supports BayesPairing

@@ -193,14 +193,35 @@ void Motif::load_from_csv(string csv_line)
 {
     vector<string> tokens;
     split(tokens, csv_line, boost::is_any_of(","));
-    atlas_id = tokens[0];
-    score_   = stoi(tokens[2]);
-    comp.push_back(Component(make_pair<int, int>(stoi(tokens[3]), stoi(tokens[4]))));
-    if (tokens[5] != "-") comp.push_back(Component(make_pair<int, int>(stoi(tokens[5]), stoi(tokens[6]))));
-    reversed_ = (tokens[1] == "True");
-    is_model_ = true;
-    PDBID     = "";
-    source_   = RNAMOTIFATLAS;
+    if (csv_line.find(string("True")) != std::string::npos or csv_line.find(string("False")) != std::string::npos) {    // This has been created by jar3d
+        atlas_id = tokens[0];
+        score_   = stoi(tokens[2]);
+        comp.push_back(Component(make_pair<int, int>(stoi(tokens[3]), stoi(tokens[4]))));
+        if (tokens[5] != "-") comp.push_back(Component(make_pair<int, int>(stoi(tokens[5]), stoi(tokens[6]))));
+        reversed_ = (tokens[1] == "True");
+        is_model_ = true;
+        PDBID     = "";
+        source_   = RNAMOTIFATLAS;
+    } else {    // this has been created by BayesPairing
+        score_ = stoi(tokens[1]);
+        // identify source:
+        if (tokens[0].find(string("rna3dmotif")) == std::string::npos) {
+            is_model_ = true;
+            PDBID     = "";
+            source_   = RNAMOTIFATLAS;
+            atlas_id  = tokens[0];
+        } else {
+            is_model_ = false;
+            PDBID     = tokens[0];
+            source_   = RNA3DMOTIF;
+            atlas_id  = "";
+        }
+        uint i = 2;
+        while (i < tokens.size()) {
+            comp.push_back(Component(make_pair<int, int>(stoi(tokens[i]), stoi(tokens[i + 1]))));
+            i += 2;
+        }
+    }
 }
 
 string Motif::pos_string(void) const
@@ -378,7 +399,7 @@ vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbo
     return posInsertionSites;
 }
 
-vector<Motif> load_jar3d_output(const string& path)
+vector<Motif> load_csv(const string& path)
 {
     vector<Motif> posInsertionSites;
     std::ifstream motifs;

@@ -41,7 +41,7 @@ class Motif
     public:
     Motif();
     Motif(const vector<Component>& v, string PDB);
-    void              load_from_csv(string csv_line);
+    void load_from_csv(string csv_line);
     // static void       build_from_desc(path descfile, string rna, vector<Motif>& final_results);
     static void       build_from_desc(args_of_parallel_func args);
     static char       is_valid_DESC(const string& descfile);
@@ -63,7 +63,7 @@ class Motif
 
 bool          is_desc_insertible(const string& descfile, const string& rna, bool verbose);
 vector<Motif> load_desc_folder(const string& path, const string& rna, bool verbose);
-vector<Motif> load_jar3d_output(const string& path);
+vector<Motif> load_csv(const string& path);
 
 // utilities to compare secondary structures:
 bool operator==(const Motif& m1, const Motif& m2);

@@ -72,12 +72,14 @@ int main(int argc, char* argv[])
     "descfolder,d",
     po::value<string>(&motifs_path_name),
     "A folder containing modules in .desc format, as produced by Djelloul & Denise's catalog program")(
-    "jar3dcsv,f",
+    "jar3dcsv",
     po::value<string>(&motifs_path_name),
-    "A file containing the output of JAR3D's search for motifs in the sequence, as produced by searchForMotifSites.py")(
-    "first-objective,c",
-    po::value<unsigned int>(&MOIP::obj_to_solve_)->default_value(1),
-    "Objective to solve in the mono-objective portions of the algorithm")("output,o", po::value<string>(&outputName), "A file to summarize the computation results")(
+    "A file containing the output of JAR3D's search for motifs in the sequence, as produced by test_on_RNAstrand.py")(
+    "bayespaircsv",
+    po::value<string>(&motifs_path_name),
+    "A file containing the output of BayesPairing's search for motifs in the sequence, as produced by "
+    "test_on_RNAstrand.py")("first-objective,c", po::value<unsigned int>(&MOIP::obj_to_solve_)->default_value(1), "Objective to solve in the mono-objective portions of the algorithm")(
+    "output,o", po::value<string>(&outputName), "A file to summarize the computation results")(
     "theta,t",
     po::value<float>(&theta_p_threshold)->default_value(0.001),
     "Pairing probability threshold to consider or not the possibility of pairing")(
@@ -108,14 +110,16 @@ int main(int argc, char* argv[])
             return EXIT_SUCCESS;
         }
         if (vm.count("verbose")) verbose = true;
-        if (!vm.count("jar3dcsv") and !vm.count("descfolder")) {
-            cerr << "\033[31mYou must provide at least --jar3dcsv or --descfolder.\033[0m See --help for more "
+        if (!vm.count("jar3dcsv") and !vm.count("bayespaircsv") and !vm.count("descfolder")) {
+            cerr << "\033[31mYou must provide at least --jar3dcsv, --bayespaircsv or --descfolder.\033[0m See --help "
+                    "for more "
                     "information."
                  << endl;
             return EXIT_FAILURE;
         }
-        if (vm.count("-d") and (obj_function_nbr == 1 or obj_function_nbr == 3)) {
-            cerr << "\033[31mYou must provide at -f to use --type 1 or --type 3.\033[0m See --help for more "
+        if (vm.count("-d") and (obj_function_nbr == 2 or obj_function_nbr == 3)) {
+            cerr << "\033[31mYou must provide --jar3dcsv or --bayespaircsv to use --type 2 or --type 3.\033[0m See "
+                    "--help for more "
                     "information."
                  << endl;
             return EXIT_FAILURE;
@@ -150,7 +154,9 @@ int main(int argc, char* argv[])
         return EXIT_FAILURE;
     }
     if (vm.count("jar3dcsv"))
-        posInsertionSites = load_jar3d_output(motifs_path_name.c_str());
+        posInsertionSites = load_csv(motifs_path_name.c_str());
+    else if (vm.count("bayespaircsv"))
+        posInsertionSites = load_csv(motifs_path_name.c_str());
     else
         posInsertionSites = load_desc_folder(motifs_path_name.c_str(), fa->seq(), verbose);