef DEBUG + printf("g_nthreads = %d\n", g_nthreads); + printf("g_unamode = %d\n", g_unamode); + printf("g_mismatch = %d\n", g_mismatch); + printf("g_prefilter_mode = %d\n", g_prefilter_mode); + printf("g_dangles = %d\n", g_dangles); + +#endif + +} + +void free_fold(int len) { + if (CONS_ENABLED) + free_constraints(len); + if (SHAPE_ENABLED){ + free_shapeArray(len); + } + + free_tables(len); + free_global_params(); +} + + +int mfe_main(int argc, char** argv) { + std::string seq; + int energy; + + parse_mfe_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + // Read in thermodynamic parameters. Always use Turner99 data (for now) + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + printRunConfiguration(seq); + + printf("\nComputing minimum free energy structure...\n"); + fflush(stdout); + + double t1 = get_seconds(); + energy = calculate(seq.length()) ; + t1 = get_seconds() - t1; + + printf("Done.\n\n"); + printf("Results:\n"); + if (energy >= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); + printf("- MFE runtime: %9.6f seconds\n", t1); + + t1 = get_seconds(); + trace(seq.length()); + t1 = get_seconds() - t1; + + printf("\n"); + print_sequence(seq.length()); + print_structure(seq.length()); + + if (CONS_ENABLED) + print_constraints(seq.length()); + + if (SHAPE_ENABLED && VERBOSE) + print_shapeArray(seq.length()); + + save_ct_file(outputFile, seq, energy); + printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); + + if(CONS_ENABLED && VERBOSE){ + printf("Verifying that structure fulfills constraint criteria... "); + if(verify_structure()){ + printf("OK\n"); + } + else{ + printf("ERROR: NOT OK!!\n"); + fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n"); + fprintf(stderr, "Structure file: %s\n", outputFile.c_str()); + fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); + } + } + + free_fold(seq.length()); + + return EXIT_SUCCESS; +} + + +void parse_mfe_options(int argc, char** argv) { + int i; + + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) { + //LIMIT_DISTANCE = true; + enable_limit_distance(true); + set_contact_distance(contactDistance); + } + else + help(); + } + else + help(); + }else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } + + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } + + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + +} + + +void printRunConfiguration(string seq) { + bool standardRun = true; + + printf("Run Configuration:\n"); + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } + if (UNAMODE == true) { + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); + standardRun = false; + } + if (b_prefilter == true) { + printf("+ running with prefilter value = %d\n",prefilter1); + standardRun = false; + } + + if(!constraintsFile.empty()) { + printf("- using constraint file: %s\n", constraintsFile.c_str()); + standardRun = false; + } + + if(!shapeFile.empty()){ + printf("- using SHAPE data file: %s\n", shapeFile.c_str()); + } + if (contactDistance != -1) { + printf("- maximum contact distance: %d\n", contactDistance); + standardRun = false; + } + + if(standardRun) + printf("- standard\n"); + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("- output file: %s\n", outputFile.c_str()); +} + +static void help() { + printf("Usage: gtmfe [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} + diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 8a9082f..30889de 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -44,6 +44,8 @@ int contactDistance = -1; /** * Print the help message and quit. */ + +/* void help() { printf("Usage: gtfold [OPTION]... FILE\n\n"); @@ -92,10 +94,12 @@ void help() { printf("\tAll other values for INT are ignored.\n"); exit(-1); } +*/ /** * Parse the options from argc and argv and save them into global state. */ +/* void parse_options(int argc, char** argv) { int i; @@ -252,12 +256,13 @@ void parse_options(int argc, char** argv) { bppOutFile += outputPrefix; bppOutFile += "_bpp.txt"; } - +*/ /** * Prints the run configuration for this run. * * The lines that start with a '-' are normal options, the '+' are beta options. */ +/* void printRunConfiguration(string seq) { bool standardRun = true; @@ -320,3 +325,4 @@ void printRunConfiguration(string seq) { printf("- sequence length: %d\n", (int)seq.length()); printf("- output file: %s\n", outputFile.c_str()); } +*/ diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc index fcbcbc5..006f8a1 100644 --- a/gtfold-mfe/src/shapereader.cc +++ b/gtfold-mfe/src/shapereader.cc @@ -14,6 +14,12 @@ using namespace std; double* SHAPEarray; int* SHAPEenergies; +static bool SHAPE_ENABLED = false; + +void enable_shape(bool b) { + SHAPE_ENABLED = b; +} + void free_shapeArray(int len){ free(SHAPEarray); } diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc index 53b2f3b..b831ff8 100644 --- a/gtfold-mfe/src/stochastic-sampling.cc +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -682,7 +682,7 @@ void batch_sample(int num_rnd, int length, double U) if (num_rnd > 0 ) { printf("\nSampling structures...\n"); - int count,nsamples =0; + int count; //nsamples =0; for (count = 1; count <= num_rnd; ++count) { memset(structure, 0, (length+1)*sizeof(int)); @@ -713,7 +713,7 @@ void batch_sample(int num_rnd, int length, double U) // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; } - std::cout << nsamples << std::endl; + //std::cout << nsamples << std::endl; int pcount = 0; int maxCount = 0; std::string bestStruct; double bestE = INFINITY; diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc new file mode 100644 index 0000000..2aff56b --- /dev/null +++ b/gtfold-mfe/src/subopt_main.cc @@ -0,0 +1,158 @@ +#include +#include +#include +#include +#include +#include +#include + +#include "loader.h" +#include "algorithms.h" +#include "subopt_traceback.h" +#include "global.h" +#include "utils.h" +#include "mfe_main.h" + + +using namespace std; + +static string seqfile = ""; +static string suboptFile = ""; +static double suboptDelta = 0; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string paramDir = ""; +static bool PARAM_DIR = false; +static void help(); + +void save_subopt_file(string outputFile, ss_map_t& ss_data, + const string& seq, int energy) +{ + ofstream outfile; + outfile.open(outputFile.c_str()); + char buff[4096]; + + sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0); + outfile << buff << std::endl; + for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) + { + sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0); + //outfile << it->first << '\t' << it->second/100.0 << std::endl; + outfile << buff << std::endl; + } + + outfile.close(); +} + +void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + +} + +static void help() { + printf("Usage: gtsubopt [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +void subopt_main(int argc, char** argv) { + + string seq = ""; + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 1, 0); + + int energy = calculate(seq.length()) ; + + double t1 = get_seconds(); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); + t1 = get_seconds() - t1; + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); + + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); + + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); + + free_fold(seq.length()); +} diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index 3e13199..6d461a8 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -47,9 +47,11 @@ void trace(int len) { printf("\n"); traceW(len); - printf("- sum of energy of Loops: %12.2f kcal/mol\n", total_en/100.0); - printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0); - return; + if (g_verbose == 1) { + printf("- sum of energy of Loops: %12.2f kcal/mol\n", total_en/100.0); + printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0); + } + return; } void traceW(int j) { diff --git a/gtfold-mfe/src/utils.cc b/gtfold-mfe/src/utils.cc index 8c6ffbe..8c218c9 100644 --- a/gtfold-mfe/src/utils.cc +++ b/gtfold-mfe/src/utils.cc @@ -1,6 +1,21 @@ #include "utils.h" -#include +#include #include +#include +#include + +double get_seconds() { + struct timeval tv; + gettimeofday(&tv, NULL); + return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; +} + +int is_valid_base(char c) { + return ( (c-'A' == 0) || (c-'a' == 0) || + (c-'C' == 0) || (c-'c' == 0) || + (c-'G' == 0) || (c-'g' == 0) || + (c-'U' == 0) || (c-'u' == 0)); +} char baseToDigit(const char* base) { if (!strcmp(base, "A")) { From 70d4e4dfce452f6d2efc575bf68bc286e140f04e Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 15 Dec 2011 22:09:55 -0500 Subject: [PATCH 184/187] adding changes in global vars --- gtfold-mfe/include/global.h | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h index c452b2a..23ec167 100644 --- a/gtfold-mfe/include/global.h +++ b/gtfold-mfe/include/global.h @@ -3,6 +3,11 @@ #include "constants.h" +#ifdef __cplusplus +#include +using namespace std; +#endif + extern unsigned char *RNA; extern int *structure; extern int* constraints; @@ -18,10 +23,10 @@ extern int g_prefilter2; extern unsigned int chPairKey; -// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). +// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) +// and (U,G). #define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) ))) - #ifdef __cplusplus extern "C" { #endif @@ -30,10 +35,17 @@ void init_global_params(int len); void free_global_params(); void print_sequence(int len); void print_structure(int len); +void print_header() ; #ifdef __cplusplus } #endif +#ifdef __cplusplus +int read_sequence_file(const char* filename, std::string& seq); +bool encodeSequence(string seq); +void save_ct_file(string outputFile, string seq, int energy) ; +#endif + void init_checkPair(); int update_checkPair(int i, int j); From 6d5a9f9e6599f8c70bcb23ae8c8b77bfac186f3d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 15 Dec 2011 22:22:31 -0500 Subject: [PATCH 185/187] removing file --- gtfold-mfe/src/global.c | 92 ----------------------------------------- 1 file changed, 92 deletions(-) delete mode 100644 gtfold-mfe/src/global.c diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c deleted file mode 100644 index 1c2d45b..0000000 --- a/gtfold-mfe/src/global.c +++ /dev/null @@ -1,92 +0,0 @@ -#include -#include - -#include "global.h" -#include "constraints.h" - -unsigned char *RNA; -int *structure; -unsigned int chPairKey; - -int g_nthreads; -int g_dangles; -int g_unamode; -int g_mismatch; -int g_verbose; -int g_prefilter_mode; -int g_prefilter1; -int g_prefilter2; - -void init_global_params(int len) { - RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char)); - if (RNA == NULL) { - perror("Cannot allocate variable 'RNA'"); - exit(-1); - } - structure = (int *) malloc((len+1) * sizeof(int)); - if (structure == NULL) { - perror("Cannot allocate variable 'structure'"); - exit(-1); - } - - init_checkPair(); -} - -void free_global_params() { - free(structure); - free(RNA); -} - -void print_sequence(int len) { - int i; - for (i = 1; i <= len; i++) { - if (RNA[i] == BASE_A) - printf("A"); - else if (RNA[i] == BASE_C) - printf("C"); - else if (RNA[i] == BASE_G) - printf("G"); - else if (RNA[i] == BASE_U) - printf("U"); - else - printf("N"); - } - printf("\n"); -} - -void print_structure(int len) { - int i = 1; - for (i = 1; i <= len; i++) - { - if (structure[i] > 0 && structure[i] > i) - printf("("); - else if (structure[i] > 0 && structure[i] < i) - printf(")"); - else - printf("."); - } - printf("\n"); -} - -void init_checkPair() { - int i, j; - chPairKey = 0; - for (i = 0; i < 4; i++) - for (j = 0; j < 4; j++) - chPairKey += checkPair(i, j) << ((i << 2) + j); -} - -int update_checkPair(int i, int j) { - int r = 0; - if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3))) - return r; - if (!(chPairKey & (1 << ((i << 2) + j)))) { - chPairKey += 1 << ((i << 2) + j); - r = 1; - } - return r; -} - -inline int canPair(int a, int b) { - return (chPairKey & (1 << (((a)<<2) + (b)))); -} From e492adcde5dc4a2a272b9ce4f62182c70bfbc473 Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Thu, 15 Dec 2011 23:13:46 -0500 Subject: [PATCH 186/187] + adding new options + script to add symlink --- gtfold-mfe/createsymlinks.sh | 8 ++++++ gtfold-mfe/src/boltzmann_main.cc | 48 +++++++++++++++++++++++++------- gtfold-mfe/src/createsymlinks.sh | 8 ++++++ gtfold-mfe/src/subopt_main.cc | 5 ++++ 4 files changed, 59 insertions(+), 10 deletions(-) create mode 100644 gtfold-mfe/createsymlinks.sh create mode 100644 gtfold-mfe/src/createsymlinks.sh diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh new file mode 100644 index 0000000..99db1bd --- /dev/null +++ b/gtfold-mfe/createsymlinks.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +BINDIR=/home/users/pgaurav/git-hub/gtfold_final/bin +echo 'creating symlinks under' $BINDIR +ln -sf gtfold $BINDIR/gtmfe +ln -sf gtfold $BINDIR/gtsubopt +ln -sf gtfold $BINDIR/gtboltzmann + diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc index f590dc6..b423c0e 100644 --- a/gtfold-mfe/src/boltzmann_main.cc +++ b/gtfold-mfe/src/boltzmann_main.cc @@ -21,6 +21,8 @@ static bool PF_COUNT_MODE = false; static bool BPP_ENABLED = false; static bool PARAM_DIR = false; static bool RND_SAMPLE = false; +static bool CALC_PF_DO = false; +static bool CALC_PF_DS = false; static string seqfile = ""; static string outputPrefix = ""; @@ -37,9 +39,13 @@ static void help() { printf("OPTIONS\n"); - printf(" --partition Calculate the partition function.\n"); + printf(" --partition Calculate the partition function (default is using sfold reccurences).\n"); + printf(" --partition -dS Calculate the partition function using sfold reccurences.\n"); + printf(" --partition -d0 Calculate the partition function using -d0 reccurences.\n"); + printf(" --partition -d2 Calculate the partition function using -d2 reccurences (Under implementation).\n"); + printf(" --sample INT Sample number of structures equal to INT\n"); - printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --pfcount Calculate the structure count using partition function and zero energy value.\n"); printf(" --bpp Calculate base pair probabilities.\n"); printf("\n"); printf(" -o, --output NAME Write output files with prefix given in NAME\n"); @@ -80,7 +86,14 @@ static void parse_options(int argc, char** argv) { } else if (strcmp(argv[i],"--partition") == 0) { CALC_PART_FUNC = true; - } else if (strcmp(argv[i],"--pf_count") == 0) { + } else if (strcmp(argv[i],"-dS") == 0) { + CALC_PF_DS = true; + } else if (strcmp(argv[i],"-d0") == 0) { + CALC_PF_DO = true; + } else if (strcmp(argv[i],"-d2") == 0) { + help(); + } + else if (strcmp(argv[i],"--pfcount") == 0) { CALC_PART_FUNC = true; PF_COUNT_MODE = true; } else if (strcmp(argv[i],"--sample") == 0) { @@ -147,11 +160,27 @@ int boltzmann_main(int argc, char** argv) { readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0); - calculate(seq.length()) ; - trace(seq.length()); - - if (CALC_PART_FUNC == true) - { + if (CALC_PART_FUNC == true && CALC_PF_DS == true) { + printf("\nComputing partition function in -dS mode ...\n"); + calculate_partition(seq.length(),0); + free_partition(); + } + else if (CALC_PART_FUNC == true && CALC_PF_DO == true) { + printf("\nCalculating partition function in -d0 mode ...\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } + else if (CALC_PART_FUNC == true) { printf("\nComputing partition function...\n"); int pf_count_mode = 0; if(PF_COUNT_MODE) pf_count_mode=1; @@ -167,8 +196,7 @@ int boltzmann_main(int argc, char** argv) { batch_sample(num_rnd, seq.length(), U); free_partition(); - } - else if(BPP_ENABLED){ + } else if(BPP_ENABLED) { printf("\n"); printf("Calculating partition function\n"); double ** Q, **QM, **QB, **P; diff --git a/gtfold-mfe/src/createsymlinks.sh b/gtfold-mfe/src/createsymlinks.sh new file mode 100644 index 0000000..e0ac203 --- /dev/null +++ b/gtfold-mfe/src/createsymlinks.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +BINDIR='.' +echo 'creating symlinks under' $BINDIR +ln -sf gtfold $BINDIR/gtmfe +ln -sf gtfold $BINDIR/gtsubopt +ln -sf gtfold $BINDIR/gtboltzmann + diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc index 2aff56b..96b2ac5 100644 --- a/gtfold-mfe/src/subopt_main.cc +++ b/gtfold-mfe/src/subopt_main.cc @@ -75,6 +75,11 @@ void parse_options(int argc, char** argv) { } } + if(seqfile.empty()) { + printf("Missing input file.\n"); + help(); + } + // If no output file specified, create one if(outputPrefix.empty()) { // base it off the input file From 1957922ab4c69fab0907d85c6ad085f931b0687d Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Fri, 16 Dec 2011 11:14:48 -0500 Subject: [PATCH 187/187] added creation of symlinks --- gtfold-mfe/createsymlinks.sh | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh index 99db1bd..1427a56 100644 --- a/gtfold-mfe/createsymlinks.sh +++ b/gtfold-mfe/createsymlinks.sh @@ -1,8 +1,14 @@ #!/bin/sh +if [ $# != 1 ] +then +echo "Usage: sh createsymlinks.sh " +exit -1 +fi -BINDIR=/home/users/pgaurav/git-hub/gtfold_final/bin +BINDIR=$1 echo 'creating symlinks under' $BINDIR -ln -sf gtfold $BINDIR/gtmfe -ln -sf gtfold $BINDIR/gtsubopt -ln -sf gtfold $BINDIR/gtboltzmann +cd $BINDIR +ln -sf gtfold gtmfe +ln -sf gtfold gtsubopt +ln -sf gtfold gtboltzmann