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New version; synchronize in repository

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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1461 331e1502-861f-0410-8da2-ba01fb791d7f
This commit is contained in:
wcancino 2009-02-24 10:36:30 +00:00
commit 5dc30552dd
4 changed files with 10 additions and 2 deletions
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5
contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEA.cpp
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@ -31,7 +31,7 @@ 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; 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; LikelihoodCalculator *lik_calc_ptr;
phylotreeIND *templatetree_ptr; phylotreeIND *templatetree_ptr;
ProbMatrixContainer *probmatrixs_ptr;
int main(int argc, char *argv[]) int main(int argc, char *argv[])
{ {
@ -64,7 +64,7 @@ int main(int argc, char *argv[])
if( datafile.size()==0 ) if( datafile.size()==0 )
{ {
if(getNodeRank()==1) parser.printHelp( cout ); if(getNodeRank()==1) parser.printHelp( cout );
return(-1); return(-1);
} }
@ -88,6 +88,7 @@ int main(int argc, char *argv[])
modelHKY.init(); modelHKY.init();
modelHKY.set_kappa(kappa); modelHKY.set_kappa(kappa);
ProbMatrixContainer probmatrixs(modelHKY); ProbMatrixContainer probmatrixs(modelHKY);
probmatrixs_ptr = &probmatrixs;
LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs,ncats); LikelihoodCalculator lik_calc(templatetree, modelHKY, probmatrixs,ncats);
lik_calc.set_alpha(alpha); lik_calc.set_alpha(alpha);
modelHKY.init(); modelHKY.init();

3
contribution/branches/PhyloMOEA/PhyloMOEA/PhyloMOEO_eval.h
View file

@ -26,6 +26,8 @@
//#include <peo> //#include <peo>
#include <iostream> #include <iostream>
extern ProbMatrixContainer *probmatrixs_ptr;
class PhyloEval : public moeoEvalFunc < PhyloMOEO > class PhyloEval : public moeoEvalFunc < PhyloMOEO >
{ {
public: public:
@ -47,6 +49,7 @@ public:
objVec[0] = parseval.fitch(); objVec[0] = parseval.fitch();
objVec[1] = -likeval.calculate_likelihood(); objVec[1] = -likeval.calculate_likelihood();
_sol.objectiveVector(objVec); _sol.objectiveVector(objVec);
probmatrixs_ptr->clear();
//} //}
} }

2
contribution/branches/PhyloMOEA/PhyloMOEA/phylotreeIND.cpp
View file

@ -1556,6 +1556,7 @@ void phylotreeIND::read_newick2(string newickstring)
if( read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1) if( read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1)
{ {
cout << "sintax error in position " << pos << endl; cout << "sintax error in position " << pos << endl;
cout << newickstring << endl;
throw ExceptionManager(11); throw ExceptionManager(11);
exit(1); exit(1);
} }
@ -1594,6 +1595,7 @@ void phylotreeIND::read_newick2(string newickstring)
if(read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1) if(read_taxonname_bl(newickstring, taxon_name, blen, pos) == -1)
{ {
cout << "sintax error at position " << pos << endl; cout << "sintax error at position " << pos << endl;
cout << newickstring << endl;
exit(1); exit(1);
} }

2
contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp
View file

@ -20,6 +20,7 @@
#include <eo> #include <eo>
#include <moeo> #include <moeo>
#include <peo>
#include <iostream> #include <iostream>
#include <fstream> #include <fstream>
#include <likoptimizer.h> #include <likoptimizer.h>
@ -88,6 +89,7 @@ void optimize_solutions( eoPop<PhyloMOEO> &pop)
void optimize_solution( PhyloMOEO &indi) void optimize_solution( PhyloMOEO &indi)
{ {
cout << "\noptimizaing tree in node " << getNodeRank() << endl;
phylotreeIND &sol = indi.get_tree(); phylotreeIND &sol = indi.get_tree();
lik_calc_ptr->set_tree(sol); lik_calc_ptr->set_tree(sol);
//cout << "\noptimizaing tree " << i+1 << " of " << n; //cout << "\noptimizaing tree " << i+1 << " of " << n;