From 8643a23b1a918859b3793c6f9c9b734cd8e50665 Mon Sep 17 00:00:00 2001
From: wcancino <wcancino@331e1502-861f-0410-8da2-ba01fb791d7f>
Date: Mon, 15 Jun 2009 13:11:43 +0000
Subject: [PATCH] git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1585
 331e1502-861f-0410-8da2-ba01fb791d7f

---
 .../PhyloMOEA/PhyloMOEA/CMakeLists.txt         | 18 ++++++++++++++++++
 .../branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp |  3 ++-
 .../PhyloMOEA/PhyloMOEA/PhyloMOEO_archive.h    |  1 +
 .../PhyloMOEA/likelihoodcalculator.cpp         | 10 +++++-----
 ...oFrontByFrontCrowdingDiversityAssignment2.h | 10 +++++-----
 .../PhyloMOEA/parsimonycalculator.cpp          |  1 +
 6 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/CMakeLists.txt b/contribution/branches/PhyloMOEA/PhyloMOEA/CMakeLists.txt
index b1c5cc324..e43eb5f3e 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/CMakeLists.txt
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/CMakeLists.txt
@@ -47,11 +47,29 @@ SET( TESTOMP_SOURCES	eigensolver.cpp
 						testomp.cpp
 )
 
+SET( UTILITARY_SOURCES	eigensolver.cpp
+						likelihoodcalculator.cpp
+						matrixutils.cpp
+						probmatrixcontainer.cpp
+						parsimonycalculator.cpp
+						ProbMatrix.cpp
+						RandomNr.cpp
+						Sequences.cpp
+						SubsModel.cpp
+						phylotreeIND.cpp
+						treeIterator.cpp
+						utils.cpp 
+						likoptimizer.cpp
+						utility.cpp
+)
+
 
 ADD_EXECUTABLE( PhyloMOEA ${PHYLOMOEA_SOURCES} )
 ADD_EXECUTABLE( testomp   ${TESTOMP_SOURCES} )
+ADD_EXECUTABLE( utility   ${UTILITARY_SOURCES} )
 
 TARGET_LINK_LIBRARIES(PhyloMOEA gsl gslcblas GTL eo eoutils ga moeo cma peo rmc_mpi xml2)
 TARGET_LINK_LIBRARIES(testomp gsl gslcblas GTL eo eoutils ga moeo cma peo rmc_mpi xml2 gomp)
+TARGET_LINK_LIBRARIES(utility gsl gslcblas GTL eo eoutils ga moeo cma peo rmc_mpi xml2 gomp)
 
 INSTALL( TARGETS PhyloMOEA RUNTIME DESTINATION bin)
\ No newline at end of file
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
index f5adf9b24..74c809017 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
@@ -103,7 +103,7 @@ int main(int argc, char *argv[])
 	eoPop<PhyloMOEO> population(popsize, initializer);
 
 	peoMoeoPopEval <PhyloMOEO> eval(byobj);
-
+	
 
 	// Only the master node read the initial trees and writes ouput files
 	if(getNodeRank()==1)
@@ -214,6 +214,7 @@ int main(int argc, char *argv[])
 		peo :: run();
 		peo :: finalize();
 		//algo(population);
+		
 	}
 
 	if (getNodeRank()==1) 
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_archive.h b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_archive.h
index 63fb70742..eb3ed542d 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_archive.h
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_archive.h
@@ -45,6 +45,7 @@ class PhyloMOEOParetoSolutionsArchive:public moeoUnboundedArchive<PhyloMOEO>
 		{
 			create_file( filename );
 			if(title.size()>0) os << title << endl;
+			os.precision(10);
 			for(int i=0; i<size(); i++)	
 				os << operator[](i) << std::endl;
 			os.close();
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/likelihoodcalculator.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/likelihoodcalculator.cpp
index a3baa7772..929a6769e 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/likelihoodcalculator.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/likelihoodcalculator.cpp
@@ -310,16 +310,16 @@ double LikelihoodCalculator::calculate_likelihood()
 	for(int i=0; i<2; i++)
 		pthread_join(threads[i],NULL);*/
 	//cout << "calculando partials..." << endl;
-	struct timeval start;
-	gettimeofday(&start,NULL);
+	//struct timeval start;
+	//gettimeofday(&start,NULL);
 	calculate_partials( a, &b);
 	calculate_partials( b, &a);
 	//cout << "somando..." << endl;
 	// sum all partials
 	lik = sum_site_liks();
-	struct timeval end;
-	gettimeofday(&end,NULL);
-	print_elapsed_time_short(&start, &end);
+	//struct timeval end;
+	//gettimeofday(&end,NULL);
+	//print_elapsed_time_short(&start, &end);
 	return lik;
 }
 
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/moeoFrontByFrontCrowdingDiversityAssignment2.h b/contribution/branches/PhyloMOEA/PhyloMOEA/moeoFrontByFrontCrowdingDiversityAssignment2.h
index f5d5f56f4..01fa9b2e4 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/moeoFrontByFrontCrowdingDiversityAssignment2.h
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/moeoFrontByFrontCrowdingDiversityAssignment2.h
@@ -1,9 +1,9 @@
 /*
 * <moeoFrontByFrontCrowdingDiversityAssignment.h>
-* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
-* (C) OPAC Team, LIFL, 2002-2007
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2009
+* (C) OPAC Team, LIFL, 2002-2009
 *
-* Arnaud Liefooghe
+* Arnaud Liefooghe, Waldo Cancino
 *
 * This software is governed by the CeCILL license under French law and
 * abiding by the rules of distribution of free software.  You can  use,
@@ -40,7 +40,7 @@
 
 #include <diversity/moeoCrowdingDiversityAssignment.h>
 #include <comparator/moeoFitnessThenDiversityComparator.h>
-#include <moeoPtrComparator.h>
+#include <comparator/moeoPtrComparator.h>
 
 
 /**
@@ -49,7 +49,7 @@
  * Tis strategy assigns diversity values FRONT BY FRONT. It is, for instance, used in NSGA-II.
  */
 template < class MOEOT >
-class moeoFrontByFrontCrowdingDiversityAssignment2 : public moeoCrowdingDiversityAssignment < MOEOT >
+class moeoFrontByFrontCrowdingDiversityAssignment : public moeoCrowdingDiversityAssignment < MOEOT >
   {
   public:
 
diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/parsimonycalculator.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/parsimonycalculator.cpp
index bc591c087..71c095303 100644
--- a/contribution/branches/PhyloMOEA/PhyloMOEA/parsimonycalculator.cpp
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/parsimonycalculator.cpp
@@ -243,6 +243,7 @@ int ParsimonyCalculator::node_parsimony( node a, node b, unsigned char *result)
 	// calculate parsimony for taxon child, just union
 	int sum_parsy = 0;
 	int num_inf_sites = SeqData->infsite_count();
+	#pragma parallel for
 	for(int j=0; j< num_inf_sites; j++)
 		sum_parsy += set_parsimony( &set_internal[a][j*5], &set_internal[b][j*5], &result[j*5]) *  SeqData->infsite_count(j);	
 	return sum_parsy;