undocumented beta release tested with beta tests

cbcrg · Apr 26, 2021 · 71bc186 · 71bc186
1 parent 0c265b2
commit 71bc186
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Showing 12 changed files with 30 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_13.45.36.eae37da #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.37.0c265b2 #_#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: 06ee2d6d2b246f3d27c709dd89fc7c1d
+config: 965255841d33ca2a3fd2f0856740535c
 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_13.45.36.eae37da',
+    VERSION: 'Version_13.45.37.0c265b2',
     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_13.45.36.eae37da documentation</title>
+  <title>T-Coffee Version_13.45.37.0c265b2 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.36.eae37da
+                Version_13.45.37.0c265b2
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.36.eae37da documentation</li>
+      <li>T-Coffee Version_13.45.37.0c265b2 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_13.45.36.eae37da' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.37.0c265b2' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.36.eae37da' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.37.0c265b2' #_#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
@@ -327,6 +327,8 @@ int **col2bsrep2 (int **colin,int **colout, int ni)
 {
   /*select maxp sites with re-sampling among the maxp sites in colin*/
   /*keep the all against all that are declared in colin*/
+  /*The total number is guarranteed, but not the total number of pairs*/
+
 
   int i, j, k;
   int p1,p2, pmax;
@@ -362,16 +364,16 @@ int **col2bsrep2 (int **colin,int **colout, int ni)
 	  if (colin[i][0]>mni)mni=colin[i][0];
 	  if (colin[i][1]>mni)mni=colin[i][1];
 	}
-      l1=(int*)vcalloc (mni+1, sizeof (int));
-      ls=(int*)vcalloc (mni+1, sizeof (int));
+      l1=(int*)vcalloc (mni+1, sizeof (int));//cache for the columns
+      ls=(int*)vcalloc (mni+1, sizeof (int));//ls: list of sites => list of used columns, collected from tghe cache
       for (i=0; i<ni; i++)
 	{
 	  l1[colin[i][0]]=1;
 	  l1[colin[i][1]]=1;
 	}
       for (ns=0,i=0; i<=mni; i++)if (l1[i])ls[ns++]=i;
-
-      pairs=declare_int (mni+1,mni+1);
+      
+      pairs=declare_int (mni+1,mni+1);//Look up 2D array of all used columns - sparse because of the distance filtering
       for (i=0; i<ni; i++)
 	{
 	  int p1=colin[i][0];
@@ -784,7 +786,8 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
   static int   distance_mode;
   static double distance_modeE;
   static int no_weights;
-
+  //4 - initial measure (1-rlativeDelta)²=> concave function, different from Kimura
+  //7 - more Kimura like: (1-rlativeDelta²)=>convex
 
   if (!setparam)
     {
@@ -849,6 +852,17 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
        we=1;
        sc=(double)(FABS((w1-w2)));
      }
+   else if ( distance_mode ==7)
+     {
+       double rdelta;
+       we=((w1>w2)?w1:w2);
+       rdelta=FABS((w1-w2))/we;
+       rdelta*=rdelta;
+       rscore[0]=1-rdelta;
+       rmax[1]=we;
+       return rscore[0];
+     }
+
 
    if (no_weights)
      we=1;

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-36
+37
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master eae37da undocumented beta release tested with beta tests
+* master 0c265b2 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.36.eae37da
+Version_13.45.37.0c265b2