Renamed objectives with chars

@@ -17,7 +17,7 @@ using std::endl;
 using std::make_pair;
 using std::vector;
 
-uint   MOIP::obj_function_nbr_ = 1;
+char   MOIP::obj_function_nbr_ = 'A';
 uint   MOIP::obj_to_solve_     = 1;
 double MOIP::precision_        = 1e-5;
 bool   MOIP::allow_pk_         = true;
@@ -145,29 +145,30 @@ MOIP::MOIP(const RNA& rna, const vector<Motif>& insertionSites, float theta, boo
     for (uint i = 0; i < insertion_sites_.size(); i++) {
         IloNum sum_k = 0;
         switch (obj_function_nbr_) {
-        case 1:
+        case 'A':
             // RNA MoIP style
             for (const Component& c : insertion_sites_[i].comp) sum_k += c.k;
             obj1 += IloNum(sum_k * sum_k) * insertion_dv_[index_of_first_components[i]];
             break;
+            
+        case 'B':
+            // everything but the Jar3D/Bayespairing score
+            for (const Component& c : insertion_sites_[i].comp) sum_k += c.k;
+            obj1 += IloNum(insertion_sites_[i].comp.size() / log2(sum_k)) * insertion_dv_[index_of_first_components[i]];
+            break;
 
-        case 2:
-            // Weighted by the JAR3D score only:
+        case 'C':
+            // Weighted by the JAR3D or BayesPairing score only:
             obj1 += IloNum(insertion_sites_[i].score_) * insertion_dv_[index_of_first_components[i]];
             break;
 
-        case 3:
+        case 'D':
             // everything
             for (const Component& c : insertion_sites_[i].comp) sum_k += c.k;
             obj1 += IloNum(insertion_sites_[i].comp.size() * insertion_sites_[i].score_ / log2(sum_k)) *
                     insertion_dv_[index_of_first_components[i]];
             break;
 
-        case 4:
-            // everything but Jar3D score
-            for (const Component& c : insertion_sites_[i].comp) sum_k += c.k;
-            obj1 += IloNum(insertion_sites_[i].comp.size() / log2(sum_k)) * insertion_dv_[index_of_first_components[i]];
-            break;
         }
     }
 

@@ -26,10 +26,10 @@ class MOIP
     void                      remove_solution(uint i);
     void                      forbid_solutions_between(double min, double max);
     IloEnv&                   get_env(void);
-    static uint               obj_function_nbr_;    // On what criteria do you want to insert motifs ?
-    static uint obj_to_solve_;  // What objective do you prefer to solve in mono-objective portions of the algorithm ?
-    static double precision_;   // decimals to keep in objective values, to avoid numerical issues. otherwise, solution with objective 5.0000000009 dominates solution with 5.0 =(
-    static bool allow_pk_;      // Wether we forbid pseudoknots (false) or allow them (true)
+    static char               obj_function_nbr_;    // On what criteria do you want to insert motifs ?
+    static uint               obj_to_solve_;  // What objective do you prefer to solve in mono-objective portions of the algorithm ?
+    static double             precision_;   // decimals to keep in objective values, to avoid numerical issues. otherwise, solution with objective 5.0000000009 dominates solution with 5.0 =(
+    static bool               allow_pk_;      // Wether we forbid pseudoknots (false) or allow them (true)
 
     private:
     bool   is_undominated_yet(const SecondaryStructure& s);

 /***
-        Biominserter, Louis Becquey, nov 2018
+        Biorseo, Louis Becquey, nov 2018
         louis.becquey@univ-evry.fr
 ***/
 
@@ -58,7 +58,7 @@ int main(int argc, char* argv[])
     string             inputName, outputName, motifs_path_name, basename;
     bool               verbose = false;
     float              theta_p_threshold;
-    int                obj_function_nbr = 3;
+    char               obj_function_nbr = 'A';
     list<Fasta>        f;
     vector<Motif>      posInsertionSites;
     ofstream           outfile;
@@ -78,9 +78,8 @@ int main(int argc, char* argv[])
     ("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")
-    ("type,f", po::value<int>(&obj_function_nbr), "What objective function to use to include motifs: square of motif size in nucleotides like "
-    "RNA-MoIP (1), jar3d score (2), motif size + jar3d score + number of components (3), motif size + number of "
-    "components (4)")
+    ("type,f", po::value<char>(&obj_function_nbr)->default_value('A'), "What objective function to use to include motifs: square of motif size in nucleotides like "
+    "RNA-MoIP (A), motif size + number of components (B), site score (C), motif size + site score + number of components (D)")
     ("disable-pseudoknots,n", "Add constraints forbidding the formation of pseudoknots")
     ("verbose,v", "Print what is happening to stdout");
     po::variables_map vm;
@@ -91,8 +90,8 @@ int main(int argc, char* argv[])
         po::store(po::parse_command_line(argc, argv, desc), vm);    // can throw
 
         if (vm.count("help") or vm.count("-h")) {
-            cout << "Biominserter, bio-objective integer linear programming framework to predict RNA secondary "
-                    "structures with included known RNA modules."
+            cout << "Biorseo, bio-objective integer linear programming framework to predict RNA secondary "
+                    "structures by including known RNA modules."
                  << endl
                  << "developped by Louis Becquey (louis.becquey@univ-evry.fr), 2019" << endl
                  << endl
@@ -100,20 +99,20 @@ int main(int argc, char* argv[])
             return EXIT_SUCCESS;
         }
         if (vm.count("version")) {
-            cout << "Biominserter RNA-MoIP special edition, 2019" << endl;
+            cout << "Biorseo v1.0, May 2019" << endl;
             return EXIT_SUCCESS;
         }
         if (vm.count("verbose")) verbose = true;
         if (vm.count("disable-pseudoknots")) MOIP::allow_pk_ = false;
         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 "
+            cerr << "\033[31mYou must provide at least one of --jar3dcsv, --bayespaircsv or --descfolder.\033[0m See --help "
                     "for more "
                     "information."
                  << endl;
             return EXIT_FAILURE;
         }
-        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 "
+        if (vm.count("-d") and (obj_function_nbr == 'C' or obj_function_nbr == 'D')) {
+            cerr << "\033[31mYou must provide --jar3dcsv or --bayespaircsv to use --type C or --type D.\033[0m See "
                     "--help for more "
                     "information."
                  << endl;