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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 MODELBIN_H
#define MODELBIN_H
#include "modelmarkov.h"
/**
Model for Binary data
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class ModelBIN : public ModelMarkov
{
public:
/**
constructor
@param model_name model name, e.g., JC, HKY.
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelBIN(const char *model_name, string model_params, StateFreqType freq, string freq_params, PhyloTree *tree);
/**
initialization, called automatically by the constructor, no need to call it
@param model_name model name, e.g., JC, HKY.
@param freq state frequency type
*/
virtual void init(const char *model_name, string model_params, StateFreqType freq, string freq_params);
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams() { return name; }
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
};
#endif
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