From 7d7dadb6c06bfca7cee48b61aa4bd877b588497e Mon Sep 17 00:00:00 2001 From: Prashant Gaurav Date: Mon, 20 Jun 2011 11:11:50 -0400 Subject: [PATCH 01/30] 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 02/30] 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 03/30] 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 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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 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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 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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 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 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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/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) . . . . . . . . . . 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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/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 04/30] 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 05/30] 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 06/30] 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 07/30] 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 08/30] 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 09/30] 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 10/30] 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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+inf inf inf inf 1.15 1.15 0.05 1.15 inf inf inf inf 1.85 1.85 0.75 1.85 +inf inf inf inf 1.15 1.15 1.15 1.15 inf inf inf inf 1.85 1.85 1.85 1.85 +inf inf inf inf 0.05 1.15 1.15 1.15 inf inf inf inf 0.75 1.85 1.85 1.85 +inf inf inf inf 1.15 1.15 1.15 0.45 inf inf inf inf 1.85 1.85 1.85 1.15 +1.85 1.85 0.75 1.85 inf inf inf inf 1.85 1.85 0.75 1.85 inf inf inf inf +1.85 1.85 1.85 1.85 inf inf inf inf 1.85 1.85 1.85 1.85 inf inf inf inf +0.75 1.85 1.85 1.85 inf inf inf inf 0.75 1.85 1.85 1.85 inf inf inf inf +1.85 1.85 1.85 1.15 inf inf inf inf 1.85 1.85 1.85 1.15 inf inf inf inf diff --git a/gtfold-mfe/data/UNAParams/tstackm.DAT b/gtfold-mfe/data/UNAParams/tstackm.DAT new file mode 100644 index 0000000..ee473db --- /dev/null +++ b/gtfold-mfe/data/UNAParams/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -1.00 -0.80 -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf -0.60 -0.70 -2.20 -0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -2.10 -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 11/30] 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 12/30] 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 13/30] 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 14/30] 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 15/30] 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 16/30] 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 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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. + +@SET_MAKE@ + +VPATH = @srcdir@ +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +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) 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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 17/30] 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 18/30] 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 19/30] 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 22/30] 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 23/30] 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 24/30] 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 25/30] 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 26/30] 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 27/30] 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 28/30] 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 @@ -0,0 +1,399 @@ +# Makefile.in generated 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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 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 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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 29/30] 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 30/30] 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; }