From dd70ee8222449d0618326155ec6db208d1c25dc9 Mon Sep 17 00:00:00 2001
From: wcancino <wcancino@331e1502-861f-0410-8da2-ba01fb791d7f>
Date: Fri, 23 Jan 2009 14:15:17 +0000
Subject: [PATCH] Small modifications

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1366 331e1502-861f-0410-8da2-ba01fb791d7f
---
 .../PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp         | 20 +++++++++++++++----
 .../PhyloMOEA/PhyloMOEA/likoptimizer.cpp      | 16 ++++++++++++---
 2 files changed, 29 insertions(+), 7 deletions(-)

diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
index 38bbf847f..c4c434dc3 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
@@ -22,7 +22,7 @@ RandomNr *rn;
 //Sequences *seq;
 long seed;
 //vector<phylotreeIND> arbores;
-string datafile,usertree, expid, path;
+string datafile,usertree, expid, path, algotype;
 double pcrossover, pmutation, kappa, alpha;
 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;
@@ -47,6 +47,7 @@ int main(int argc, char *argv[])
 	datafile = parser.createParam(string(), "data", "Datafile", 'd',"Param").value();
 	usertree = parser.createParam(string(), "treef", "Treefile", 't',"Param").value();
 	path = parser.createParam(string(), "path", "Treefile", 'p',"Param").value();
+	algotype = parser.createParam(string("nsgaii"), "algo", "Algorith, Type", 'b',"Param").value();
  	ostringstream convert;
  	convert << seed;
 	expid = parser.createParam(convert.str(), "expid", "Experiment ID", 'e',"Param").value();
@@ -158,9 +159,20 @@ int main(int argc, char *argv[])
 	
 //	apply<PhyloMOEO> ( byobj, population );
 //	population.printOn(cout);
-	moeoNSGAII2 < PhyloMOEO > nsgaII (cp, byobj, operadores);
-	
-	nsgaII(population);
+	if(algotype == "ibea")
+	{
+		moeoAdditiveEpsilonBinaryMetric < ObjectiveVector > metric;
+		moeoIBEA < PhyloMOEO > algo (cp, byobj, operadores, metric);
+		cout << "\n\nRunning IBEA ..." << endl;	
+		algo(population);
+	}	
+	else
+	{
+		moeoNSGAII < PhyloMOEO > algo (cp, byobj, operadores);
+		cout << "\n\nRunning NSGA-II ..." << endl;	
+		algo(population);
+
+	}
 	
 	cout << "\nCalculating Final Solutions...";
 	cout << "  done\n";
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/likoptimizer.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/likoptimizer.cpp
index 25e8b0c79..c3ccd20ca 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/likoptimizer.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/likoptimizer.cpp
@@ -31,10 +31,11 @@ void Step_LikOptimizer::optimize()
 	oldroot = invalid_node;
 
 	// calculate conditional likelihood
+	double likinit=Lik_calc->calculate_likelihood();
 	//cout << "likelihood inicial" << Lik_calc->calculate_likelihood() << endl;
 
 	graph::edge_iterator it_end = tree_ptr->TREE.edges_end();
-	
+	int niterations=0;
 	double sum,aux;
 	do{
 		it = tree_ptr->TREE.edges_begin();
@@ -70,9 +71,18 @@ void Step_LikOptimizer::optimize()
 			oldroot = a;
 			++it;
 		}
-		cout << '.';
+		if(niterations>=30) 
+		{
+			if(niterations == 30)cout << "\n probable problematic tree we will print the sum value for ten iterations more and quit this tree\n";
+			cout << sum << endl;
+		}
+		else cout << '.';
 		cout.flush();
-	}while(sum>=0.0001);
+		niterations++;
+		
+	}while(sum>=0.0001 && niterations<40);
+	double likfin = Lik_calc->calculate_likelihood();
+	cout << likinit << " -->" << likfin << endl;
 	//cout << "\nlikelihood final" << Lik_calc->calculate_likelihood() << endl;
 }