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/SubsModel.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 SUBSMODEL_H
+#define SUBSMODEL_H
+// substitution model class
+// only nucleotides
+#include "eigensolver.h"
+#include "Patterns.h"
+#include <iostream>
+
+class SubstModel
+{
+	private:
+			
+		// instantaneus rate matrix 4x4
+		double rate[16]; // rate matrix
+		double **ievec; // inverse eigenvectors
+		double *frequences;
+		double a,b,c,d,e; // model parameterss
+		double kappa;
+		int model;
+		Sequences *patterns;
+		EigenSolver *eigensystem;
+		// define the substituion model
+		void construct_rate_matrix();
+		void setsubstmodel( int );
+		void calculatepmatrix(double);
+		void mult_frequences();
+		void set_diagonal();
+		void normalize();
+		void set_equal_frequences();
+		void init_rate_matrix();
+		void f81();
+		void k2p();
+		void jc69();
+		void hky85();
+		void gtr();
+		inline double get_rate(int i, int j) { return rate[4*i+j]; }
+		inline void set_rate( int i, int j, double val) { rate[4*i +j] = val; }
+	public:
+		enum models { JC69, F81, K2P, HKY85, GTR };
+		friend class ProbMatrix;
+		~SubstModel() { delete eigensystem; for(int i=0; i<4; i++) delete[] ievec[i]; delete [] ievec; }
+		SubstModel(Sequences &p, int m = 0);
+		void init();
+		void  set_kappa(double t) { kappa = t; init(); }
+		double get_kappa() { return kappa; }
+		void print_rate_matrix();
+};
+#endif
+
+
+
+
+
+