Loading the recombination parameters to MutationParams

src/libaevol/io/parameters/ParamLoader.cpp

@@ -249,6 +249,10 @@ void ParamLoader::load(const ParamValues& param_values,
   param_mut->set_deletion_proportion(param_values.deletion_proportion_);
   param_mut->set_translocation_proportion(param_values.translocation_proportion_);
   param_mut->set_inversion_proportion(param_values.inversion_proportion_);
+  #ifdef __EUKARYOTE
+  param_mut->set_max_tries(param_values.max_tries_);
+  param_mut->set_min_align_score(param_values.min_align_score_);
+  #endif
 
   exp_s->set_mutation_parameters(param_mut);
 

src/libaevol/mutation/MutationParams.cpp

@@ -85,6 +85,12 @@ MutationParams::MutationParams()
   translocation_proportion_ = 0.0;
   inversion_proportion_     = 0.0;
 
+  // ----------------------------------------------- Recombination parameters
+  #ifdef __EUKARYOTE
+  max_tries_ = 0;
+  min_align_score_ = 0;
+  #endif
+
   // ------------------------------------------------------------ Alignements
   align_fun_shape_    = SIGMOID;
   align_sigm_lambda_  = 4;
@@ -129,6 +135,12 @@ MutationParams::MutationParams(const MutationParams & model)
   translocation_proportion_ = model.translocation_proportion_;
   inversion_proportion_     = model.inversion_proportion_;
 
+  // ----------------------------------------------- Recombination parameters
+  #ifdef __EUKARYOTE
+  max_tries_ = model.max_tries_;
+  min_align_score_ = model.min_align_score_;
+  #endif
+
   // ------------------------------------------------------------ Alignements
   align_fun_shape_    = model.align_fun_shape_;
   align_sigm_lambda_  = model.align_sigm_lambda_;
@@ -177,6 +189,12 @@ MutationParams::MutationParams(gzFile backup_file)
   gzread(backup_file, &translocation_proportion_, sizeof(translocation_proportion_));
   gzread(backup_file, &inversion_proportion_,     sizeof(inversion_proportion_));
 
+  // ----------------------------------------------- Recombination parameters
+  #ifdef __EUKARYOTE
+  gzread(backup_file, &max_tries_,        sizeof(max_tries_));
+  gzread(backup_file, &min_align_score_,  sizeof(min_align_score_));
+  #endif
+
   // ------------------------------------------------------------ Alignements
   gzread(backup_file, &align_fun_shape_,     sizeof(align_fun_shape_));
   gzread(backup_file, &align_sigm_lambda_,   sizeof(align_sigm_lambda_));
@@ -245,6 +263,12 @@ void MutationParams::save(gzFile backup_file) const
   gzwrite(backup_file, &translocation_proportion_, sizeof(translocation_proportion_));
   gzwrite(backup_file, &inversion_proportion_,     sizeof(inversion_proportion_));
 
+  // ----------------------------------------------- Recombination parameters
+  #ifdef __EUKARYOTE
+  gzwrite(backup_file, &max_tries_,        sizeof(max_tries_));
+  gzwrite(backup_file, &min_align_score_,  sizeof(min_align_score_));
+  #endif
+
   // ------------------------------------------------------------ Alignements
   gzwrite(backup_file, &align_fun_shape_,     sizeof(align_fun_shape_));
   gzwrite(backup_file, &align_sigm_lambda_,   sizeof(align_sigm_lambda_));

src/libaevol/mutation/MutationParams.h

@@ -105,6 +105,12 @@ class MutationParams
     inline double translocation_proportion() const;
     inline double inversion_proportion() const;
 
+    // ----------------------------------------------- Recombination parameters
+    #ifdef __EUKARYOTE
+    inline int32_t max_tries() const;
+    inline int16_t min_align_score() const;
+    #endif
+
     // ------------------------------------------------------------ Alignements
     inline AlignmentFunctionShape align_fun_shape() const;
     inline double  align_sigm_lambda() const;
@@ -153,6 +159,12 @@ class MutationParams
     inline void set_translocation_proportion(double translocation_proportion);
     inline void set_inversion_proportion(double inversion_proportion);
 
+    // ----------------------------------------------- Recombination parameters
+    #ifdef __EUKARYOTE
+    inline void set_max_tries(int32_t max_tries);
+    inline void set_min_align_score(int16_t min_align_score);
+    #endif
+
     // ------------------------------------------------------------ Alignements
     inline void set_align_fun_shape(AlignmentFunctionShape align_fun_shape);
     inline void set_align_sigm_lambda(double align_sigm_lambda);
@@ -235,6 +247,12 @@ class MutationParams
     double translocation_proportion_;
     double inversion_proportion_;
 
+    // ----------------------------------------------- Recombination parameters
+    #ifdef __EUKARYOTE
+    int32_t max_tries_;
+    int16_t min_align_score_;
+    #endif
+
     // ------------------------------------------------------------ Alignements
     AlignmentFunctionShape align_fun_shape_;
     double  align_sigm_lambda_;
@@ -357,6 +375,18 @@ inline double MutationParams::inversion_proportion() const
   return inversion_proportion_;
 }
 
+// ----------------------------------------------- Recombination parameters
+#ifdef __EUKARYOTE
+inline int32_t MutationParams::max_tries() const
+{
+  return max_tries_;
+}
+inline int16_t MutationParams::min_align_score() const
+{
+  return min_align_score_;
+}
+#endif
+
 // ---------------------------------------------------------------- Alignements
 inline AlignmentFunctionShape MutationParams::align_fun_shape() const
 {
@@ -511,6 +541,18 @@ inline void MutationParams::set_inversion_proportion(double inversion_proportion
   inversion_proportion_ = inversion_proportion;
 }
 
+// ----------------------------------------------- Recombination parameters
+#ifdef __EUKARYOTE
+inline void MutationParams::set_max_tries(int32_t max_tries)
+{
+  max_tries_ = max_tries;
+}
+inline void MutationParams::set_min_align_score(int16_t min_align_score)
+{
+  min_align_score_ = min_align_score;
+}
+#endif
+
 // ---------------------------------------------------------------- Alignements
 inline void MutationParams::set_align_fun_shape(
     AlignmentFunctionShape align_fun_shape)