Removed k-pareto sets (reason: too slow)

@@ -9,7 +9,7 @@ TARGET   = biominserter
 
 CC	   = clang++
 # compiling flags here
-CFLAGS   = -Icppsrc/ -I/usr/local/include -I$(ICONCERT) -I$(ICPLEX) -I$(INUPACK) -I$(IEIGEN) -O3
+CFLAGS   = -Icppsrc/ -I/usr/local/include -I$(ICONCERT) -I$(ICPLEX) -I$(INUPACK) -I$(IEIGEN) -O3  
 CXXFLAGS = --std=c++17 -Wall -Wpedantic -Wextra -Wno-ignored-attributes -Wno-unused-variable
 
 LINKER   = clang++

@@ -14,17 +14,18 @@ class MOIP
 {
     public:
     MOIP(void);
-    MOIP(const RNA& rna, const vector<Motif>& motifSites, uint nsets, float pthreshold, bool verbose);
+    MOIP(const RNA& rna, const vector<Motif>& motifSites, float pthreshold, bool verbose);
     ~MOIP(void);
-    SecondaryStructure        solve_objective(int o, double min, double max, const vector<IloConstraint>& F);
+    SecondaryStructure        solve_objective(int o, double min, double max, const IloConstraintArray& F);
     SecondaryStructure        solve_objective(int o);
     uint                      get_n_solutions(void) const;
     const SecondaryStructure& solution(uint i) const;
-    void                      search_between(double lambdaMin, double lambdaMax, const vector<IloConstraint>& F_);
+    void                      search_between(double lambdaMin, double lambdaMax, const IloConstraintArray& F_);
     bool                      allowed_basepair(size_t u, size_t v) const;
     void                      add_solution(const SecondaryStructure& s);
     void                      remove_solution(uint i);
-    vector<IloConstraint>     forbid_solutions_between(double min, double max);
+    IloConstraintArray        forbid_solutions_between(double min, double max);
+    IloEnv&                   get_env(void);
     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 double epsilon_;
@@ -46,7 +47,7 @@ class MOIP
     RNA                        rna_;                // RNA object
     vector<Motif>              insertion_sites_;    // Potential Motif insertion sites
     vector<SecondaryStructure> pareto_;             // Vector of results
-    uint                       n_sets_;             // number of Pareto sets to return
+    // uint                       n_sets_;             // number of Pareto sets to return
 
     // Objectives related
     float theta_;    // theta parameter for the probability function
@@ -69,6 +70,7 @@ inline IloNumExprArg&            MOIP::y(size_t u, size_t v) { return basepair_d
 inline IloNumExprArg&            MOIP::C(size_t x, size_t i) { return insertion_dv_[get_Cpxi_index(x, i)]; }
 inline SecondaryStructure        MOIP::solve_objective(int o)
 {
-    return solve_objective(o, 0, rna_.get_RNA_length(), vector<IloConstraint>());
+    return solve_objective(o, 0, rna_.get_RNA_length(), IloConstraintArray(env_));
 }
+inline IloEnv&                   MOIP::get_env(void) { return env_; }
 #endif    // MOIP_H_
\ No newline at end of file

@@ -14,7 +14,7 @@ SecondaryStructure::SecondaryStructure() {}
 
 
 SecondaryStructure::SecondaryStructure(const RNA& rna)
-: objective_scores_(vector<double>(2)), n_(rna.get_RNA_length()), nBP_(0), k_(0), rna_(rna)
+: objective_scores_(vector<double>(2)), n_(rna.get_RNA_length()), nBP_(0), rna_(rna)
 {
     is_empty_structure = false;
 }

@@ -49,8 +49,8 @@ class SecondaryStructure
     void   insert_motif(const Motif& m);
     double get_objective_score(int i) const;
     void   set_objective_score(int i, double s);
-    void   set_pareto_set(uint k);
-    uint   get_pareto_set(void) const;
+    // void   set_pareto_set(uint k);
+    // uint   get_pareto_set(void) const;
     uint   get_n_motifs(void) const;
     uint   get_n_bp(void) const;
     void   print(void) const;
@@ -63,7 +63,7 @@ class SecondaryStructure
     vector<Motif> motif_info_;    // information about known motives in this secondary structure and their positions
     size_t        n_;             // length of the RNA
     size_t        nBP_;           // number of basepairs
-    uint          k_;             // Secondary Structure belongs to the kth Pareto set
+    // uint          k_;             // Secondary Structure belongs to the kth Pareto set
     RNA           rna_;           // RNA object which is folded
     bool          is_empty_structure;    // Empty structure, returned when the solver does not find solutions anymore
     IloConstraint forbid_this_;          // Add it to a cplex model to forbid that solution
@@ -90,7 +90,7 @@ inline double SecondaryStructure::get_objective_score(int i) const { return obje
 inline void   SecondaryStructure::set_objective_score(int i, double s) { objective_scores_[i - 1] = s; }
 inline uint   SecondaryStructure::get_n_motifs(void) const { return motif_info_.size(); }
 inline uint   SecondaryStructure::get_n_bp(void) const { return nBP_; }
-inline uint   SecondaryStructure::get_pareto_set(void) const { return k_; }
-inline void   SecondaryStructure::set_pareto_set(uint k) { k_ = k; }
+// inline uint   SecondaryStructure::get_pareto_set(void) const { return k_; }
+// inline void   SecondaryStructure::set_pareto_set(uint k) { k_ = k; }
 
 #endif

@@ -116,20 +116,18 @@ int main(int argc, char* argv[])
 
     /*  FIND K-PARETO SETS  */
 
-    MOIP myMOIP = MOIP(myRNA, posInsertionSites, 1, theta_p_threshold, verbose);
+    MOIP               myMOIP = MOIP(myRNA, posInsertionSites, theta_p_threshold, verbose);
+    double             min, max;
+    IloConstraintArray F(myMOIP.get_env());
+
     try {
-        bestSSO1 = myMOIP.solve_objective(1, -__DBL_MAX__, __DBL_MAX__, vector<IloConstraint>());
-        bestSSO2 = myMOIP.solve_objective(2, -__DBL_MAX__, __DBL_MAX__, vector<IloConstraint>());
-        bestSSO1.set_pareto_set(1);
-        bestSSO2.set_pareto_set(1);
+        bestSSO1 = myMOIP.solve_objective(1, -__DBL_MAX__, __DBL_MAX__, F);
+        bestSSO2 = myMOIP.solve_objective(2, -__DBL_MAX__, __DBL_MAX__, F);
         if (verbose) {
             cout << endl << "Best solution according to objective 1 :" << bestSSO1.to_string() << endl;
             cout << "Best solution according to objective 2 :" << bestSSO2.to_string() << endl;
         }
 
-        double                min, max;
-        vector<IloConstraint> F;
-
         // extend the Pareto set on top
         if (MOIP::obj_to_solve_ == 1) {
             myMOIP.add_solution(bestSSO1);
@@ -144,8 +142,9 @@ int main(int argc, char* argv[])
         }
 
         if (verbose)
-            cout << std::setprecision(8) << "\nSolving objective function " << MOIP::obj_to_solve_ << ", on top of "
-                 << min << ": Obj" << 3 - MOIP::obj_to_solve_ << "  being in [" << min << ", " << max << "]..." << endl;
+            cout << std::setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function "
+                 << MOIP::obj_to_solve_ << ", on top of " << min << ": Obj" << 3 - MOIP::obj_to_solve_ << "  being in ["
+                 << min << ", " << max << "]..." << endl;
         myMOIP.search_between(min, max, F);    // F is empty
 
 
@@ -162,35 +161,33 @@ int main(int argc, char* argv[])
         F.clear();
         F = myMOIP.forbid_solutions_between(min, max);
         if (verbose)
-            cout << std::setprecision(8) << "\nSolving objective function " << MOIP::obj_to_solve_ << ", below (or eq. to) "
-                 << max << ": Obj" << 3 - MOIP::obj_to_solve_ << "  being in [" << min << ", " << max << "]..." << endl
-                 << "\t>forbidding " << F.size() << " solutions found in [" << std::setprecision(10)
+            cout << std::setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function "
+                 << MOIP::obj_to_solve_ << ", below (or eq. to) " << max << ": Obj" << 3 - MOIP::obj_to_solve_
+                 << "  being in [" << min << ", " << max << "]..." << endl
+                 << "\t>forbidding " << F.getSize() << " solutions found in [" << std::setprecision(10)
                  << min - MOIP::precision_ << ", " << max + MOIP::precision_ << ']' << endl;
         myMOIP.search_between(min, max, F);
 
-    } catch (IloAlgorithm::NotExtractedException& e) {
-        cerr << e << endl;
-        exit(EXIT_FAILURE);
     } catch (IloCplex::Exception& e) {
-        cerr << e << endl;
+        cerr << "Cplex Exception: " << e.getMessage() << endl;
         exit(EXIT_FAILURE);
     }
 
     /*  REMOVE SOLUTIONS WITH TOO HIGH LABEL  */
 
-    vector<size_t> to_remove;
-    if (verbose) cout << endl;
-    for (uint i = 0; i < myMOIP.get_n_solutions(); i++)
-        if (myMOIP.solution(i).get_pareto_set() > 1) {    // Some solution is fromm a Pareto set of too high order
-            if (verbose)
-                cout << "Removing structure from Pareto set " << myMOIP.solution(i).get_pareto_set() << " : "
-                     << myMOIP.solution(i).to_string() << endl;
-            to_remove.push_back(i);
-        }
-    if (to_remove.size()) {
-        for (size_t i = to_remove.size() - 1; i != 0; i--) myMOIP.remove_solution(to_remove[i]);
-        myMOIP.remove_solution(to_remove[0]);
-    }
+    // vector<size_t> to_remove;
+    // if (verbose) cout << endl;
+    // for (uint i = 0; i < myMOIP.get_n_solutions(); i++)
+    //     if (myMOIP.solution(i).get_pareto_set() > 1) {    // Some solution is fromm a Pareto set of too high order
+    //         if (verbose)
+    //             cout << "Removing structure from Pareto set " << myMOIP.solution(i).get_pareto_set() << " : "
+    //                  << myMOIP.solution(i).to_string() << endl;
+    //         to_remove.push_back(i);
+    //     }
+    // if (to_remove.size()) {
+    //     for (size_t i = to_remove.size() - 1; i != 0; i--) myMOIP.remove_solution(to_remove[i]);
+    //     myMOIP.remove_solution(to_remove[0]);
+    // }
 
     /*  DISPLAY RESULTS  */