undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.17.4d93b67 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.18.e57994d #_#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:

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: 95a093d02ab14c2a2eadb0e970d0fd0a
+config: 3ddbdc944649c0a2d1c675dfff0c3663
 tags: 33eac41acc08762151beb8f3b7b86c8f

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_13.45.17.4d93b67',
+    VERSION: 'Version_13.45.18.e57994d',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/.html/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.17.4d93b67 documentation</title>
+  <title>T-Coffee Version_13.45.18.e57994d documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.17.4d93b67
+                Version_13.45.18.e57994d
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.17.4d93b67 documentation</li>
+      <li>T-Coffee Version_13.45.18.e57994d documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.17.4d93b67' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.18.e57994d' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.17.4d93b67' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.18.e57994d' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

lib/util_lib/reformat.c

@@ -367,21 +367,19 @@ int seq_reformat ( int argc, char **in_argv)
 		fprintf ( stdout, "\n     +remove_nuc.x........Remove Position 1, 2 or 3 of every codon");
 		fprintf ( stdout, "\n     +phylo3D.<tree|gtree>...Replaces evaluate3D for the estimation of 3D trees\n");
 		fprintf ( stdout, "\n     ........................The parameters below must be set BEFORE +phylo3D\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|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");
-		fprintf ( stdout, "\n        +phylo3d_dm..........distance mode (def=4)\n");
-		fprintf ( stdout, "\n        +phylo3d_exp.........distance exponentiation (def=2)\n");
-		fprintf ( stdout, "\n        +phylo3d_exp.........distance exponentiation (def=2)\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|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        +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");
+		fprintf ( stdout, "\n        +print_nsites...........adds to the dm output a line specifying the number of sites used\n");
+		fprintf ( stdout, "\n        +phylo3d_dm.............distance mode (def=4)\n");
+		fprintf ( stdout, "\n        +phylo3d_exp............distance exponentiation (def=2)\n");
+		fprintf ( stdout, "\n        +phylo3d_no_weight......unweighted distance_mode\n");
+		fprintf ( stdout, "\n        +ref_tree <file>........specifies the ref tree when +maxd=scan\n");
 
-
-
-		fprintf ( stdout, "\n        +ref_tree <file>..specifies the ref tree when +maxd=scan\n");
 		fprintf ( stdout, "\n     +evaluate3D..........strike|distances|contacts");
 		fprintf ( stdout, "\n     .....................Uses the -in2 contact_lib or the +pdb2contacts +seq2contacts ");
 		fprintf ( stdout, "\n     .....................If none, uses +seq2contacts ");
@@ -11729,7 +11727,13 @@ 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, "align_method"))cputenv ("align_method_4_TCOFFEE=%s",ACTION(1));
+       else if ( strm(action, "align_method"))
+	 {
+	   char *ml=NULL;
+	   int xx;
+	   for (xx=1; xx<n_actions; xx++)ml=csprintf (ml, "%s%s ", (ml)?ml:"",ACTION(xx));
+	   cputenv ("align_method_4_TCOFFEE=%s",ml);
+	 }
        else if ( strm(action, "gap"))cputenv ("gap_4_TCOFFEE=%s",ACTION(1));
        else if ( strm(action, "phylo3d_dm"))cputenv ("THREED_TREE_MODE=%s",ACTION(1));
        else if ( strm(action, "phylo3d_exp"))cputenv ("THREED_TREE_MODE_EXP=%s",ACTION(1));

lib/version/build_version.version

@@ -1 +1 @@
-17
+18

lib/version/github.version

@@ -1 +1 @@
-* master 4d93b67 undocumented beta release tested with beta tests
+* master e57994d undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.17.4d93b67
+Version_13.45.18.e57994d