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// $Id: givenRatesMLDistance.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___GIVEN_RATES_ML_DISTANCE_H
#define ___GIVEN_RATES_ML_DISTANCE_H
#include "definitions.h"
#include "countTableComponent.h"
#include "likeDist.h"
#include "stochasticProcess.h"
#include "logFile.h"
#include <cmath>
using namespace std;
class givenRatesMLDistance : public likeDist {
public:
explicit givenRatesMLDistance(const stochasticProcess& sp,
const Vdouble& rates,
const MDOUBLE toll =0.0001,
const MDOUBLE maxPairwiseDistance = 5.0
)
: likeDist(sp, toll,maxPairwiseDistance),_rates(rates) {}
explicit givenRatesMLDistance(stochasticProcess& sp,
const Vdouble& rates,
const MDOUBLE toll =0.0001,
const MDOUBLE maxPairwiseDistance = 5.0
)
: likeDist(sp, toll,maxPairwiseDistance),_rates(rates) {}
explicit givenRatesMLDistance(const stochasticProcess& sp,
const MDOUBLE toll =0.0001,
const MDOUBLE maxPairwiseDistance = 5.0
)
: likeDist(sp, toll,maxPairwiseDistance),_rates(0) {}
explicit givenRatesMLDistance(stochasticProcess& sp,
const MDOUBLE toll =0.0001,
const MDOUBLE maxPairwiseDistance = 5.0
)
: likeDist(sp, toll,maxPairwiseDistance),_rates(0) {}
givenRatesMLDistance(const givenRatesMLDistance& other):
likeDist(static_cast<likeDist>(other)), _rates(other._rates) {}
virtual givenRatesMLDistance* clone() const {return new givenRatesMLDistance(*this);}
void setRates(const Vdouble &rates) {_rates = rates;}
// Returns the estimated ML distance between the 2 sequences.
// if score is given, it will be assigned the log-likelihood.
const MDOUBLE giveDistance(const sequence& s1,
const sequence& s2,
const vector<MDOUBLE> * weights,
MDOUBLE* score=NULL) const;
private:
Vdouble _rates;
};
#endif
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