undocumented beta release tested with beta tests

build/web-readme.txt

@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.13.4992314 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.14.76e2591 #_#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:

compile/makefile

@@ -498,6 +498,7 @@ DP_LIB_OBJECTS = \
 		evaluate_for_domain.o_$(OSNAME)\
 		evaluate_dirichlet.o_$(OSNAME)\
 		evaluate.o_$(OSNAME)\
+		phylo3d.o_$(OSNAME)\
 		showpair.o_$(OSNAME)\
 		fsa_dp.o_$(OSNAME)\
 		pavie_dp.o_$(OSNAME)

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: e31befbc5973b1d48ccf8d56ed99189b
+config: 193a0537723e280fd6e2e13db1b51573
 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_13.45.13.4992314',
+    VERSION: 'Version_13.45.14.76e2591',
     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_13.45.13.4992314 documentation</title>
+  <title>T-Coffee Version_13.45.14.76e2591 documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.13.4992314
+                Version_13.45.14.76e2591
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.13.4992314 documentation</li>
+      <li>T-Coffee Version_13.45.14.76e2591 documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

docs/conf.py

@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.13.4992314' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.14.76e2591' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.13.4992314' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.14.76e2591' #_#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/evaluate.c

@@ -1912,20 +1912,17 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
     {
       scan3D_max=atoigetenv("scan3D");
       unsetenv ("scan3D");
-      imaxD=tune_imaxD(A,CL,mode,(float)scan3D_max,enb,in_matrix_name);//Scan to maximize fit to cw 1D tree
+      imaxD=tune_imaxD(A,CL,mode,(float)scan3D_max,enb,in_matrix_name);//Scan to maximize fit to some pre-defined 3D tree
     }
 
   //Get arguments passed via environement
-  if (getenv ("TREE_GAP_4_TCOFFEE"))
-    {
-      max_gap  =atofgetenv("TREE_GAP_4_TCOFFEE");
-    }
+  if (getenv ("TREE_GAP_4_TCOFFEE")){max_gap  =atofgetenv("TREE_GAP_4_TCOFFEE");}
   else max_gap=0.5;
 
   if (getenv ("TREE_MODE_4_TCOFFEE"))tree_mode=getenv("TREE_MODE_4_TCOFFEE");
   else tree_mode="nj";
 
-
+  
   if (getenv ("REPLICATES_4_TCOFFEE"))
     {
       if ( strm (getenv ("REPLICATES_4_TCOFFEE"), "columns"))
@@ -1948,10 +1945,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
   if (!mode || strm (mode, "strike"))modeM=strikeM;
   else if (strm (mode, "distances"))modeM=distancesM;
   else if (strm (mode, "contacts"))modeM=contactsM;
-  else 	
-    {
-      printf_exit ( EXIT_FAILURE,stderr, "\nERROR: struc_evaluate4tcoffe::mode %s is unknown", (mode)?mode:"unset");
-    }
+  else {printf_exit ( EXIT_FAILURE,stderr, "\nERROR: struc_evaluate4tcoffe::mode %s is unknown", (mode)?mode:"unset");}
 
 
 
@@ -2041,7 +2035,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 
 
 
-  //Set the right evlaution matrix for proteins or RNA
+  //Set the right evaluation matrix for proteins or RNA
   if (modeM==strikeM)
     {
       matrix_name=(char*)vcalloc ((strlen(in_matrix_name)+2), sizeof (char));
@@ -2287,8 +2281,7 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 		//Fine if S2 has no structure for strike
 		if (modeM!=strikeM && !s2_has_contacts)continue;
 
-		//Now do the all against all
-
+		//Now do the all against all		
 
 		ic1=0;
 
@@ -2545,15 +2538,15 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
 
 
 
-	  //This is where the distance between two sequences gets turned into a % between 0 and a 100. 0: very similar, 100 maximal relative distance
+	  //This is where the distance between two sequences gets turned into a % between 0 and a 100. 0: very similar, 100 maximal relative distance, -100 missing value
 
 
 	  for (s1=0; s1<A->nseq; s1++)
 	      {
 		for (s2=0; s2<A->nseq; s2++)
 		  {
 		    if (s1==s2)tot_pw_sc[s1][s2]=0;
-		    else if (max_pw_sc[s1][s2]>0.000000001)
+		    else if (max_pw_sc[s1][s2]>MY_EPSILON)
 		      {
 			tot_pw_sc[s1][s2]/=max_pw_sc[s1][s2];
 			tot_pw_sc[s1][s2]=(double)100*((double)1-tot_pw_sc[s1][s2]);
@@ -2811,6 +2804,12 @@ Alignment *struc_evaluate4tcoffee (Alignment *A, Constraint_list *CL, char *mode
   return OUT;
 }   	
 
+
+
+
+
+
+
 Alignment *msa2distances (Alignment *A, Constraint_list *CL, float radius, float clus_th, int clus_min)
 {