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/*
* modelcodonparametric.h
*
* Created on: May 29, 2013
* Author: minh
*/
#ifndef MODELCODONPARAMETRIC_H_
#define MODELCODONPARAMETRIC_H_
#include "modelcodon.h"
/**
* parametric codon model (e.g., Goldman-Yang, Muse-Gaut)
*/
class ModelCodonParametric: virtual public ModelCodon {
public:
/**
constructor
@param model_name model name, e.g., GY,YN
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelCodonParametric(const char *model_name, string model_params, StateFreqType freq, string freq_params,
PhyloTree *tree, bool count_rates = true);
/**
* destructor
*/
virtual ~ModelCodonParametric();
/**
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);
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
protected:
/** initialize Muse-Gaut 1994 model */
void initMG94();
/** initialize Goldman-Yang 1994 model (simplified version with 2 parameters omega and kappa */
void initGY94();
};
#endif /* MODELCODONPARAMETRIC_H_ */
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