aa33715685
git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
111 lines
3.7 KiB
C++
111 lines
3.7 KiB
C++
/***************************************************************************
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* Copyright (C) 2008 by Waldo Cancino *
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* wcancino@icmc.usp.br *
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* *
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* This program is free software; you can redistribute it and/or modify *
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* it under the terms of the GNU General Public License as published by *
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* the Free Software Foundation; either version 2 of the License, or *
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* (at your option) any later version. *
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* *
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* This program is distributed in the hope that it will be useful, *
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* but WITHOUT ANY WARRANTY; without even the implied warranty of *
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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* GNU General Public License for more details. *
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* *
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* You should have received a copy of the GNU General Public License *
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* along with this program; if not, write to the *
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* Free Software Foundation, Inc., *
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* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
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***************************************************************************/
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#include <eo>
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#include <moeo>
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#include <iostream>
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#include <fstream>
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#include <likoptimizer.h>
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#include <utils.h>
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extern gsl_rng *rn2;
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extern RandomNr *rn;
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//Sequences *seq;
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extern long seed;
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//vector<phylotreeIND> arbores;
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extern string datafile,usertree, expid, path;
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extern double pcrossover, pmutation, kappa, alpha;
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extern unsigned int ngenerations, popsize, ncats;
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void welcome_message()
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{
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cout << "\nPhyloMOEA, a program for multi-criteria phylogenetic inference\n";
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cout << "using maximum parsimony and maximum likelihood\n";
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cout << "Version 0.2 (ParadisEO backend) (c) 2009, Waldo Cancino";
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cout << "\n";
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}
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void save_exp_params(ostream &of=cout)
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{
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of << "PhyloMOEA Experiment Parameters" << endl;
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of << "--------------------------------------------" << endl;
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of << "Sequence Datafile : " << datafile << endl;
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of << "Initial Trees File : " << usertree << endl;
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of << "N. Generations : " << ngenerations << endl;
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of << "Population Size : " << popsize << endl;
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of << "Crossover Rate : " << pcrossover << endl;
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of << "Mutation Rate : " << pmutation << endl;
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of << "Discrete-Gamma Categs: " << ncats << endl;
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of << "Gamma Shape : " << alpha << endl;
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of << "HKY85+GAmma Kappa : " << kappa << endl;
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of << "Experiment ID : " << expid << endl;
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of << "Ramdom Seed : " << seed << endl;
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of << "Working Path : " << path << endl;
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}
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void optimize_solutions( eoPop<PhyloMOEO> &pop, LikelihoodCalculator &lik_calc)
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{
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int n = pop.size();
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for(int i=0; i<n; i++)
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{
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phylotreeIND &sol = pop[i].get_tree();
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lik_calc.set_tree(sol);
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cout << "\noptimizaing tree " << i+1 << " of " << n;
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// cout << endl << "likelihood inicial:" << lik_calc->calculate_likelihood() << endl;
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Newton_LikOptimizer test(lik_calc);
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test.optimize();
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pop[i].invalidate();
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//lik_calc->maximizelikelihood();
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//lik_calc->set_tree(*sol);
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// lik_calc->set_tree( *sol);
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// cout << endl << "likelihood final:" << lik_calc->calculate_likelihood() << endl;
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}
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}
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void readtrees(const char *fname, eoPop<PhyloMOEO> &poptree)
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{
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int ntrees;
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string s;
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fstream in_file;
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try{
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in_file.open(fname, ios::in);
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if(!in_file.is_open())
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{
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cout << fname << endl;
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throw ExceptionManager(10);
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}
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poptree.readFrom( in_file );
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return;
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}
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catch(ExceptionManager e)
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{
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e.Report();
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}
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in_file.close();
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}
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