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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* minh.bui@univie.ac.at *
* *
* 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 MODELNONREV_H
#define MODELNONREV_H
#include "phylotree.h"
#include "modelgtr.h"
/**
The general non-reversible model
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class ModelNonRev : public ModelGTR
{
public:
ModelNonRev(PhyloTree *tree, bool count_rates = true);
/**
@return TRUE if model is time-reversible, FALSE otherwise
*/
virtual bool isReversible() { return false; };
/**
@return the number of rate entries, equal to the number of non-diagonal elements
of the rate matrix (since model is NOT reversible)
*/
virtual int getNumRateEntries() { return num_states*(num_states-1); }
virtual void getQMatrix(double *rate_mat);
/**
decompose the rate matrix into eigenvalues and eigenvectors
*/
virtual void decomposeRateMatrix();
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
/**
compute the transition probability matrix.
@param time time between two events
@param trans_matrix (OUT) the transition matrix between all pairs of states.
Assume trans_matrix has size of num_states * num_states.
*/
virtual void computeTransMatrix(double time, double *trans_matrix);
/**
compute the transition probability between two states
@param time time between two events
@param state1 first state
@param state2 second state
*/
virtual double computeTrans(double time, int state1, int state2);
protected:
virtual void freeMem();
/**
unrestricted Q matrix. Note that Q is normalized to 1 and has row sums of 0.
no state frequencies are involved here since Q is a general matrix.
*/
double *rate_matrix;
/**
temporary working space
*/
double *temp_space;
};
#endif
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