undocumented beta release tested with beta tests

cbcrg · May 4, 2021 · fac255e · fac255e
1 parent eb089e8
commit fac255e
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Showing 12 changed files with 28 additions and 15 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_13.45.38.71bc186 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.39.eb089e8 #_#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: d9dadaf5dc63b804dcf95244b0afdaec
+config: 4470041d5544e0f34e41a87ca629c317
 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_13.45.38.71bc186',
+    VERSION: 'Version_13.45.39.eb089e8',
     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_13.45.38.71bc186 documentation</title>
+  <title>T-Coffee Version_13.45.39.eb089e8 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.38.71bc186
+                Version_13.45.39.eb089e8
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.38.71bc186 documentation</li>
+      <li>T-Coffee Version_13.45.39.eb089e8 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_13.45.38.71bc186' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.39.eb089e8' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.38.71bc186' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.39.eb089e8' #_#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
@@ -801,6 +801,8 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
       if (getenv ("THREED_TREE_NO_WEIGHTS"))no_weights=atoigetenv ("THREED_TREE_NO_WEIGHTS");
       else no_weights=1;
     }
+
+
 
    //first attempt-- Major issue because non symetrical and therefore not a distance
    if (!distance_mode)
@@ -852,23 +854,34 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
        we=1;
        sc=(double)(FABS((w1-w2)));
      }
-   else if ( distance_mode ==7)
+   else if ( distance_mode ==7)//Convexb -- Kimura like: 1-D^2 -- assiumes that D is over-estimated
      {
        double rdelta;
        we=((w1>w2)?w1:w2);
        rdelta=FABS((w1-w2))/we;
+
        rdelta*=rdelta;
        rscore[0]=1-rdelta;
-       rmax[1]=we;
+       rmax[0]=1;
        return rscore[0];
      }
-   else if ( distance_mode ==8)
+   else if ( distance_mode ==8)//Linear -- 1-D -- No assumption on D
+     {
+       double rdelta;
+       we=((w1>w2)?w1:w2);
+       rdelta=FABS((w1-w2))/we;
+       rscore[0]=1-rdelta;
+       rmax[0]=1;
+       return rscore[0];
+     }	 
+   else if  (distance_mode ==9)//concave -- (1-D)^2 -- Asumes D is iunder- estimated
      {
        double rdelta;
        we=((w1>w2)?w1:w2);
        rdelta=FABS((w1-w2))/we;
        rscore[0]=1-rdelta;
-       rmax[1]=we;
+       rscore[0]*=rscore[0];
+       rmax[0]=1;
        return rscore[0];
      }	 
 

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-38
+39
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 71bc186 undocumented beta release tested with beta tests
+* master eb089e8 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.38.71bc186
+Version_13.45.39.eb089e8