Different criteria as a command line option

@@ -17,8 +17,9 @@ using std::endl;
 using std::make_pair;
 using std::vector;
 
-uint   MOIP::obj_to_solve_ = 1;
-double MOIP::precision_    = 1e-5;
+uint   MOIP::obj_function_nbr_ = 1;
+uint   MOIP::obj_to_solve_     = 1;
+double MOIP::precision_        = 1e-5;
 
 unsigned getNumConstraints(IloModel& m)
 {
@@ -127,21 +128,41 @@ MOIP::MOIP(const RNA& rna, const vector<Motif>& insertionSites, float theta, boo
     model_ = IloModel(env_);
     define_problem_constraints();
     if (verbose_) cout << "A total of " << getNumConstraints(model_) << " constraints are used." << endl;
+    if (getNumConstraints(model_) > 1500) {
+        cerr << "\033[31m Quitting because too hard for me (too many constraints). Srry. \033[0m" << endl;
+        exit(1);
+    }
+
 
     // Define the motif objective function:
     obj1 = IloExpr(env_);
     for (uint i = 0; i < insertion_sites_.size(); i++) {
-        // objective f_1A
-        // IloNum n_compo_squared = IloNum(insertion_sites_[i].comp.size() * insertion_sites_[i].comp.size());
-        // obj1 += n_compo_squared * insertion_dv_[index_of_first_components[i]];
-
-        // Weighted by the JAR3D score:
-        // obj1 += IloNum(insertion_sites_[i].score) * insertion_dv_[index_of_first_components[i]];
-
-        // RNA MoIP style
         IloNum sum_k = 0;
-        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]];
+        switch (obj_function_nbr_) {
+        case 1:
+            // 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 2:
+            // Weighted by the JAR3D score only:
+            obj1 += IloNum(insertion_sites_[i].score_) * insertion_dv_[index_of_first_components[i]];
+            break;
+
+        case 3:
+            // 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;
+        }
     }
 
     // Define the expected accuracy objective function:
@@ -470,7 +491,6 @@ bool MOIP::exists_vertical_outdated_labels(const SecondaryStructure& s) const
     return result;
 }
 
-
 bool MOIP::exists_horizontal_outdated_labels(const SecondaryStructure& s) const
 {
     bool result = false;
@@ -490,6 +510,10 @@ void MOIP::add_solution(const SecondaryStructure& s)
 {
     if (verbose_) cout << "\t>adding structure to Pareto set :\t" << s.to_string() << endl;
     pareto_.push_back(s);
+    if (pareto_.size() > 300) {
+        cerr << "\033[31m Quitting because combinatorial issues. \033[0m";
+        exit(1);
+    }
 }
 
 size_t MOIP::get_yuv_index(size_t u, size_t v) const

@@ -26,6 +26,7 @@ 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 =(
 

@@ -57,6 +57,7 @@ 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;
     list<Fasta>        f;
     vector<Motif>      posInsertionSites;
     ofstream           outfile;
@@ -79,7 +80,12 @@ int main(int argc, char* argv[])
     "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")("verbose,v", "Print what is happening to stdout");
+    "Pairing probability threshold to consider or not the possibility of pairing")(
+    "type",
+    po::value<int>(&obj_function_nbr),
+    "If -f is provided, 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)")("verbose,v", "Print what is happening to stdout");
     po::variables_map vm;
     po::store(po::parse_command_line(argc, argv, desc), vm);
     basename = remove_ext(inputName.c_str(), '.', '/');
@@ -103,23 +109,33 @@ int main(int argc, char* argv[])
         }
         if (vm.count("verbose")) verbose = true;
         if (!vm.count("jar3dcsv") and !vm.count("descfolder")) {
-            cerr << "You must provide at least --jar3dcsv or --descfolder. See --help for more information." << endl;
+            cerr << "\033[31mYou must provide at least --jar3dcsv 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 "
+                    "information."
+                 << endl;
             return EXIT_FAILURE;
         }
 
         po::notify(vm);    // throws on error, so do after help in case there are any problems
     } catch (po::error& e) {
-        cerr << "ERROR: " << e.what() << endl;
+        cerr << "ERROR: \033[31m" << e.what() << "\033[0m" << endl;
         cerr << desc << endl;
         return EXIT_FAILURE;
     }
 
+    MOIP::obj_function_nbr_ = obj_function_nbr;
+
     /*  FILE PARSING  */
 
     // load fasta file
     if (verbose) cout << "Reading input files..." << endl;
     if (access(inputName.c_str(), F_OK) == -1) {
-        cerr << inputName << " not found" << endl;
+        cerr << "\033[31m" << inputName << " not found\033[0m" << endl;
         return EXIT_FAILURE;
     }
     Fasta::load(f, inputName.c_str());
@@ -130,7 +146,7 @@ int main(int argc, char* argv[])
 
     // load CSV file
     if (access(motifs_path_name.c_str(), F_OK) == -1) {
-        cerr << motifs_path_name << " not found" << endl;
+        cerr << "\033[31m" << motifs_path_name << " not found\033[0m" << endl;
         return EXIT_FAILURE;
     }
     if (vm.count("jar3dcsv"))
@@ -190,7 +206,7 @@ int main(int argc, char* argv[])
         myMOIP.search_between(min, max);
 
     } catch (IloCplex::Exception& e) {
-        cerr << "Cplex Exception: " << e.getMessage() << endl;
+        cerr << "\033[31mCplex Exception: " << e.getMessage() << "\033[0m" << endl;
         exit(EXIT_FAILURE);
     }