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

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git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1335 331e1502-861f-0410-8da2-ba01fb791d7f
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wcancino 2009-01-15 15:27:23 +00:00
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contribution/branches/PhyloMOEA/PhyloMOEA/ProbMatrix.h Normal file
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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 PROBMATRIX_H
#define PROBMATRIX_H
#include "SubsModel.h"
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_chebyshev.h>
#include <map>
// store a set of the probability matric according some brach-lenght
class ProbMatrix
{
private:
SubstModel *model;
double branchlenght;
double *tmpexp;
static gsl_cheb_series **cs;
bool calculate_derivate;
void calculatepmatrix();
void calculatepmatrixchev();
void calculate_p1d_matrix();
void calculate_p2d_matrix();
public:
double *p, *p1d, *p2d;
ProbMatrix( SubstModel *m, double bl );
~ProbMatrix() { delete [] tmpexp; delete [] p; delete [] p1d; delete [] p2d; }
inline void init() { calculatepmatrix(); }
//void init();
void init_derivate();
inline double p_ij_t(int i, int j) { return p[i*4+j]; }
inline double p1d_ij_t(int i, int j) { return p1d[i*4+j]; }
inline double p2d_ij_t(int i, int j) { return p2d[i*4+j]; }
void set_branch_length(double l);
};
struct params { ProbMatrix *pmatrix; int i; int j; };
#endif