64 lines
2.4 KiB
C++
64 lines
2.4 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 PROBMATRIX_H
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#define PROBMATRIX_H
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#include "SubsModel.h"
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#include <gsl/gsl_linalg.h>
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#include <gsl/gsl_math.h>
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#include <gsl/gsl_chebyshev.h>
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#include <map>
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// store a set of the probability matric according some brach-lenght
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class ProbMatrix
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{
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private:
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SubstModel *model;
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double branchlenght;
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double *tmpexp;
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static gsl_cheb_series **cs;
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bool calculate_derivate;
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void calculatepmatrix();
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void calculatepmatrixchev();
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void calculate_p1d_matrix();
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void calculate_p2d_matrix();
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public:
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double *p, *p1d, *p2d;
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ProbMatrix( SubstModel *m, double bl );
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~ProbMatrix() { delete [] tmpexp; delete [] p; delete [] p1d; delete [] p2d; }
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inline void init() { calculatepmatrix(); }
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//void init();
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void init_derivate();
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inline double p_ij_t(int i, int j) { return p[i*4+j]; }
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inline double p1d_ij_t(int i, int j) { return p1d[i*4+j]; }
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inline double p2d_ij_t(int i, int j) { return p2d[i*4+j]; }
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void set_branch_length(double l);
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};
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struct params { ProbMatrix *pmatrix; int i; int j; };
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#endif
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