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/*
* modelmorphology.h
*
* Created on: Apr 15, 2014
* Author: minh
*/
#ifndef MODELMORPHOLOGY_H_
#define MODELMORPHOLOGY_H_
#include "modelmarkov.h"
/**
* This class implement ML model for morphological data. Such models are:
* - Mk (Lewis 2001) a JC-type model
* - ORDERED: allowing only transition from state i to i-1 and i+1
* TODO: Mkv to account for absence of constant sites
*/
class ModelMorphology: public ModelMarkov {
public:
/**
constructor
@param model_name model name, e.g., JC, HKY.
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelMorphology(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 the number of dimensions
*/
virtual int getNDim();
/**
start structure for checkpointing
*/
virtual void startCheckpoint();
/**
save object into the checkpoint
*/
virtual void saveCheckpoint();
/**
restore object from the checkpoint
*/
virtual void restoreCheckpoint();
/**
* @return model name with parameters in form of e.g. GTR{a,b,c,d,e,f}
*/
virtual string getNameParams();
/**
write information
@param out output stream
*/
virtual void writeInfo(ostream &out);
/**
write parameters, used with modeltest
@param out output stream
*/
virtual void writeParameters(ostream &out);
/**
read the rates from an input stream. it will throw error messages if failed
@param in input stream
*/
virtual void readRates(istream &in) throw(const char*, string);
virtual ~ModelMorphology();
};
#endif /* MODELMORPHOLOGY_H_ */
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