undocumented beta release tested with beta tests

cbcrg · Jan 18, 2022 · fa6a283 · fa6a283
1 parent c355d11
commit fa6a283
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Showing 13 changed files with 193 additions and 131 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_13.45.57.844f401 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.58.c355d11 #_#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: 77274e6f4dace44b936a99cb345421da
+config: 60d874a2e32c885e354c8281edc22a84
 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_13.45.57.844f401',
+    VERSION: 'Version_13.45.58.c355d11',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'singlehtml',

diff --git a/docs/.html/index.html b/docs/.html/index.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>T-Coffee Version_13.45.57.844f401 documentation</title>
+  <title>T-Coffee Version_13.45.58.c355d11 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
@@ -28,7 +28,7 @@
             <a href="#" class="icon icon-home"> T-Coffee
           </a>
               <div class="version">
-                Version_13.45.57.844f401
+                Version_13.45.58.c355d11
               </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <ul>
@@ -61,7 +61,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="#" class="icon icon-home"></a> &raquo;</li>
-      <li>T-Coffee Version_13.45.57.844f401 documentation</li>
+      <li>T-Coffee Version_13.45.58.c355d11 documentation</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>

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_13.45.57.844f401' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.58.c355d11' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.57.844f401' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.58.c355d11' #_#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
@@ -186,8 +186,7 @@ Alignment * main_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL, con
 {
 
   Alignment *TopS=NULL, *LastS=NULL, *CurrentS=NULL;
-
-
+
   if ( IN->A){IN=IN->A;}
   while (IN)
     {
@@ -225,11 +224,11 @@ Alignment * main_coffee_evaluate_output2 ( Alignment *IN,Constraint_list *CL, co
    else if ( strm (mode, "no"))return NULL;
    else if ( strstr( mode, "triplet") || strstr (mode, "tcs"))
      {
+
        return triplet_coffee_evaluate_output ( IN,CL);
      }
    else if ( strstr ( mode, "fast"))
      {
-
        return fast_coffee_evaluate_output ( IN,CL);
      }
    else if ( strstr ( mode, "slow"))