undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.58.c355d11 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.59.fa6a283 #_#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: 60d874a2e32c885e354c8281edc22a84
+config: 1af7f06c93fc56c46f26e0dba51d3e65
 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_13.45.58.c355d11',
+    VERSION: 'Version_13.45.59.fa6a283',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'singlehtml',

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_13.45.58.c355d11 documentation</title>
+  <title>T-Coffee Version_13.45.59.fa6a283 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_13.45.58.c355d11
+                Version_13.45.59.fa6a283
               </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_13.45.58.c355d11 documentation</li>
+      <li>T-Coffee Version_13.45.59.fa6a283 documentation</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.58.c355d11' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.59.fa6a283' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.58.c355d11' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.59.fa6a283' #_#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/dp_lib/phylo3d.c

@@ -443,12 +443,22 @@ Alignment * addtree (p3D *D,Alignment *A)
   FILE *fp;
   int s1, s2;
   Alignment *TREEA=A->Tree;
-
+  int dotree=1;
+  if (!getenv ("THREED_TREE_DM"))dotree=0;
+
 
-  if (A->nseq>2)dist2nj_tree (D->dm, A->name, A->nseq, treeF);
-  TREEA->seq_al[TREEA->nseq]=file2string(treeF);
-  sprintf (TREEA->name[TREEA->nseq], "%d",TREEA->nseq+1); 	    
-  TREEA->seq_al[TREEA->nseq]=file2string(treeF);
+  if (A->nseq>2 && dotree)
+    {
+      dist2nj_tree (D->dm, A->name, A->nseq, treeF);
+      TREEA->seq_al[TREEA->nseq]=file2string(treeF);
+      sprintf (TREEA->name[TREEA->nseq], "%d",TREEA->nseq+1); 	    
+
+    }
+  else
+    {
+      sprintf (TREEA->name[TREEA->nseq], "%d",TREEA->nseq+1); 
+      TREEA->seq_al[TREEA->nseq]=csprintf (TREEA->seq_al[TREEA->nseq], "uncomputedtree");
+    }
   fp=vfopen (TREEA->dmF_list[TREEA->nseq], "w");
 
   fprintf ( fp, "%d \n", A->nseq);
@@ -690,6 +700,7 @@ Alignment *aln2trim3d (Alignment *A, Constraint_list *CL)
 
 int aln2dm (p3D *D, Alignment *A)
 {
+  // Turns A into either a distance matrix or a similarity matrix
   int rv=1;
   int s1, s2;
   int c1,c2, t;
@@ -728,7 +739,7 @@ int aln2dm (p3D *D, Alignment *A)
 double pair2dist(p3D *D, int s1, int s2)
 { 
   //s1 and s2 match the D->dm3d 
-  // check the offseet of the residue index - starts at 1 or 0
+  //check the offseet of the residue index - starts at 1 or 0
   double score=0;
   double max=0;
   double rscore, rmax;
@@ -775,7 +786,16 @@ double pair2dist(p3D *D, int s1, int s2)
 
     }
   if (max<MY_EPSILON)score=-100;
+  else if (getenv ("THREED_TREE_DM"))
+    {
+      if(atoigetenv ("THREED_TREE_DM")==1)
+	score=score/max;
+      else
+	score=sqrt(score/max);
+    }
   else score=(double)100*((double)1 - (score/max));
+
+
   return score;
 }
 double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
@@ -883,7 +903,25 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
        rscore[0]*=rscore[0];
        rmax[0]=1;
        return rscore[0];
-     }	 
+     }
+   else if (distance_mode==10)
+     {
+       static int setv=0;
+       if (!setv){cputenv ("THREED_TREE_DM=1");setv=1;}
+       rscore[0]=FABS((w1-w2));
+       rmax[0]=1;
+
+       return rscore[0];
+     }
+   else if (distance_mode==11)
+     {
+       static int setv=0;
+       if (!setv){cputenv ("THREED_TREE_DM=2");setv=1;}
+       rscore[0]=(w1-w2)*(w1-w2);
+       rmax[0]=1;
+       return rscore[0];
+     }
+
 
    if (no_weights)
      we=1;

lib/version/build_version.version

@@ -1 +1 @@
-58
+59

lib/version/github.version

@@ -1 +1 @@
-* master c355d11 undocumented beta release tested with beta tests
+* master fa6a283 undocumented beta release tested with beta tests

lib/version/version_number.version

@@ -1 +1 @@
-Version_13.45.58.c355d11
+Version_13.45.59.fa6a283