undocumented beta release tested with beta tests

cbcrg · Nov 24, 2020 · 7b3f015 · 7b3f015
1 parent 2a569b9
commit 7b3f015
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Showing 13 changed files with 56 additions and 41 deletions.
diff --git a/binaries/macosx/t_coffee b/binaries/macosx/t_coffee
diff --git a/build/web-readme.txt b/build/web-readme.txt
@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.22.40c4fd3 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.23.2a569b9 #_#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:

diff --git a/docs/.html/.buildinfo b/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: 38b0d66f9661303241a3c46516c62985
+config: 7e7906b9710f0cffff5485a53a1771b9
 tags: 33eac41acc08762151beb8f3b7b86c8f
diff --git a/docs/.html/.doctrees/environment.pickle b/docs/.html/.doctrees/environment.pickle
diff --git a/docs/.html/_static/documentation_options.js b/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_13.45.22.40c4fd3',
+    VERSION: 'Version_13.45.23.2a569b9',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/.html/index.html b/docs/.html/index.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.22.40c4fd3 documentation</title>
+  <title>T-Coffee Version_13.45.23.2a569b9 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.22.40c4fd3
+                Version_13.45.23.2a569b9
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.22.40c4fd3 documentation</li>
+      <li>T-Coffee Version_13.45.23.2a569b9 documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

diff --git a/docs/.html/objects.inv b/docs/.html/objects.inv
diff --git a/docs/conf.py b/docs/conf.py
@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.22.40c4fd3' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.23.2a569b9' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.22.40c4fd3' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.23.2a569b9' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/lib/dp_lib/phylo3d.c b/lib/dp_lib/phylo3d.c
@@ -27,6 +27,7 @@ Alignment *phylo3d (Alignment *inA, Constraint_list *CL)
 
   //Filter columns with distances
   if (D->maxd<MY_EPSILON)D->maxd=scan_maxd(D);
+
   D->N=filter_columns_with_dist (A,D->pos, D->col,D->dm3d,D->maxd);
 
   //Compute the first tree or DM
@@ -56,7 +57,7 @@ double scan_maxd (p3D *D)
   int bnsites=0;
   int scan3D_min=(getenv("min_maxd_4_TCOFFEE"))?atof(getenv("min_maxd_4_TCOFFEE")):5;
   int scan3D_max=(getenv("max_maxd_4_TCOFFEE"))?atof(getenv("max_maxd_4_TCOFFEE")):D->extremed;
-
+  int start, end;
   int a;
 
   if (!getenv ("REFERENCE_TREE"))
@@ -81,44 +82,54 @@ double scan_maxd (p3D *D)
   brf=0;
   bmaxd=D->extremed;
 
+
+  if (getenv ("soft_maxd_4_TCOFFEE")){start=0; end=0;}
+  else if ( getenv ("strict_maxd_4_TCOFFEE")){start=1; end=1;}
+  else{start=0; end=1;}
+
   for (a=scan3D_min; a<scan3D_max; a++)
-    for (strict=0; strict<=1; strict++)
-      {
-      static char *treeF=vtmpnam (NULL);
-      D->maxd=(double)a*100;
-      makerep(D,0);
-      filter_columns_with_dist (A,D->pos, D->colrep, D->dm3d, D->maxd);
-
-      cputenv ("strict_maxd_4_TCOFFEE=%d", strict);
-
-
-      if (aln2dm(D,A))
+    {
+
+      for (strict=start; strict<=end; strict++)
 	{
-	  dist2nj_tree (D->dm, A->name, A->nseq, treeF);
-	  T=main_read_tree(treeF);
-	  rf=simple_tree_cmp(RT,T, S, 1);
-	  if (verbose())fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> %6.2f %% Similiarity with ref_tree -- Nsites: %d strict_maxd: %d", a, rf, D->nsites, strict) ;
+	  static char *treeF=vtmpnam (NULL);
+	  D->maxd=(double)a*100;
+	  cputenv ("strict_maxd_4_TCOFFEE=%d", strict);
+	  makerep(D,0);
+	  filter_columns_with_dist (A,D->pos, D->colrep, D->dm3d, D->maxd);
 
-	  if ( rf>=brf)
+
+
+
+	  if (aln2dm(D,A))
+	    {
+	      dist2nj_tree (D->dm, A->name, A->nseq, treeF);
+	      T=main_read_tree(treeF);
+	      rf=simple_tree_cmp(RT,T, S, 1);
+
+	      if (verbose())fprintf ( stderr, "\n!# scan       : +maxd %3d %-12s ==> RF vs reftree %5.2f Nsites: %5d", a, (strict)?"+strict_maxd":"+soft_maxd", (float) 100-rf,D->nsites);
+
+	      if ( rf>=brf)
+		{
+		  brf=rf;
+		  bmaxd=(double)a;
+		  bstrict=strict;
+		  bnsites=D->nsites;
+		}
+	    }
+	  else
 	    {
-	      brf=rf;
-	      bmaxd=(double)a;
-	      bstrict=strict;
-	      bnsites=D->nsites;
+	      if (verbose())fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> Missing Values in the distance matrix", a) ;
 	    }
 	}
-      else
-	{
-	  if (verbose())fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> Missing Values in the distance matrix", a) ;
-	}
     }
   if (brf>0)
     {
-      if (verbose())fprintf ( stderr, "\n!# Optimal Threshold: %d Angstrom  ==> %.2f %% RF similarity with ref_tree +strict_maxd: %d Nsites: %d\n", (int)bmaxd, brf,bstrict,bnsites);
+      if (verbose())fprintf ( stderr, "\n!# scan result: +maxd %3d %-12s ==> RF vs reftree %5.2f Nsites: %5d\n", (int)bmaxd, (strict)?"strict_maxd":"soft_maxd", (float) 100-brf,bnsites);
     }
   else
     {
-      if (verbose())fprintf ( stderr, "\n!# WARNING -- Missing Values -- Could not find any suitable threshold - Use max value %d Angstrom -use a higher value for scan3D_max ", (int)bmaxd);
+      if (verbose())fprintf ( stderr, "\n!# WARNING -- Missing Values -- Could not find any suitable threshold - Use max value %d Angstrom", (int)bmaxd);
     }
   free_sequence (S, -1);
   cputenv ("strict_maxd_4_TCOFFEE=%d", bstrict);
@@ -365,8 +376,8 @@ Alignment * addtree (p3D *D,Alignment *A)
 
 
       fprintf (fp, "!# MAXD: %.2f  Angstrom",(float)D->maxd/100);
-      if (D->nsites >-1)   fprintf (fp, "-- NSITES: %d  %.2f%%",D->nsites, p1);
-      if (D->nsitepairs>-1)fprintf (fp, "-- NSITEPAIRS: %d %.2f%%", D->nsitepairs,p2);
+      if (D->nsites >-1)   fprintf (fp, " -- NSITES: %d  %.2f%%",D->nsites, p1);
+      if (D->nsitepairs>-1)fprintf (fp, " -- NSITEPAIRS: %d %.2f%%", D->nsitepairs,p2);
       fprintf (fp, "\n");
     }
   for ( s1=0; s1<A->nseq;s1++)

diff --git a/lib/util_lib/reformat.c b/lib/util_lib/reformat.c
@@ -370,7 +370,9 @@ int seq_reformat ( int argc, char **in_argv)
 		fprintf ( stdout, "\n        +enb <int>..............Specifies the number of excluded nb (def=3)\n");
 		fprintf ( stdout, "\n        +replicates <int>.......Specifies the number of replicates (def=0)\n");
 		fprintf ( stdout, "\n        +maxd <int|scan>........Specifies the distance cutoff (def=maximum distance on provided PDBs)\n");
-		fprintf ( stdout, "\n        +strict_maxd............ALL distances within pairs of columns must be <=maxd to be kept\n");
+		fprintf ( stdout, "\n        +strict_maxd............ALL distances within pairs of columns must be <=maxd for a pair to be kept\n");
+		fprintf ( stdout, "\n        +soft_maxd..............ANY distances within pairs of columns must be <=maxd for a pair to be kept\n");
+
 		fprintf ( stdout, "\n        +align_method.<st1 st2>.Specifies which T-Coffee method in gtree, use sa_pair for struc based aln\n");
 		fprintf ( stdout, "\n        +columns4tree.<file>....Specifies the columns to be used <c1> <c2> on each line (1-len_aln)\n");
 		fprintf ( stdout, "\n        +max_gap.<float>........Specifies the maximum fraction of gaps for columns to be considered (<=)\n");
@@ -11727,6 +11729,8 @@ void modify_data  (Sequence_data_struc *D1in, Sequence_data_struc *D2in, Sequenc
        else if ( strm(action, "max_maxd"))cputenv ("max_maxd_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "min_maxd"))cputenv ("min_maxd_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "strict_maxd"))cputenv ("strict_maxd_4_TCOFFEE=%s",ACTION(1));
+       else if ( strm(action, "soft_maxd"))cputenv ("soft_maxd_4_TCOFFEE=%s",ACTION(1));
+
        else if ( strm(action, "align_method"))
 	 {
 	   char *ml=NULL;

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-22
+23
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 40c4fd3 undocumented beta release tested with beta tests
+* master 2a569b9 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.22.40c4fd3
+Version_13.45.23.2a569b9