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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 MODELDNA_H
#define MODELDNA_H
#include "modelmarkov.h"
#include <string>
/**
* return name and other information of an input model_name
* @param model_name DNA model name
* @param full_name (OUT) full model name with citation
* @param rate_type (OUT) a 6-digit string showing 6 rate constraints
* @param def_freq (OUT) base frequency type, either FREQ_UNNOWN, FREQ_EQUAL, or FREQ_ESIMATE
* @return unique model name or "" (empty string) if model_name is unrecognized
*/
string getDNAModelInfo(string model_name, string &full_name, string &rate_type, StateFreqType &def_freq);
/**
All DNA models are managed here
@author BUI Quang Minh <minh.bui@univie.ac.at>
*/
class ModelDNA : public ModelMarkov
{
friend class ModelPoMo;
public:
/**
constructor
@param tree associated tree for the model
*/
ModelDNA(PhyloTree *tree);
/**
constructor
@param model_name model name, e.g., JC, HKY.
@param freq state frequency type
@param tree associated phylogenetic tree
*/
ModelDNA(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);
/**
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();
/**
Read the rate parameters from a comma-separated string
It will throw error messages if failed
@param in input stream
*/
virtual void readRates(string str) throw(const char*);
/**
set the substitution rate parameters by a specification
@param rate_spec a string of six letters describing how rates are related
@return TRUE if successful, FALSE otherwise
*/
bool setRateType(string rate_spec);
/**
return the number of dimensions
*/
virtual int getNDim();
/**
write parameters, used with modeltest
@param out output stream
*/
virtual void writeParameters(ostream &out);
protected:
/**
this function is served for the multi-dimension optimization. It should pack the model parameters
into a vector that is index from 1 (NOTE: not from 0)
@param variables (OUT) vector of variables, indexed from 1
*/
virtual void setVariables(double *variables);
/**
this function is served for the multi-dimension optimization. It should assign the model parameters
from a vector of variables that is index from 1 (NOTE: not from 0)
@param variables vector of variables, indexed from 1
@return TRUE if parameters are changed, FALSE otherwise (2015-10-20)
*/
virtual bool getVariables(double *variables);
/**
rate parameter specification, a string of 6 characters
*/
string param_spec;
/** vector of boolean, TRUE if corresponding parameter is fixed and FALSE otherwise */
vector<bool> param_fixed;
};
#endif
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