changes for --rnafold option

Author: pgaurav

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);

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;

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";

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);
 

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;