From 18ad6927d2510fd39f0d1de66f04f7e7e3a1761d Mon Sep 17 00:00:00 2001
From: wcancino <wcancino@331e1502-861f-0410-8da2-ba01fb791d7f>
Date: Mon, 15 Jun 2009 14:25:25 +0000
Subject: [PATCH] git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1586
 331e1502-861f-0410-8da2-ba01fb791d7f

---
 .../branches/PhyloMOEA/PhyloMOEA/utility.cpp  | 106 ++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 contribution/branches/PhyloMOEA/PhyloMOEA/utility.cpp

diff --git a/contribution/branches/PhyloMOEA/PhyloMOEA/utility.cpp b/contribution/branches/PhyloMOEA/PhyloMOEA/utility.cpp
new file mode 100644
index 000000000..d660ef7b3
--- /dev/null
+++ b/contribution/branches/PhyloMOEA/PhyloMOEA/utility.cpp
@@ -0,0 +1,106 @@
+#include <eo>
+#include <moeo>
+#include <PhyloMOEO.h>
+#include <PhyloMOEO_init.h>
+#include <PhyloMOEO_eval.h>
+#include <PhyloMOEO_archive.h>
+#include <PhyloMOEOProbMatrixContainerUpdater.h>
+#include <utils/moeoBestObjVecStat.h>
+#include <utils/moeoAverageObjVecStat.h>
+#include <omp.h>
+#include <utils.h>
+#include <apply.h>
+
+gsl_rng *rn2;
+RandomNr *rn;
+//Sequences *seq;
+long seed;
+//vector<phylotreeIND> arbores;
+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;
+LikelihoodCalculator *lik_calc_ptr;
+phylotreeIND *templatetree_ptr;
+ProbMatrixContainer *probmatrixs_ptr;
+
+int main(int argc, char *argv[])
+{
+	// measures execution time
+	struct timeval tempo1, tempo2, result;
+	eoParser parser(argc, argv);
+	datafile = parser.createParam(string(), "data", "Datafile", 'd',"Param").value();
+	int nthreads = parser.createParam(omp_get_max_threads(), "nthreads", "Numthreads", 't',"Param").value();
+	int nexp = parser.createParam(10, "nexps", "NumExps", 'e',"Param").value();
+	kappa = parser.createParam((double)(4.0), "kappa", "Kappa value", 'k',"Param").value();
+	alpha = parser.createParam((double)(2.0), "alpha", "Alpha value", 'a',"Param").value();
+	ncats = parser.createParam((unsigned int)(4), "nCat", "Number of Categories", 'r',"Param").value();
+	datafile = parser.createParam(string(), "data", "Datafile", 'd',"Param").value();
+	path = parser.createParam(string(), "path", "Treefile", 'p',"Param").value();
+
+	cout << "\n\nReading Sequence Datafile..." << path+datafile;
+
+	datafile = path+datafile;
+	Sequences seq6(datafile.c_str());
+//	Sequences seq7("/home/wcancino/experimentos/PhyloMOEA_0.2/omp_tests/datasets/TEST.500_5000");
+	cout << " done.\n";
+	// calculate datafile
+	cout << "calculating pattersn..." << endl;
+
+	seq6.calculate_patterns();
+	seq6.calculate_frequences();
+
+
+ 	gsl_rng *rn2 = gsl_rng_alloc(gsl_rng_default);
+ 	RandomNr *rn = new RandomNr(time(NULL));
+	omp_set_num_threads(nthreads);
+	phylotreeIND templatetree6( rn, seq6, rn2);
+	SubstModel modelHKY6( seq6, SubstModel::HKY85);
+	modelHKY6.init();
+	ProbMatrixContainer probmatrixs6(modelHKY6);
+	LikelihoodCalculator lik_calc6(templatetree6, modelHKY6, probmatrixs6, 4);
+	lik_calc6.set_alpha(alpha);
+	modelHKY6.init();
+ 	modelHKY6.set_kappa(kappa); 
+	Phyloraninit initializer6(templatetree6);
+
+	PhyloMOEOParetoSolutionsArchive pareto_solutions;
+	ParsimonyCalculator parsi_calc6(templatetree6);
+	PhyloEval byobj( parsi_calc6, lik_calc6 );
+
+	probmatrixs_ptr = &probmatrixs6;
+
+	moeoBestObjVecStat <PhyloMOEO> bestfit;
+	eoFileMonitor statfile(datafile + "_total_stats.txt");
+	statfile.add(bestfit);
+	for(int i=0; i < 2*nexp; i++)
+	{
+		eoPop<PhyloMOEO> population6(60, initializer6);
+
+		ostringstream os;
+		if(i<nexp) os << datafile << "_pareto_trees_serial_ibea";
+		else os << datafile << "_pareto_trees_serial_nsga";
+		os.fill('0');
+		os.width(2);
+		if(i<nexp) os << i+1 << ".txt";
+		else os << i+1-nexp << ".txt";
+		cout << "reading " << os.str() << endl;
+		readtrees(os.str().c_str(),population6);
+		//ofstream if(os.str().c_str());
+		cout << "filtering solutions....." << endl;
+		apply<PhyloMOEO> (byobj, population6);
+		pareto_solutions.operator()(population6);
+
+		bestfit.operator()(population6);
+		statfile.operator()();
+		cout.precision(15);
+	}
+	pareto_solutions.save_trees( datafile+"_total_pareto_trees.txt");
+	pareto_solutions.save_scores( datafile+"_total_pareto_scores.txt");
+
+//	of.close();
+	gsl_rng_free(rn2);
+	//	delete probmatrixs;
+	delete rn;
+	return 0;
+}
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