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