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/*
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) 2012 BUI Quang Minh <email>
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 3 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, see <http://www.gnu.org/licenses/>.
*/
#ifndef RATEKATEGORY_H
#define RATEKATEGORY_H
#include "rateheterogeneity.h"
class PhyloTree;
/**
among-site-rate model that sites are categorized into K categories of equal proportion
where the K rates are optimized by ML instead of the Gamma distribution
*/
class RateKategory : virtual public RateHeterogeneity
{
public:
/**
constructor
@param ncat number of rate categories
@param tree associated phylogenetic tree
*/
RateKategory(int ncat, PhyloTree *tree);
/**
destructor
*/
virtual ~RateKategory();
/**
@return the number of rate categories
*/
virtual int getNRate() { return ncategory; }
/**
get the number of rate categories for site-specific category model
@return the number of rate categories
*/
virtual int getNDiscreteRate() { return ncategory; }
/**
@param category category ID from 0 to #category-1
@return the rate of the specified category
*/
virtual double getRate(int category) { return rates[category]; }
/**
Compute site-specific rates. Override this for Gamma model
@param pattern_rates (OUT) pattern rates. Resizing if necesary
@return total number of categories
*/
virtual int computePatternRates(DoubleVector &pattern_rates, IntVector &pattern_cat);
/**
the target function which needs to be optimized
@param x the input vector x
@return the function value at x
*/
virtual double targetFunk(double x[]);
/**
optimize model parameters
@return the best likelihood
*/
virtual double optimizeParameters(double epsilon);
/**
return the number of dimensions
*/
virtual int getNDim() { return (ncategory-1); }
/**
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);
protected:
/**
number of rate categories
*/
int ncategory;
/**
rates, containing ncategory elements
*/
double *rates;
/**
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);
};
#endif // RATEKATEGORY_H
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