fixed warnings and tables in the doc

docs/tcoffee_installation.rst

@@ -353,7 +353,7 @@ If you want to have your own BLAST server to run your own databases, you should
 
 
 
-.. warning:: Note that T-Coffee is compliant with BLAST+, the latest NCBI Blast.
+.. tip:: T-Coffee is compliant with BLAST+, the latest NCBI Blast.
 
 Using a BLAST local version on Windows/cygwin
 ---------------------------------------------

docs/tcoffee_reference.rst

@@ -309,8 +309,6 @@ In general, you can set any environment variable using the -setenv flag. You can
 
 
 
-.. warning:: IMPORTANT:
-
 .. warning:: export > -setenv > -proxy, -email > t_coffee_env > default environment
 
 Note that when you use -setenv for PATH, the value you provide is concatenated TO THE BEGINNING of the current PATH value. This way you can force T-Coffee to use a specific version of an aligner.
@@ -616,7 +614,7 @@ Sequence Input
 
    *This flag sets the type of the sequences. If omitted, the type is guessed automatically. This flag is compatible with ClustalW.*
 
-.. warning:: Warning: In case of low complexity or short sequences, it is recommended to set the type manually.
+.. warning:: In case of low complexity or short sequences, it is recommended to set the type manually.
 
 -seq
 ^^^^
@@ -712,7 +710,7 @@ Structures, Sequences Methods and Library Input via the -in Flag
 
    *Default: -in=Mlalign_id_pair,Mclustalw_pair*
 
-.. warning:: Note: -in can be replaced with the combined usage of -aln, iprofile, .pdb, .lib, -method.
+.. note:: Note: -in can be replaced with the combined usage of -aln, iprofile, .pdb, .lib, -method.
 
    *See the box for an explanation of the -in flag. The following argument passed via -in*
 
@@ -775,7 +773,7 @@ Structures, Sequences Methods and Library Input via the -in Flag
 
    *This command results in a progressive alignment carried out on the sequences in seqfile. The procedure does not use any more the T-Coffee concistency based algorithm, but switches to a standard progressive alignment algorithm (like ClustalW or Pileup) much less accurate. In this context, appropriate gap penalties should be provided. The matrices are in the file source/matrices.h. Add-Hoc matrices can also be provided by the user (see the matrices format section at the end of this manual).*
 
-.. warning:: Warning: Xmatrix does not have the same effect as using the -matrix flag. The -matrix defines the matrix that will be used while compiling the library while the Xmatrix defines the matrix used when assembling the final alignment.
+.. warning:: **X**matrix does not have the same effect as using the -matrix flag. The -matrix defines the matrix that will be used while compiling the library while the Xmatrix defines the matrix used when assembling the final alignment.
 
 Profile Input
 -------------
@@ -2178,9 +2176,7 @@ Structural Analysis
 ===================
 APDB, iRMSD and tRMSD Parameters
 --------------------------------
-.. warning:: Warning: These flags will only work within the APDB package that can be invoked via the -other_pg parameter of T-Coffee:
-
-.. warning::  t_coffee -other_pg apdb -aln <your aln>
+.. warning:: These flags will only work within the APDB package that can be invoked via the -other_pg parameter of T-Coffee: t_coffee -other_pg apdb -aln <your aln>
 
 -quiet [Same as T-Coffee]
 ^^^^^^^^^^^^^^^^^^^^^^^^^

lib/dp_lib/evaluate.c

@@ -5052,7 +5052,7 @@ int get_domain_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1,
 	return score;
 	} 
 
-int column2sankoff_score (int *lu, NT_node T, int nseq, int **matrix, int gep);
+int* column2sankoff_score (int *lu, NT_node T, int nseq, int **matrix, int gep);
 int get_dp_cost_sankoff_tree ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL)
 	{
 	  int a, s, rs,r;
@@ -5061,18 +5061,19 @@ int get_dp_cost_sankoff_tree ( Alignment *A, int**pos1, int ns1, int*list1, int
 	  static int **matrix;
 
 	  NT_node N;
-	  int gep=-1;
+	  int gep=-10;
 	  int nseq=(CL->S)->nseq;
 	  int score;
-
+	  int *sa;
+
 	  if (T==NULL)
 	    {
 	      T=main_read_tree (A->tname);
 	      T=recode_tree    (T, (CL->S));
 	      matrix=read_matrice ("blosum62mt");
 	      key=(int*)vcalloc ((CL->S)->nseq, sizeof (int));
 	    }
-
+	 
 	  for ( a=0; a< ns1; a++)
 	    {
 	      s=list1[a];
@@ -5087,8 +5088,14 @@ int get_dp_cost_sankoff_tree ( Alignment *A, int**pos1, int ns1, int*list1, int
 	      r =pos2[s][col1];
 	      key[s]=(r>0)?(CL->S)->seq[s][r-1]:'-';
 	    }
+
 	  N=find_node_in_tree (key, nseq, T);
-	  score=column2sankoff_score (key, N, nseq, matrix,gep);
+
+	  sa=column2sankoff_score (key, N, nseq,matrix,gep);
+	  score=sa[0];
+	  for (a=1; a<=26; a++)score=MAX(sa[a],score);
+	  vfree(sa);
+
 	  for ( a=0; a< ns1; a++)
 	    {
 	      s=list1[a];
@@ -5103,11 +5110,62 @@ int get_dp_cost_sankoff_tree ( Alignment *A, int**pos1, int ns1, int*list1, int
 	      r =pos2[s][col1];
 	      key[s]=(r>0)?(CL->S)->seq[s][r-1]:'-';
 	    }
-	  return score;
+	  score*=SCORE_K;
+	  return score*SCORE_K;
 	}
-int column2sankoff_score (int *lu, NT_node T, int nseq, int **matrix, int gep)
+int* column2sankoff_score (int *lu, NT_node T, int nseq, int **c, int gep)
 {
-  return 1;
+  int inf=-999999;
+  if (!T)return NULL;
+  else if (T->isseq)
+    {
+      int *S=(int*)vcalloc (27, sizeof (int));
+      S=(int*)memset ((void*)S,inf, 27*sizeof(int));
+      char r=lu[T->lseq[0]];
+
+      if (r=='-')S[26]=gep;
+      else
+	{
+	  r=tolower(r)-'a';
+	  S[r]=c[r][r];
+	}
+      return S;
+    }
+  else
+    {
+      int i, j, k;
+      int *S =(int*)vcalloc (27, sizeof (int));
+      int *Sl=column2sankoff_score(lu,T->left , nseq, c, gep);
+      int *Sr=column2sankoff_score(lu,T->right, nseq, c, gep);
+
+      for (i=0; i<=26; i++)
+	{
+	  int max_j=inf;
+	  int max_k=inf;
+	  int mc;
+	  for (j=0; j<=26;j++)
+	    {
+
+	      if (i==26 || j==26)mc=gep;
+	      else mc=c[i][j];
+
+	      int v=((Sl[j])==inf)?inf:(mc+Sl[j]);
+	      if (v>max_j)max_j=v;
+	    }
+	  for (k=0; k<=26;k++)
+	    {
+	      if (i==26 || k==26)mc=gep;
+	      else mc=c[i][k];
+
+	      int v=(Sr[k]==inf)?inf:(mc+Sr[k]);
+	      if (v>max_k)max_k=v;
+	    }
+	  S[i]=(max_k==inf || max_j==inf)?inf:(max_k+max_j);
+	}
+      vfree(Sl);
+      vfree(Sr);
+      return S;
+    }
 }
 /*********************************************************************************************/
 /*                                                                                           */

lib/dp_lib/util_dp_gotoh_nw.c

@@ -789,6 +789,7 @@ int gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL)
 	static int sample=0;//road==0, random tie; road=1: upper road; road=2 lower road;
 	static int set_sample;
 
+
 	/********Prepare penalties*******/
 	gop=CL->gop*SCORE_K;
 	gep=CL->gep*SCORE_K;
@@ -902,7 +903,7 @@ int gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL)
 			    {
 
 			      sub=(CL->get_dp_cost) (A, pos0, ns[0], l_s[0], i-1, pos0, ns[1], l_s[1],j-1,CL);
-
+			      
 			      /*get the best Insertion*/
 			      l_gop=(i==lenal[0] || i==1 )?((TG_MODE==0)?gop:0):gop;
 			      l_gep=(i==lenal[0] || i==1)?((TG_MODE==2)?0:gep):gep;

lib/t_coffee_lib/t_coffee.c

@@ -5069,9 +5069,11 @@ get_cl_param(\
 		   if ( A->nseq==1);
 		   else if ( strm ( msa_mode, "sankoff_aln"))
 		     {
-
-		       CL->get_dp_cost=get_dp_cost_sankoff_tree;
+
+		       //CL->get_dp_cost=get_dp_cost_sankoff_tree;
+		       CL->get_dp_cost=slow_get_dp_cost;
 		       CL->pair_wise=gotoh_pair_wise;
+
 		       pc=tree_file;
 		       if ( strm (tree_file, "default") || !check_file_exists (tree_file))
 			 {