[med-svn] r203 - trunk/packages/probcons/branches/upstream/current

[Charles Plessy]

Author: charles-guest
Date: 2007-02-14 15:12:19 +0100 (Wed, 14 Feb 2007)
New Revision: 203

Modified:
   trunk/packages/probcons/branches/upstream/current/Main.cc
   trunk/packages/probcons/branches/upstream/current/Makefile
   trunk/packages/probcons/branches/upstream/current/README
Log:
Load /tmp/tmp.Y9DaNA/probcons-1.11 into
trunk/packages/probcons/branches/upstream/current.


Modified: trunk/packages/probcons/branches/upstream/current/Main.cc
===================================================================
--- trunk/packages/probcons/branches/upstream/current/Main.cc	2007-02-10 03:26:03 UTC (rev 202)
+++ trunk/packages/probcons/branches/upstream/current/Main.cc	2007-02-14 14:12:19 UTC (rev 203)
@@ -1023,7 +1023,10 @@
 
   MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices, model);
 
+  SafeVector<int> oldOrdering;
   if (enableAlignOrder){
+    for (int i = 0; i < alignment->GetNumSequences(); i++)
+      oldOrdering.push_back (alignment->GetSequence(i)->GetSortLabel());
     alignment->SaveOrdering();
     enableAlignOrder = false;
   }
@@ -1037,6 +1040,12 @@
 
   cerr << endl;
 
+  if (oldOrdering.size() > 0){
+    for (int i = 0; i < (int) oldOrdering.size(); i++){
+      alignment->GetSequence(i)->SetSortLabel(oldOrdering[i]);
+    }
+  }
+
   // return final alignment
   return alignment;
 }
@@ -1402,6 +1411,9 @@
   for (int i = 0; i < numSeqs; i++) seqs[i] = alignment->GetSequence(i)->GetDataPtr();
   SafeVector<pair<int,int> > active;
   active.reserve (numSeqs);
+
+  SafeVector<int> lab;
+  for (int i = 0; i < numSeqs; i++) lab.push_back(alignment->GetSequence(i)->GetSortLabel());
   
   // for every column
   for (int i = 1; i <= alignLength; i++){
@@ -1410,10 +1422,11 @@
     active.clear();
     for (int j = 0; j < numSeqs; j++){
       if (seqs[j][i] != '-'){
-	active.push_back (make_pair(j, ++position[j]));
+	active.push_back (make_pair(lab[j], ++position[j]));
       }
     }
     
+    sort (active.begin(), active.end());
     outfile << setw(4) << ComputeScore (active, sparseMatrices) << endl;
   }
   

Modified: trunk/packages/probcons/branches/upstream/current/Makefile
===================================================================
--- trunk/packages/probcons/branches/upstream/current/Makefile	2007-02-10 03:26:03 UTC (rev 202)
+++ trunk/packages/probcons/branches/upstream/current/Makefile	2007-02-14 14:12:19 UTC (rev 203)
@@ -15,7 +15,7 @@
 #    c) RELEASE mode
 ################################################################################
 
-OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
+OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.11"
 
 # debug mode    
 #CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)

Modified: trunk/packages/probcons/branches/upstream/current/README
===================================================================
--- trunk/packages/probcons/branches/upstream/current/README	2007-02-10 03:26:03 UTC (rev 202)
+++ trunk/packages/probcons/branches/upstream/current/README	2007-02-14 14:12:19 UTC (rev 203)
@@ -105,3 +105,6 @@
    -- Reduced memory consumption by
       -- not storing posterior matrix transposes
       -- restricting consistency-derived posterior matrices to original posterior matrix
+
+1.11, 12/1/2006 (Chuong Do)
+   -- Fixed bug with conflict between --annot and -a options
\ No newline at end of file