Merge branch 'master' of github.com:stephaneguindon/phyml

stephaneguindon · Jun 12, 2018 · 66b622f · 66b622f
2 parents 46f9c7c + fade7b6
commit 66b622f
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Showing 3 changed files with 28 additions and 2 deletions.
diff --git a/src/mixt.c b/src/mixt.c
@@ -145,12 +145,18 @@ void MIXT_Chain_Sprs(t_tree *mixt_tree)
       if(tree->next_mixt) tree->best_spr->next_mixt = tree->next_mixt->best_spr;
       if(tree->prev_mixt) tree->best_spr->prev_mixt = tree->prev_mixt->best_spr;
 
-      For(i,2*tree->n_otu-2)
+      for(i=0;i<2*tree->n_otu-2;++i)
         {
           if(tree->next)      tree->spr_list_one_edge[i]->next      = tree->next->spr_list_one_edge[i];
           if(tree->prev)      tree->spr_list_one_edge[i]->prev      = tree->prev->spr_list_one_edge[i];
           if(tree->next_mixt) tree->spr_list_one_edge[i]->next_mixt = tree->next_mixt->spr_list_one_edge[i];
           if(tree->prev_mixt) tree->spr_list_one_edge[i]->prev_mixt = tree->prev_mixt->spr_list_one_edge[i];
+
+          if(tree->next)      tree->spr_list_all_edge[i]->next      = tree->next->spr_list_all_edge[i];
+          if(tree->prev)      tree->spr_list_all_edge[i]->prev      = tree->prev->spr_list_all_edge[i];
+          if(tree->next_mixt) tree->spr_list_all_edge[i]->next_mixt = tree->next_mixt->spr_list_all_edge[i];
+          if(tree->prev_mixt) tree->spr_list_all_edge[i]->prev_mixt = tree->prev_mixt->spr_list_all_edge[i];
+
         }
       tree = tree->next;
     }
@@ -1576,6 +1582,25 @@ void MIXT_Graft_Subtree(t_edge *mixt_target, t_node *mixt_link, t_node *mixt_lin
 //////////////////////////////////////////////////////////////
 //////////////////////////////////////////////////////////////
 
+void MIXT_Multiply_Scalar_Dbl(scalar_dbl *this, phydbl scalar)
+{
+  if(this == NULL) return;
+  else
+    {
+      scalar_dbl *buff;
+      buff = this;
+      do
+        {
+          buff->v *= scalar;
+          buff = buff->next;
+        }
+      while(buff);
+    }
+}
+
+//////////////////////////////////////////////////////////////
+//////////////////////////////////////////////////////////////
+
 void MIXT_Br_Len_Opt(t_edge *mixt_b, t_tree *mixt_tree)
 {
   t_tree *tree;

diff --git a/src/mixt.h b/src/mixt.h
@@ -103,5 +103,6 @@ void MIXT_Backup_Partial_Scale(t_node *mixt_d, t_edge *mixt_b, t_tree *mixt_tree
 void MIXT_Restore_Partial_Scale(t_node *mixt_d, t_edge *mixt_b, t_tree *mixt_tree);
 void MIXT_Set_Both_Sides(int yesno, t_tree *mixt_tree);
 void MIXT_Set_Br_Len(phydbl val, t_edge *mixt_b, t_tree *mixt_tree);
+void MIXT_Multiply_Scalar_Dbl(scalar_dbl *this, phydbl scalar);
 
 #endif
diff --git a/src/spr.c b/src/spr.c
@@ -791,7 +791,7 @@ void Global_Spr_Search(t_tree *tree)
   iter = 0;
   do
     {
-      if(iter) for(int i=0;i<2*tree->n_otu-3;++i) tree->a_edges[i]->l->v *= Rgamma((phydbl)(0.2*iter+1),(phydbl)(1./(0.2*iter+1)));
+      if(iter) for(int i=0;i<2*tree->n_otu-3;++i) MIXT_Multiply_Scalar_Dbl(tree->a_edges[i]->l,Rgamma((phydbl)(0.2*iter+1),(phydbl)(1./(0.2*iter+1))));
       Spr(tree->c_lnL,1.0,tree);
       Optimize_Br_Len_Serie(2,tree);