undocumented beta release tested with beta tests

cbcrg · Nov 24, 2020 · 2a569b9 · 2a569b9
1 parent 40c4fd3
commit 2a569b9
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Showing 12 changed files with 28 additions and 18 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_13.45.21.8ddb065 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.22.40c4fd3 #_#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: 31e400220cdb90ea995e1b98806c4ee5
+config: 38b0d66f9661303241a3c46516c62985
 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_13.45.21.8ddb065',
+    VERSION: 'Version_13.45.22.40c4fd3',
     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_13.45.21.8ddb065 documentation</title>
+  <title>T-Coffee Version_13.45.22.40c4fd3 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.21.8ddb065
+                Version_13.45.22.40c4fd3
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.21.8ddb065 documentation</li>
+      <li>T-Coffee Version_13.45.22.40c4fd3 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_13.45.21.8ddb065' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.22.40c4fd3' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.21.8ddb065' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.22.40c4fd3' #_#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
@@ -51,6 +51,9 @@ double scan_maxd (p3D *D)
   float bmaxd=1500;
   Sequence *S=aln2seq(D->A);
   Alignment *A=D->A;
+  int strict;
+  int bstrict=0;
+  int bnsites=0;
   int scan3D_min=(getenv("min_maxd_4_TCOFFEE"))?atof(getenv("min_maxd_4_TCOFFEE")):5;
   int scan3D_max=(getenv("max_maxd_4_TCOFFEE"))?atof(getenv("max_maxd_4_TCOFFEE")):D->extremed;
 
@@ -79,23 +82,29 @@ double scan_maxd (p3D *D)
   bmaxd=D->extremed;
 
   for (a=scan3D_min; a<scan3D_max; a++)
-    {
+    for (strict=0; strict<=1; strict++)
+      {
       static char *treeF=vtmpnam (NULL);
       D->maxd=(double)a*100;
       makerep(D,0);
       filter_columns_with_dist (A,D->pos, D->colrep, D->dm3d, D->maxd);
 
+      cputenv ("strict_maxd_4_TCOFFEE=%d", strict);
+
+
       if (aln2dm(D,A))
 	{
 	  dist2nj_tree (D->dm, A->name, A->nseq, treeF);
 	  T=main_read_tree(treeF);
 	  rf=simple_tree_cmp(RT,T, S, 1);
-	  if (verbose())fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> %6.2f %% Similiarity with ref_tree -- Nsites: %d", a, rf, D->nsites) ;
+	  if (verbose())fprintf ( stderr, "\n!# Threshold = %3d Angstrom ==> %6.2f %% Similiarity with ref_tree -- Nsites: %d strict_maxd: %d", a, rf, D->nsites, strict) ;
 
 	  if ( rf>=brf)
 	    {
 	      brf=rf;
 	      bmaxd=(double)a;
+	      bstrict=strict;
+	      bnsites=D->nsites;
 	    }
 	}
       else
@@ -105,14 +114,14 @@ double scan_maxd (p3D *D)
     }
   if (brf>0)
     {
-      if (verbose())fprintf ( stderr, "\n!# Optimal Threshold: %d Angstrom  ==> %.2f %% RF similarity with ref_tree\n", (int)bmaxd, brf);
+      if (verbose())fprintf ( stderr, "\n!# Optimal Threshold: %d Angstrom  ==> %.2f %% RF similarity with ref_tree +strict_maxd: %d Nsites: %d\n", (int)bmaxd, brf,bstrict,bnsites);
     }
   else
     {
       if (verbose())fprintf ( stderr, "\n!# WARNING -- Missing Values -- Could not find any suitable threshold - Use max value %d Angstrom -use a higher value for scan3D_max ", (int)bmaxd);
     }
   free_sequence (S, -1);
-
+  cputenv ("strict_maxd_4_TCOFFEE=%d", bstrict);
   return bmaxd*100;//in picometers
 }
 
@@ -375,7 +384,7 @@ Alignment * addtree (p3D *D,Alignment *A)
 }
 int filter_columns_with_dist(Alignment *B, int **pos,int **col, int***dm, double maxd)
 {
-  if ( getenv ("strict_maxd_4_TCOFFEE"))return filter_columns_with_dist_strict(B,pos,col,dm,maxd);
+  if ( getenv ("strict_maxd_4_TCOFFEE") && atoi(getenv ("strict_maxd_4_TCOFFEE"))==1)return filter_columns_with_dist_strict(B,pos,col,dm,maxd);
   else return filter_columns_with_dist_relaxed(B,pos,col,dm,maxd);
 } 
 
@@ -750,10 +759,11 @@ double phylo3d2score (double w1, double w2, double *rscore, double *rmax)
    //If 
    rmax[0]=we;
    rscore[0]=pow(sc,distance_modeE)*we;
-   return rscore[0]/rmax[0];
-
+   return rscore[0]/rmax[0];   
 }
 
 
 
+
+
 
diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-21
+22
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 8ddb065 undocumented beta release tested with beta tests
+* master 40c4fd3 undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.21.8ddb065
+Version_13.45.22.40c4fd3