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Add the option to perform branch lenght optimization

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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1552 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino 2009-03-17 09:29:10 +00:00
commit 8516b58dec
1 changed files with 12 additions and 9 deletions
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21
contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
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@ -25,7 +25,7 @@ RandomNr *rn;
//Sequences *seq;
long seed;
//vector<phylotreeIND> arbores;
string datafile,usertree, expid, path, algotype;
string datafile,usertree, expid, path, algotype, optimize_branch;
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;
@ -58,6 +58,7 @@ int main(int argc, char *argv[])
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();
optimize_branch = parser.createParam(string("yes"), "opt", "Optimize Branch Lenght", 'o',"Param").value();
ostringstream convert;
convert << seed;
expid = parser.createParam(convert.str(), "expid", "Experiment ID", 'e',"Param").value();
@ -237,14 +238,16 @@ int main(int argc, char *argv[])
//finalsolutions[0].get_tree().printNewick(cout);
lik_calc_ptr = &lik_calc;
// make the optimization phase also in parallel
peo :: init (argc, argv);
peoMultiStart <PhyloMOEO> ParallelLKOptimizationInit (optimize_solution);
peoWrapper ParallelLKOptimization (ParallelLKOptimizationInit, finalsolutions);
ParallelLKOptimizationInit.setOwner(ParallelLKOptimization);
if (getNodeRank()==1) cout << "\nOptimizing tree branch lenghts...\n";
peo :: run( );
peo :: finalize( );
if(optimize_branch=="yes")
{
peo :: init (argc, argv);
peoMultiStart <PhyloMOEO> ParallelLKOptimizationInit (optimize_solution);
peoWrapper ParallelLKOptimization (ParallelLKOptimizationInit, finalsolutions);
ParallelLKOptimizationInit.setOwner(ParallelLKOptimization);
if (getNodeRank()==1) cout << "\nOptimizing tree branch lenghts...\n";
peo :: run( );
peo :: finalize( );
}
if (getNodeRank()==1)
{