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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1586 331e1502-861f-0410-8da2-ba01fb791d7f

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wcancino 2009-06-15 14:25:25 +00:00
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contribution/branches/PhyloMOEA/PhyloMOEA/utility.cpp Normal file
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#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;
}