74 lines
2.7 KiB
C++
74 lines
2.7 KiB
C++
/***************************************************************************
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* Copyright (C) 2005 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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#ifndef SUBSMODEL_H
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#define SUBSMODEL_H
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// substitution model class
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// only nucleotides
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#include "eigensolver.h"
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#include "Patterns.h"
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#include <iostream>
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class SubstModel
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{
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private:
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// instantaneus rate matrix 4x4
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double rate[16]; // rate matrix
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double **ievec; // inverse eigenvectors
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double *frequences;
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double a,b,c,d,e; // model parameterss
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double kappa;
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int model;
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Sequences *patterns;
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EigenSolver *eigensystem;
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// define the substituion model
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void construct_rate_matrix();
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void setsubstmodel( int );
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void calculatepmatrix(double);
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void mult_frequences();
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void set_diagonal();
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void normalize();
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void set_equal_frequences();
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void init_rate_matrix();
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void f81();
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void k2p();
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void jc69();
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void hky85();
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void gtr();
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inline double get_rate(int i, int j) { return rate[4*i+j]; }
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inline void set_rate( int i, int j, double val) { rate[4*i +j] = val; }
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public:
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enum models { JC69, F81, K2P, HKY85, GTR };
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friend class ProbMatrix;
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~SubstModel() { delete eigensystem; for(int i=0; i<4; i++) delete[] ievec[i]; delete [] ievec; }
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SubstModel(Sequences &p, int m = 0);
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void init();
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void set_kappa(double t) { kappa = t; init(); }
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double get_kappa() { return kappa; }
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void print_rate_matrix();
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};
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#endif
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