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

git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f

contribution/branches/PhyloMOEA/PhyloMOEA/likelihoodcalculator.h

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+/***************************************************************************
+ *   Copyright (C) 2005 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.             *
+ ***************************************************************************/
+#ifndef LIKELIHOODCALCULATOR_H
+#define LIKELIHOODCALCULATOR_H
+#include <phylotreeIND.h>
+#include <SubsModel.h>
+#include <probmatrixcontainer.h>
+//#include <pthread.h>
+#include <tree_limits.h>
+/**
+@author Waldo Cancino
+*/
+
+
+class LikelihoodCalculator{
+private:
+	edge bfocus;	// branch focus
+	node a,b;	// bfocus vertices (b can be a taxon, a never can be)
+	double **prob;	// point to the probability matrix associated to bfocus
+	int worker;		// for threading, not used really
+	int nrates;
+	double *rates_prob; // rate probabilities
+	double *rates_freq; // rate frequences
+	double alpha;
+	node root; // root of the likelihood calculator	
+	node oldroot, invalid_node; // old root and first root when change the focus of the likelihood calculations
+
+	// continous allocated memory to store partial results
+	double *part_memory_internal, // conditional likelihood of internal nodes 
+		*part_memory_taxons,  // conditional likelihood of internal nodes, no longer used
+		*part_memory_factors; // correction factors for nodes
+	
+	double *site_liks; // site likelihoods
+
+	// maps nodes to the continous memory	
+	node_map< double *> Partials; // maps nodes to the corresponding conditional likelihood 
+	node_map<double *> Factors;   // maps node to the corresponding correct factors
+
+	// external data	
+	phylotreeIND *tree_ptr; // point to the tree
+	SubstModel *model; // substitution model
+	ProbMatrixContainer *probmatrixs; // container of probmatrixs
+	Sequences *SeqData; // sequence data
+
+	
+	bool invalid_partials_taxons; // when received a new tree, the partials are invalidated
+	
+	// init partials memory
+	void init_partials();
+	
+	// prepare the post-order tree iterator
+	void calculate_partials(node n, node *);
+	// calculate conditional likelihood for the node father, from the son conditionals
+	void calculate_node_partial( node father, node son, edge edgeaux);
+
+	// likelihood sum of partial for the focus branch
+	double sum_partials( int pos);
+	double sum_partials_a_to_taxon( int pos );
+	double sum_partials_a_to_b_notaxon( int pos);
+
+	// sum the site likelihoods 
+	double sum_site_liks();
+
+	// allocate partial memory
+	void allocate_partials()
+	{
+		long total_pos = SeqData->pattern_count();
+		int ntaxons = SeqData->num_seqs();
+		part_memory_internal = new double[ (ntaxons-2) * nrates * total_pos * 4 ];
+		part_memory_factors = new double [ (2*ntaxons-2)  * total_pos];
+		site_liks = new double[total_pos];
+	}
+
+	// destroy partial memory
+	void deallocate_partials()
+	{
+		delete [] part_memory_internal;
+		delete [] part_memory_factors;
+		delete [] site_liks;
+	}
+
+	
+
+	// deprecated
+	double sum_partials2( node a, node b, edge edgeaux, int pos, int which=0);
+	void build_rates_sites();
+
+public:
+	bool corrected;
+	LikelihoodCalculator( phylotreeIND &ind, SubstModel &m, ProbMatrixContainer &p, unsigned int nr=1);
+	LikelihoodCalculator( phylotreeIND &ind, Sequences &Seqs, SubstModel &m, ProbMatrixContainer &p, unsigned int nr=1);
+
+	// main functions, prepare the object to calculate likelihood
+	double calculate_likelihood();
+	double get_site_lik(int i) { return site_liks[i]; }
+	double calculate_likelihood_exp(edge focus);
+	double calculate_all_likelihoods();
+	void update_partials();
+	void recalculate_cj(node n, node father);
+	void set_alpha(double a) { alpha = a; build_rates_sites(); };
+	// change the tree '
+	void set_tree( phylotreeIND &ind );
+	double rate_probabilities(int i) { return rates_prob[i]; }
+	int number_rates() { return nrates; }
+
+	
+	~LikelihoodCalculator()
+	{
+		//cout << "deallocando partialas" << endl;
+		deallocate_partials();
+		//cout << "deallocando o restante" << endl;
+		if(prob!=NULL) delete[] prob;
+		if(rates_prob!=NULL) delete [] rates_prob;
+		if(rates_freq!=NULL) delete [] rates_freq;
+	}
+
+	// change the dataset
+	void set_data( const Sequences &seqs);
+	
+	friend void* lik_slave_class(void *);
+
+	// frind class to do optimizations
+	friend class Step_LikOptimizer;
+};
+#endif