undocumented beta release tested with beta tests

cbcrg · Nov 19, 2020 · 4d93b67 · 4d93b67
1 parent 8d1d86e
commit 4d93b67
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Showing 12 changed files with 14 additions and 16 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_13.45.14.76e2591 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.15.8d1d86e #_#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: 193a0537723e280fd6e2e13db1b51573
+config: d98a586a128ba1c5e51040b0f0f3da4d
 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_13.45.14.76e2591',
+    VERSION: 'Version_13.45.15.8d1d86e',
     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_13.45.14.76e2591 documentation</title>
+  <title>T-Coffee Version_13.45.15.8d1d86e documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.14.76e2591
+                Version_13.45.15.8d1d86e
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.14.76e2591 documentation</li>
+      <li>T-Coffee Version_13.45.15.8d1d86e 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_13.45.14.76e2591' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.15.8d1d86e' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.14.76e2591' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.15.8d1d86e' #_#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/util_lib/reformat.c b/lib/util_lib/reformat.c
@@ -367,11 +367,12 @@ int seq_reformat ( int argc, char **in_argv)
 		fprintf ( stdout, "\n     +phylo3D.<tree|gtree>Replaces evaluate3D for the estimation of 3D trees\n");
 		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>..........Specifies the distance cutoff (def=maximum distance on provided PDBs)\n");
+		fprintf ( stdout, "\n        +maxd <int|scan>.....Specifies the distance cutoff (def=maximum distance on provided PDBs)\n");
 		fprintf ( stdout, "\n        +strict_maxsd........ALL distances within pairs of coolumns must be <=maxd to be kept\n");
 		fprintf ( stdout, "\n        +align_method.<st>...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");
+		fprintf ( stdout, "\n        +print_nsites........adds to the dm output a line specifying the number of sites used\n");
 
 
 
@@ -11712,10 +11713,7 @@ 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, "print_nsites"))cputenv ("PRINT_NSITES=1");
        else if ( strm(action, "ref_tree"))cputenv ("REFERENCE_TREE=%s", ACTION(1));
        else if ( strm(action, "replicates"))cputenv ("REPLICATES_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "enb"))cputenv ("enb_4_TCOFFEE=%s",ACTION(1));

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-14
+15
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 76e2591 undocumented beta release tested with beta tests
+* master 8d1d86e undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.14.76e2591
+Version_13.45.15.8d1d86e