recombine on alignment if enabled

src/libaevol/7/ExpManager_7.cpp

@@ -30,6 +30,7 @@
 #include "Promoter.h"
 #include "Protein.h"
 #include "Rna.h"
+#include "alignments/RecombAlignmentSearcher.h"
 #include "phenotype/fuzzy/AbstractFuzzy.h"
 #include "phenotype/fuzzy/Discrete_Double_Fuzzy.h"
 #include "phenotype/fuzzy/FuzzyFactory_7.h"
@@ -607,11 +608,24 @@ auto ExpManager_7::create_offspring(
     recombination_info[parent_idx].chrsm_end =
         recombination_info[parent_idx].chrsm_start == Chrsm::B ? Chrsm::A : Chrsm::B;
 
-    // Pick random points for recombination
-    recombination_info[parent_idx].recomb_pos_1 = prng.random(
-        individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_start).length());
-    recombination_info[parent_idx].recomb_pos_2 =
-        prng.random(individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_end).length());
+    // Pick points for recombination, either alignment-based or at random
+    auto alignment_params = exp_setup->alignment_params();
+    if (alignment_params) {
+      // Search for an alignement to determine the breakpoints for recombination
+      const auto& alignment = align::RecombAlignmentSearcher::find_alignment(
+          {&individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_start),
+           &individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_end)},
+          prng,
+          *alignment_params);
+      recombination_info[parent_idx].recomb_pos_1 = alignment.posA;
+      recombination_info[parent_idx].recomb_pos_2 = alignment.posB;
+    } else {
+      // Pick random points for recombination
+      recombination_info[parent_idx].recomb_pos_1 = prng.random(
+          individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_start).length());
+      recombination_info[parent_idx].recomb_pos_2 = prng.random(
+          individuals_[reproducers_info[parent_idx]]->dna(recombination_info[parent_idx].chrsm_end).length());
+    }
   }
 
   // Create recombinant chromosomes