manage mutations on linear chromosomes

src/libaevol/7/Dna_7.cpp

@@ -237,7 +237,11 @@ Mutation* Dna_7::do_switch(size_type pos
 
   // Look for potential new promoters containing the switched base
   if (length() >= PROM_SIZE)
+  #ifdef __EUKARYOTE
+    ann_chrsm_->promoter_list().look_for_new_promoters_around(*this, pos, pos + 1);
+  #else
     ann_chrsm_->promoter_list().look_for_new_promoters_around(*this, pos, Utils::mod(pos + 1, length()));
+  #endif
 
   #ifdef BASE_2
     return new PointMutation(pos);
@@ -247,6 +251,13 @@ Mutation* Dna_7::do_switch(size_type pos
 }
 
 Mutation* Dna_7::do_small_insertion(size_type pos, int16_t nb_insert, char* seq) {
+  size_type end_look;
+  #ifdef __EUKARYOTE
+    end_look = std::max(length_, pos + nb_insert);
+  #else
+    end_look = Utils::mod(pos + nb_insert, length_);
+  #endif
+
   // Remove the promoters that will be broken
   ann_chrsm_->promoter_list().remove_promoters_around(pos, length_);
 
@@ -264,7 +275,7 @@ Mutation* Dna_7::do_small_insertion(size_type pos, int16_t nb_insert, char* seq)
     }
     else {
       ann_chrsm_->promoter_list().move_all_promoters_after(pos, nb_insert, length_);
-      ann_chrsm_->promoter_list().look_for_new_promoters_around(*this, pos, Utils::mod(pos + nb_insert, length_));
+      ann_chrsm_->promoter_list().look_for_new_promoters_around(*this, pos, end_look);
     }
   }
 
@@ -298,6 +309,10 @@ Mutation* Dna_7::do_small_deletion(size_type pos, int16_t nb_del) {
     }
   }
   else { // the deletion contains the origin of replication
+  #ifdef __EUKARYOTE
+    printf("Deleting across position 0 : not permitted in linear chromosomes");
+    assert(false);
+  #endif
     // Do the deletion
     int32_t nb_del_at_pos_0 = nb_del - length() + pos;
 
@@ -413,6 +428,11 @@ Mutation* Dna_7::do_duplication(size_type pos_1, size_type pos_2, size_type pos_
 }
 
 Mutation* Dna_7::do_translocation(size_type pos_1, size_type pos_2, size_type pos_3, size_type pos_4, bool invert) {
+  #ifdef __EUKARYOTE
+    printf("Code not tested with translocation in eukaryote. Are you sure ?");
+    assert(false);
+  #endif
+
   auto pos_min = std::min(pos_1, std::min(pos_2, std::min(pos_3, pos_4)));
 
   if (not invert) {
@@ -463,6 +483,10 @@ Mutation* Dna_7::do_inversion(size_type pos_1, size_type pos_2) {
   //                                             pos_2    <-'
   //
 
+  #ifdef __EUKARYOTE
+    assert(pos_1 <= pos_2);
+  #endif
+
         if (length_ == 1)
         {
             printf("*** genome of size 1 ; inversion not done *** \n");
@@ -509,6 +533,10 @@ Mutation* Dna_7::do_inversion(size_type pos_1, size_type pos_2) {
 
 
 Mutation* Dna_7::do_deletion(size_type pos_1, size_type pos_2) {
+  #ifdef __EUKARYOTE
+    assert(pos_1 <= pos_2);
+  #endif
+
   // Delete segment going from pos_1 (included) to pos_2 (excluded)
     if (length_ == 1)
     {