added the -et_mode=et|sp|sankoff|id and -msa_mode=etcoffee

cbcrg · Dec 9, 2015 · 3628a4c · 3628a4c
1 parent 031e5a2
commit 3628a4c
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Showing 2 changed files with 49 additions and 16 deletions.
diff --git a/lib/dp_lib/evaluate.c b/lib/dp_lib/evaluate.c
@@ -5070,6 +5070,8 @@ int col2, Constraint_list *CL)
 	  int score;
 	  int *sa;
 
+	  static char *mode;
+
 	  int sp=0;
 	  int et=0;
 	  int sankoff=1;
@@ -5078,6 +5080,18 @@ int col2, Constraint_list *CL)
 	  int debug=0;
 	  int cons=-1;
 
+
+
+	  if (!mode)
+	    {
+	      mode=get_string_variable ("et_mode");
+	      if (!mode)
+		{
+		  mode=(char*)vcalloc (100, sizeof (char));
+		  sprintf (mode, "et");
+		}
+	    }
+
 	  if (T==NULL)
 	    {
 	      T=main_read_tree (A->tname);	      
@@ -5137,35 +5151,35 @@ int col2, Constraint_list *CL)
 
 	  if (!N)return 0;
 
-	  if (sp)
+	  if (strm (mode, "sp"))
 	    {
-
+	      //sp score: debug
 	      score=column2sp_score(CL->S, key, N, nseq, matrix, gep);
 	    }
-	  else if (id)
+	  else if (strm (mode, "id"))
 	    {
+	      //id score based on tree topology
 	      sa=column2sankoff_score_id (key, N, nseq,matrix,gep);	      
-
 	      score=sa[27];
 	      score=score*-1+100;
 	      vfree(sa);
 	    }
 
-	  else if (et)
+	  else if (strm (mode,"et"))
 	    {
+	      //ET Score based on the sub tree
 	      score=column2et_score(CL->S, key, N, nseq, matrix, gep);
 
 	    }
-	  else if (sankoff)
+	  else if (strm (mode, "sankoff"))
 	    {
+	      //Sankoff tree score, cf Felsenstein
 	      int *sa=column2sankoff_score (key, N, nseq,matrix,gep);
 	      score=sa[0];
 	      for (a=1; a<27; a++)score=MAX(score, sa[a]);
-	      //score-=30;
-	      //fprintf ( stderr, "Pos: %3d %3d -> %4d\n", col1, col2, score);
 	      vfree (sa);
 	    }
-		
+	  
 	  for (a=0; a<nseq; a++)key[a]='\0';
 	  return score*SCORE_K;
 	}
@@ -5204,14 +5218,14 @@ int column2et_score (Sequence *S,int *lu, NT_node T, int nseq, int **c, int gep)
   if (!A)
     {
       A=declare_Alignment(S);
-      //treeF=vtmpnam (NULL);
-      //alnF=vtmpnam  (NULL);
-      alnF=(char*)vcalloc (100, sizeof(char));
-      treeF=(char*)vcalloc (100, sizeof(char));
+      treeF=vtmpnam (NULL);
+      alnF=vtmpnam  (NULL);
+      //alnF=(char*)vcalloc (100, sizeof(char));
+      //treeF=(char*)vcalloc (100, sizeof(char));
     }
 
-  sprintf (treeF, "cedricT");
-  sprintf (alnF, "cedricA");
+  //sprintf (treeF, "cedricT");
+  //sprintf (alnF, "cedricA");
 
   vfclose (print_ordered_tree (T,S, "newick", vfopen (treeF, "w")));
 

diff --git a/lib/t_coffee_lib/t_coffee.c b/lib/t_coffee_lib/t_coffee.c
@@ -414,6 +414,7 @@ int batch_main ( int argc, char **argv)
 	char *master_mode;
 	Sequence *MASTER_SEQ=NULL;
 	Sequence *TEMP_SEQ=NULL;
+	char *et_mode;
 
 	int blast_maxnseq;
 
@@ -3155,7 +3156,24 @@ declare_name (msa_mode);
 			    /*Min_value*/ "any"         ,\
 			    /*Max Value*/ "any"          \
 		   );
-
+declare_name (et_mode);
+ get_cl_param(\
+			    /*argc*/      argc          ,\
+			    /*argv*/      argv          ,\
+			    /*output*/    &le           ,\
+			    /*Name*/      "-et_mode"    ,\
+			    /*Flag*/      &garbage      ,\
+			    /*TYPE*/      "S"         ,\
+			    /*OPTIONAL?*/ OPTIONAL      ,\
+			    /*MAX Nval*/  1             ,\
+			    /*DOC*/       "Algorithm used to the et score: id, et, sankoff, sp"          ,\
+			    /*Parameter*/ &et_mode      ,\
+			    /*Def 1*/    "et"      ,\
+			    /*Def 2*/    "et"      ,		\
+			    /*Min_value*/ "any"         ,	\
+			    /*Max Value*/ "any"			\
+					  );
+
 declare_name (master_mode);
 get_cl_param(\
 			    /*argc*/      argc          ,\
@@ -5069,6 +5087,7 @@ get_cl_param(\
 		   if ( A->nseq==1);
 		   else if ( strm ( msa_mode, "etcoffee"))
 		     {
+		       set_string_variable ("et_mode", et_mode);
 		       //CL->get_dp_cost=slow_get_dp_cost;
 		       if (!CL->M)
 			 {