undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.10.0ca201d #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.11.849521a #_#UPDATE_VERSION -- Populated by edit_version.pl
 The version ID is organized as follows: <Major Release>.<Latest Stable>.<Latest Beta>.<Github version tag>
 Content of this directory: 
 Linux Installation:

docs/.html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 0ecea4818fdec1a51e2a5269ad19920a
+config: 1998801ac93a32b98bcb9d9fb2982687
 tags: 33eac41acc08762151beb8f3b7b86c8f

docs/.html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'Version_13.45.10.0ca201d',
+    VERSION: 'Version_13.45.11.849521a',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/.html/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.10.0ca201d documentation</title>
+  <title>T-Coffee Version_13.45.11.849521a documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.10.0ca201d
+                Version_13.45.11.849521a
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.10.0ca201d documentation</li>
+      <li>T-Coffee Version_13.45.11.849521a documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.10.0ca201d' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.11.849521a' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.10.0ca201d' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.11.849521a' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

lib/dp_lib/evaluate.c

@@ -1885,6 +1885,9 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
   int **  ColPair=NULL;
   int n_col_pair;
   int scan3D_max;
+  int *used_sites;
+  int nsites=0;
+  int print_nsites=(getenv ("PRINT_NSITES")?1:0);
 
   //receives an alignment and a constraint list file in which contacts are declared
   //can produce scores, trees and score caches to colr MSAs
@@ -2010,6 +2013,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 
   max_col_sc=(double*)vcalloc (A->len_aln, sizeof (double));
   tot_col_sc=(double*)vcalloc (A->len_aln, sizeof (double));
+  used_sites=(int*)vcalloc (A->len_aln, sizeof (int*));
 
   max_sc=0;
   tot_sc=0;
@@ -2406,7 +2410,8 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 			   in=we;
 			   sc=pow(sc,distance_modeE)*we;
 
-
+			   used_sites[c1]=1;
+			   used_sites[c2]=1;
 			 }
 		   else if (modeM==contactsM)
 		     {
@@ -2503,11 +2508,19 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 		   max_randsc[A->nseq]+=in;
 		   tot_randsc[A->nseq]+=randsc;
 		  }
+
 		for (c1=0; c1<A->len_aln; c1++)for (c2=0; c2<A->len_aln; c2++)dm2[c1][c2]=0;
 	      }
 	    for (c1=0; c1<A->len_aln; c1++)for (c2=0; c2<A->len_aln; c2++)dm1[c1][c2]=0;
 	    }
-
+	  //Report the number of used columns
+
+	  for (nsites=0,c1=0; c1<A->len_aln; c1++)
+	    {
+	      nsites+=used_sites[c1];
+	      used_sites[c1]=0;
+	    }
+
 	  //Estimate Phylogenetic Tree Replicates
 	  if (tree)
 	    {
@@ -2555,6 +2568,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 	    sprintf (T->name[T->nseq], "%d",T->nseq); 
 
 	    fp=vfopen (T->dmF_list[T->nseq]=vtmpnam (NULL), "w");
+	    if (print_nsites)fprintf (fp, "# NSITES: %d\n", nsites);
 	    fprintf ( fp, "%d \n", A->nseq);
 	    for ( s1=0; s1<A->nseq;s1++)
 	      {
@@ -2585,6 +2599,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 	      }
 	    else 
 	      {
+		OUT->nsites=nsites;
 		OUT->dm=tot_pw_sc;
 	      }
 
@@ -2721,7 +2736,8 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 
   A->score=A->score_aln=OUT->score=OUT->score_aln=(int)(max_sc==0)?0:(tot_sc*1000)/max_sc;
 
-
+
+  vfree (used_sites);
   free_int (lu,  -1);
   free_int (dm1, -1);
   free_int (dm2, -1);

lib/io_lib/io_structures.h

@@ -275,7 +275,7 @@ struct Alignment
       int  **RepColList;//last item set to -1
       char **dmF_list;
 /*Score*/
-
+    int       nsites;  
     double ** dm;   
     int   *  score_seq;
     int   ** score_res;

lib/util_lib/reformat.c

@@ -11722,7 +11722,10 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
 	   if (!ACTION(1))cputenv ("scan3D=100");
 	   else cputenv ("scan3D=%s",ACTION(1));
 	 }
-
+       else if (strm (action, "print_nsites"))
+	 {
+	   cputenv ("PRINT_NSITES=1");
+	 }
        else if ( strm(action, "tree"))
 	 {
 	   if      (!ACTION(1))cputenv ("REPLICATES_4_TCOFFEE=1");

lib/version/build_version.version

@@ -1 +1 @@
-10
+11

lib/version/github.version

@@ -1 +1 @@
-* master 0ca201d undocumented beta release tested with beta tests
+* master 849521a undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.10.0ca201d
+Version_13.45.11.849521a