fixed fs_matrix not making it into probab_pair

lib/dp_lib/util_dp_drivers.c

@@ -198,17 +198,22 @@ Constraint_list *seq2list     ( Job_TC *job)
 		   || strm ( mode, "blast_pair")    || strm (mode, "lalign_blast_pair") \
 		   || strm ( mode, "viterbi_pair")  || strm (mode, "slow_pair")      || strm(mode, "glocal_pair") || strm (mode, "biphasic_pair") \
 		   || strm ( mode, "islow_pair")    || strm (mode, "tm_slow_pair") || strm (mode, "r_slow_pair") \
-		    || strm ( mode, "lalign_id_pair")|| strm (mode, "tm_lalign_id_pair") || strm (mode , "lalign_len_pair") || strm(mode, "fs_lalign_id_pair") \
+		    || strm ( mode, "lalign_id_pair")|| strm (mode, "tm_lalign_id_pair") || strm (mode , "lalign_len_pair")\
 		   || strm (mode, "prrp_aln")       || strm ( mode, "test_pair") \
 		   || strm (mode, "cdna_fast_pair") || strm (mode, "diaa_slow_pair") || strm (mode, "monoaa_slow_pair")\
 		   || strncmp (mode,"cdna_fast_pair",14)==0	\
 		   )
 	{
-
 	  A=fast_pair (job);
 	  RCL=aln2constraint_list ((A->A)?A->A:A, CL,weight);
 	}
-
+      else if ( strm (mode, "fs_lalign_id_pair"))
+	{
+	  set_string_variable ("fix_seq_seq_with_template", "_E_");
+	  A=fast_pair (job);
+	  RCL=aln2constraint_list ((A->A)?A->A:A, CL,weight);
+	  unset_string_variable ("fix_seq_seq_with_template");
+	}
       else if ( strm ( mode, "subop1_pair") || strm ( mode, "subop_pair") )
 	{
 	  A=fast_pair (job);
@@ -552,11 +557,11 @@ Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL)
 	      PW_CL->evaluate_residue_pair=evaluate_matrix_score;
 	      PW_CL->extend_jit=0;
 
-	      if (get_string_variable ("fs_matrix"))
-		PW_CL->M=read_matrice (get_string_variable ("fs_matrix"));
-	      else
-		PW_CL->M=read_matrice ("idmat");
+	      if (get_string_variable ("fs_matrix"))sprintf (PW_CL->method_matrix,"%s",get_string_variable ("fs_matrix"));
+	      else sprintf (PW_CL->method_matrix,"idmat");
 
+
+
 	      if (int_variable_isset ("fs_gop") && get_int_variable("fs_gop")<0)
 		PW_CL->gop=get_int_variable("fs_gop");
 	      else
@@ -2585,7 +2590,7 @@ Alignment * fast_pair      (Job_TC *job)
 		    }
 		  else
 		    buf[s]=S->seq[s];
-		  
+
 		  A->seq_al[a]=csprintf (A->seq_al[a], "%s", S->seq[s]);
 		  A->name[a]=csprintf (A->name[a], "%s", (CL->S)->name[s]);
 
@@ -4079,7 +4084,7 @@ int sa_align_groups (Alignment *A, Constraint_list *CL, int *used, int minid, in
   if (A->nseq==n) return -1;
   if (!ls){ls=declare_int (2, n); ns=(int*)vcalloc (3, sizeof (int));}
   if (!f)f=declare_int (n,n);
-  HERE ("***** 1******");
+
 
   sa_get_next_group (A, CL,used,&s0, &s1,f);
   if (g0==-1) return -1;
@@ -5816,12 +5821,13 @@ int pair_wise   (Alignment *A, int*ns, int **l_s,Constraint_list *CL )
 	Pwfunc function;
 
 
-
+	
 	if (read_size_int (ns, sizeof (int))==3 && ns[2]!=-1)
 	  {
+
 	    return pair_wise_ms(A,ns,l_s,CL);
 	  }
-
+	
 	/*Make sure evaluation functions update their cache if needed*/
 	A=update_aln_random_tag (A);
 

lib/dp_lib/util_dp_suboptimal_nw.c

@@ -1436,7 +1436,8 @@ Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixT
   int a;
   static float F=4; //potential number of full suboptimal alignmnents incorporated in the library
   static int tot_old, tot_new;
-
+
+
   if (!A)
     {
       free_int (list, -1);list=NULL;
@@ -1445,7 +1446,7 @@ Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixT
       vfree(entry); entry=NULL;
       return NULL;
     }
-  
+
   I=strlen (A->seq_al[ls[0][0]]);
   J=strlen (A->seq_al[ls[1][0]]);
 
@@ -1465,18 +1466,20 @@ Constraint_list *ProbaMatrix2CL (Alignment *A, int *ns, int **ls, int NumMatrixT
 
 
   totalProb = ComputeTotalProbability (I,J,NumMatrixTypes, NumInsertStates,forward, backward);
-
+  
   ij = 0;
   for (list_n=0,ij=0,i =0; i <= I; i++)
     {
       for (j =0; j <= J; j++, ij+=NumMatrixTypes)
 	{
 	  v= EXP (MIN(LOG_ONE,(forward[ij] + backward[ij] - totalProb)));
+
 	  if (v>thr)//Conservative reduction of the list size to speed up the sorting
 	    {
 	      list[list_n][0]=i;
 	      list[list_n][1]=j;
 	      list[list_n][2]=(int)((float)v*(float)NORM_F);
+
 	      list_n++;
 	    }
 	  if (v>0.01)old_n++;
@@ -2002,7 +2005,7 @@ float ** get_emitPairs (char *mat, char *alp, float **p, float *s)
     else if (strm (rmat, mat))return p;
 
     sprintf (rmat,"%s", mat);
-
+    
     M=read_matrice (mat);
     l=strlen (alp);
 

lib/util_lib/aln_convertion_util.c

@@ -5579,6 +5579,9 @@ int **fix_seq_seq (Sequence *S0, Sequence *Sx)
   char *use_template;
 
   //Trigger fixing with a template rather than the sequence itself
+  //currently not used
+
+
   use_template=get_string_variable ("fix_seq_seq_with_template");
 
   index=(int**)vcalloc ( S0->nseq, sizeof (int*));
@@ -5591,7 +5594,10 @@ int **fix_seq_seq (Sequence *S0, Sequence *Sx)
       if (i!=-1)
 	{
 	  seq=Sx->seq[i];
-	  if (use_template)seq=seq2E_template_string (Sx,i);
+	  if (use_template)
+	    {
+	      seq=seq2E_template_string (Sx,i);
+	    }
 	  if (!seq) seq=Sx->seq[i];
 	}
 
@@ -5609,8 +5615,9 @@ int **fix_seq_seq (Sequence *S0, Sequence *Sx)
 	  int nr0=0;
 	  int nr1=0;
 	  Alignment *B;
-
+	  //HERE ("\n%s\n%s\n\n",S0->seq[s0],seq);
 	  B=align_two_sequences (S0->seq[s0], seq, const_cast<char*>( (strm(S0->type, "PROTEIN"))?"blosum62mt":"idmat"), -4,-1, "myers_miller_pair_wise");
+	  //print_aln (B);
 	  for (c=0; c<B->len_aln; c++)
 	    {