From 5dc30552ddd5d3ced1ceed5735f060350837b2f8 Mon Sep 17 00:00:00 2001
From: wcancino <wcancino@331e1502-861f-0410-8da2-ba01fb791d7f>
Date: Tue, 24 Feb 2009 10:36:30 +0000
Subject: [PATCH] New version; synchronize in repository

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1461 331e1502-861f-0410-8da2-ba01fb791d7f
---
 contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp    | 5 +++--
 contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h | 3 +++
 contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp | 2 ++
 contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp        | 2 ++
 4 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
index 2db46165a..ce309f1b2 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
@@ -31,7 +31,7 @@ unsigned int ngenerations,  popsize, ncats;
 ofstream exp_data,evolution_data, best_media_scores, final_trees, final_pareto_trees, clades_pareto, clades_final,final_scores,pareto_scores;
 LikelihoodCalculator *lik_calc_ptr;
 phylotreeIND *templatetree_ptr;
-
+ProbMatrixContainer *probmatrixs_ptr;
 
 int main(int argc, char *argv[])
 {
@@ -64,7 +64,7 @@ int main(int argc, char *argv[])
 	if( datafile.size()==0 )
 	{
 		
-	 	if(getNodeRank()==1) parser.printHelp( cout );
+	  	if(getNodeRank()==1) parser.printHelp( cout );
 		return(-1);
 	}
 	
@@ -88,6 +88,7 @@ int main(int argc, char *argv[])
  	modelHKY.init();
  	modelHKY.set_kappa(kappa); 
  	ProbMatrixContainer probmatrixs(modelHKY);
+	probmatrixs_ptr = &probmatrixs;
 	LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs,ncats);
 	lik_calc.set_alpha(alpha);
  	modelHKY.init();
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h
index 5c3c88b2f..4181d7588 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h
@@ -26,6 +26,8 @@
 //#include <peo>
 #include <iostream>
 
+extern ProbMatrixContainer *probmatrixs_ptr;
+
 class PhyloEval : public moeoEvalFunc < PhyloMOEO >
 {
 public:
@@ -47,6 +49,7 @@ public:
         objVec[0] = parseval.fitch();
         objVec[1] = -likeval.calculate_likelihood();
         _sol.objectiveVector(objVec);
+	probmatrixs_ptr->clear();
 		//}
     }
 
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp
index f4022d05f..6f9353931 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp
@@ -1556,6 +1556,7 @@ void phylotreeIND::read_newick2(string newickstring)
 				if( read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1)
 				{
 					cout << "sintax error in position " << pos << endl;
+					cout << newickstring << endl;
 					throw ExceptionManager(11);
 					exit(1);
 				}
@@ -1594,6 +1595,7 @@ void phylotreeIND::read_newick2(string newickstring)
 				if(read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1)
 				{
 					cout << "sintax error at position " << pos << endl;
+					cout << newickstring << endl;
 					exit(1);
 			
 				}
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp
index fa3eda77a..1c4390695 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp
@@ -20,6 +20,7 @@
 
 #include <eo>
 #include <moeo>
+#include <peo>
 #include <iostream>
 #include <fstream>
 #include <likoptimizer.h>
@@ -88,6 +89,7 @@ void optimize_solutions( eoPop<PhyloMOEO> &pop)
 
 void optimize_solution( PhyloMOEO &indi)
 {
+	cout << "\noptimizaing tree in node " << getNodeRank() << endl;
 	phylotreeIND &sol = indi.get_tree();
 	lik_calc_ptr->set_tree(sol);
 	//cout << "\noptimizaing tree " << i+1 << " of " << n;