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First commit of PhyloMOEO files with some additions to Paradiseo-MOEO

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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino 2009-01-15 15:27:23 +00:00
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contribution/branches/PhyloMOEA/PhyloMOEA/utils.cpp Normal file
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/***************************************************************************
* Copyright (C) 2008 by Waldo Cancino *
* wcancino@icmc.usp.br *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include <eo>
#include <moeo>
#include <iostream>
#include <fstream>
#include <likoptimizer.h>
#include <utils.h>
extern gsl_rng *rn2;
extern RandomNr *rn;
//Sequences *seq;
extern long seed;
//vector<phylotreeIND> arbores;
extern string datafile,usertree, expid, path;
extern double pcrossover, pmutation, kappa, alpha;
extern unsigned int ngenerations, popsize, ncats;
void welcome_message()
{
cout << "\nPhyloMOEA, a program for multi-criteria phylogenetic inference\n";
cout << "using maximum parsimony and maximum likelihood\n";
cout << "Version 0.2 (ParadisEO backend) (c) 2009, Waldo Cancino";
cout << "\n";
}
void save_exp_params(ostream &of=cout)
{
of << "PhyloMOEA Experiment Parameters" << endl;
of << "--------------------------------------------" << endl;
of << "Sequence Datafile : " << datafile << endl;
of << "Initial Trees File : " << usertree << endl;
of << "N. Generations : " << ngenerations << endl;
of << "Population Size : " << popsize << endl;
of << "Crossover Rate : " << pcrossover << endl;
of << "Mutation Rate : " << pmutation << endl;
of << "Discrete-Gamma Categs: " << ncats << endl;
of << "Gamma Shape : " << alpha << endl;
of << "HKY85+GAmma Kappa : " << kappa << endl;
of << "Experiment ID : " << expid << endl;
of << "Ramdom Seed : " << seed << endl;
of << "Working Path : " << path << endl;
}
void optimize_solutions( eoPop<PhyloMOEO> &pop, LikelihoodCalculator &lik_calc)
{
int n = pop.size();
for(int i=0; i<n; i++)
{
phylotreeIND &sol = pop[i].get_tree();
lik_calc.set_tree(sol);
cout << "\noptimizaing tree " << i+1 << " of " << n;
// cout << endl << "likelihood inicial:" << lik_calc->calculate_likelihood() << endl;
Newton_LikOptimizer test(lik_calc);
test.optimize();
pop[i].invalidate();
//lik_calc->maximizelikelihood();
//lik_calc->set_tree(*sol);
// lik_calc->set_tree( *sol);
// cout << endl << "likelihood final:" << lik_calc->calculate_likelihood() << endl;
}
}
void readtrees(const char *fname, eoPop<PhyloMOEO> &poptree)
{
int ntrees;
string s;
fstream in_file;
try{
in_file.open(fname, ios::in);
if(!in_file.is_open())
{
cout << fname << endl;
throw ExceptionManager(10);
}
poptree.readFrom( in_file );
return;
}
catch(ExceptionManager e)
{
e.Report();
}
in_file.close();
}