nojhan/paradiseo
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Small modifications

Browse source 
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1366 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino 2009-01-23 14:15:17 +00:00
commit dd70ee8222
2 changed files with 29 additions and 7 deletions
Download patch file Download diff file Expand all files Collapse all files

20
contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
View file

@ -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";

16
contribution/branches/PhyloMOEA/PhyloMOEA/likoptimizer.cpp
View file

@ -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;
}