undocumented beta release tested with beta tests

cbcrg · Nov 25, 2020 · e3f346d · e3f346d
1 parent 7b3f015
commit e3f346d
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Showing 12 changed files with 17 additions and 22 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_13.45.23.2a569b9 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.24.7b3f015 #_#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: 7e7906b9710f0cffff5485a53a1771b9
+config: c122ad66236c9fbda053fb251bddea29
 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_13.45.23.2a569b9',
+    VERSION: 'Version_13.45.24.7b3f015',
     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_13.45.23.2a569b9 documentation</title>
+  <title>T-Coffee Version_13.45.24.7b3f015 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.23.2a569b9
+                Version_13.45.24.7b3f015
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.23.2a569b9 documentation</li>
+      <li>T-Coffee Version_13.45.24.7b3f015 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_13.45.23.2a569b9' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.24.7b3f015' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.23.2a569b9' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.24.7b3f015' #_#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
@@ -86,30 +86,25 @@ double scan_maxd (p3D *D)
   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=start; strict<=end; strict++)
     {
-
-      for (strict=start; strict<=end; strict++)
+      for (a=scan3D_min; a<scan3D_max; a++)
 	{
 	  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 (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 (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)
+	      if ( rf>brf || (rf==brf && D->nsites>bnsites) || (rf==brf && (double)a>=bmaxd))
 		{
 		  brf=rf;
 		  bmaxd=(double)a;
@@ -125,11 +120,11 @@ double scan_maxd (p3D *D)
     }
   if (brf>0)
     {
-      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);
+      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", (int)bmaxd);
+      if (verbose())fprintf ( stderr, "\n!# WARNING -- Missing Values -- Could not find any suitable threshold - Use max value +maxd %d Angstrom", (int)bmaxd);
     }
   free_sequence (S, -1);
   cputenv ("strict_maxd_4_TCOFFEE=%d", bstrict);

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-23
+24
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 2a569b9 undocumented beta release tested with beta tests
+* master 7b3f015 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.23.2a569b9
+Version_13.45.24.7b3f015