undocumented beta release tested with beta tests

cbcrg · Oct 19, 2020 · fb0821a · fb0821a
1 parent c3b4b29
commit fb0821a
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Showing 12 changed files with 56 additions and 24 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_13.45.3.f9661f5 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.4.c3b4b29 #_#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: a6b57a8c372452bf173b5ec65b296940
+config: 3bf7aeab773b9c2b78c14b0fafaab000
 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_13.45.3.f9661f5',
+    VERSION: 'Version_13.45.4.c3b4b29',
     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_13.45.3.f9661f5 documentation</title>
+  <title>T-Coffee Version_13.45.4.c3b4b29 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.3.f9661f5
+                Version_13.45.4.c3b4b29
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.3.f9661f5 documentation</li>
+      <li>T-Coffee Version_13.45.4.c3b4b29 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_13.45.3.f9661f5' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.4.c3b4b29' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.3.f9661f5' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.4.c3b4b29' #_#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/evaluate.c b/lib/dp_lib/evaluate.c
@@ -1731,11 +1731,13 @@ float tune_imaxD (Alignment *A, Constraint_list *CL, char *mode, float scan3D_ma
 {
   NT_node RT, T;
   float rf, brf,bimaxD;
-  int a;
+  int a, b,c;
   Sequence *S=aln2seq(A);
   Alignment *B;
+  int scan3D_min=5;
 
-
+  HERE ("BEFORE---REP=%s", getenv ("REPLICATES_4_TCOFFEE"));
+
   buffer_env ("REPLICATES_4_TCOFFEE");
   cputenv("REPLICATES_4_TCOFFEE=1");
 
@@ -1762,27 +1764,57 @@ float tune_imaxD (Alignment *A, Constraint_list *CL, char *mode, float scan3D_ma
   bimaxD=0;
   brf=0;
 
-  for (a=5; a<scan3D_max; a++)
+  for (a=scan3D_min; a<scan3D_max; a++)
     {
+      int process=1;
       B=struc_evaluate4tcoffee(A,CL, mode, (float)a, enb, in_matrix_name);
+
+      for (b=0; b<A->nseq; b++)
+	{
+	  for (c=0; c<A->nseq; c++)
+	    if (B->dm[b][c]<-99)
+	      {
+		b=A->nseq;
+		c=A->nseq;
+		process=0;
+	      }
+	}
+
+
       B=B->A;
       if (A->Tree && (A->Tree)->seq_al && (A->Tree)->seq_al[0])
 	{
-
-	  T=newick_string2tree((A->Tree)->seq_al[0]);
-	  rf=simple_tree_cmp(RT,T, S, 1);
-	  free_tree(T);
-	  fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> %6.2f %% Similiarity with ref_tree", a, rf) ;
-	  if ( rf>brf)
+	  if (process)
 	    {
-	      brf=rf;
-	      bimaxD=(float)a;
+	      T=newick_string2tree((A->Tree)->seq_al[0]);
+	      rf=simple_tree_cmp(RT,T, S, 1);
+	      free_tree(T);
+	      fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> %6.2f %% Similiarity with ref_tree", a, rf) ;
+	      if ( rf>brf)
+		{
+		  brf=rf;
+		  bimaxD=(float)a;
+		}
+	    }
+	  else
+	    {
+	      fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> Missing Values in the distance matrix", a) ;
 	    }
 	  free_aln (A->Tree); A->Tree=NULL;
-	}
+	}     
+    }
+  if (brf>0)
+    {
+      fprintf ( stderr, "\n!# Optimal Threshold: %d Angstrom  ==> %.2f %% RF similarity with ref_tree\n", (int)bimaxD, brf);
+    }
+  else
+    {
+      bimaxD=150000;
+      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)bimaxD);
     }
-  fprintf ( stderr, "\n!# Optimal Threshold: %d Angstrom  ==> %.2f %% RF similarity with ref_tree\n", (int)bimaxD, brf);
   restore_env ("REPLICATES_4_TCOFFEE");
+
+  HERE ("AFTER---REP=%s", getenv ("REPLICATES_4_TCOFFEE"));
   free_sequence (S,-1);
   return bimaxD;
 }

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-3
+4
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master f9661f5 [ahead 2] Merge branch 'master' of https://github.com/cbcrg/tcoffee
+* master c3b4b29 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.3.f9661f5
+Version_13.45.4.c3b4b29