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/likoptimizer.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 LIK_OPTIMIZER_H
+#define LIK_OPTIMIZER_H
+#include "likelihoodcalculator.h"
+#include <gsl/gsl_math.h>
+
+
+// base class for all kind of Likelihood Optimizers
+
+class Lik_Optimizer
+{
+	protected:
+		LikelihoodCalculator *Lik_calc; // point to the calculator
+		
+	public:
+		Lik_Optimizer( LikelihoodCalculator &Lc) { Lik_calc = &Lc; }
+		virtual ~Lik_Optimizer() {  };
+		// call ot the optimize function
+		virtual void optimize() = 0;
+};
+
+// branch by branch optimizer
+
+class Step_LikOptimizer:public Lik_Optimizer
+{
+	protected:
+		edge current_edge;
+		node a, b, oldroot;
+		node invalid_node;
+		void update_partials();
+		void recalculate_cj(node root, node father);
+
+		Sequences *SeqData;
+		phylotreeIND *tree_ptr;
+		int nrates;
+
+		ProbMatrixContainer *probmatrixs; // container of probmatrixs
+		node_map< double *> *Partials, *Factors; //points to partials
+
+		ProbMatrix **p_current;
+	public:
+		virtual ~Step_LikOptimizer() { if(p_current!=NULL) delete [] p_current; };
+
+		Step_LikOptimizer( LikelihoodCalculator &Lc) : Lik_Optimizer(Lc) 
+		{
+			tree_ptr = Lc.tree_ptr;
+			probmatrixs = Lc.probmatrixs;
+			
+			Partials = &Lc.Partials;
+			Factors = &Lc.Factors;
+			SeqData = Lc.SeqData;
+			nrates = Lc.number_rates();
+			p_current = new ProbMatrix*[nrates]; // points to the matrixs for each rate
+		};
+		void optimize();
+		virtual void optimize_branch() = 0;
+		inline double 	recalculate_likelihood(double tnext)
+		{
+			for(int i=0; i< nrates; i++)
+			{
+				double len = tnext*Lik_calc->rate_probabilities(i);
+				//len = len < BL_MIN ? BL_MIN : len;
+				p_current[i]->set_branch_length(len);
+			}
+			return Lik_calc->sum_site_liks(); 
+		}
+		inline double sum_partials(int pos)
+		{ 
+			for(int i=0; i< nrates; i++)
+				Lik_calc->prob[i] = (p_current[i])->p;
+			return Lik_calc->sum_partials(pos); 
+		}
+		inline double sum_partials1d( int pos )	
+		{
+			for(int i=0; i< nrates; i++)
+				Lik_calc->prob[i] = (p_current[i])->p1d;
+			return  Lik_calc->sum_partials( pos);
+		}
+		inline double sum_partials2d( int pos )	
+		{
+			for(int i=0; i< nrates; i++)
+				Lik_calc->prob[i] = (p_current[i])->p2d;
+			return  Lik_calc->sum_partials( pos);
+		}
+};
+
+
+// Newton Step by Step optimizer:
+class Newton_LikOptimizer:public Step_LikOptimizer
+{
+	private:
+		double fnext; //likelihoods
+		double f1d, f2d; // derivates
+		double dk;	// search direction		
+		double linear_decreasing(); 
+	public:
+		virtual ~Newton_LikOptimizer() {};
+		Newton_LikOptimizer(LikelihoodCalculator &Lc): Step_LikOptimizer(Lc) {};
+		void calculate_1d2d_loglikelihood();
+		void optimize_branch();
+};
+#endif