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/*
* modelcodonempirical.h
*
* Created on: May 29, 2013
* Author: minh
*/
#ifndef MODELCODONEMPIRICAL_H_
#define MODELCODONEMPIRICAL_H_
#include "modelcodon.h"
/**
* empirical codon model (e.g., Kosiol et al. 2007)
*/
class ModelCodonEmpirical: virtual public ModelCodon {
public:
/**
constructor
@param model_name model name, e.g., GY,YN
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelCodonEmpirical(const char *model_name, string model_params, StateFreqType freq, string freq_params,
PhyloTree *tree, bool count_rates = true);
/**
* destructor
*/
virtual ~ModelCodonEmpirical();
/**
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);
/**
* read codon model from a stream, modying rates and state_freq accordingly
* @param in input stream containing lower triangular matrix of rates, frequencies and list of codons
*/
void readCodonModel(istream &in);
};
#endif /* MODELCODONEMPIRICAL_H_ */
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