mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:10:24 +08:00
64 lines
2.0 KiB
C++
64 lines
2.0 KiB
C++
// $Id: pairwiseGammaDistance.h 962 2006-11-07 15:13:34Z privmane $
|
|
|
|
#ifndef PAIRWISE_GAMMA_DISTANCE_H
|
|
#define PAIRWISE_GAMMA_DISTANCE_H
|
|
|
|
#include "likeDist.h"
|
|
#include "stochasticProcess.h"
|
|
#include "definitions.h"
|
|
#include "sequence.h"
|
|
#include "gammaDistribution.h"
|
|
#include "logFile.h"
|
|
|
|
#include <cmath>
|
|
using namespace std;
|
|
|
|
// Finds ML distance with a gamma-ASRV stochasticProcess for a pair of
|
|
// sequences while optimizing the alpha parameter for the given pair of
|
|
// sequences.
|
|
// Was called "njGamma::giveDistanceOptAlphaForPairOfSequences"
|
|
class pairwiseGammaDistance : public likeDist {
|
|
public:
|
|
explicit pairwiseGammaDistance(const stochasticProcess & sp,
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0)
|
|
: likeDist(sp,toll,maxPairwiseDistance) {}
|
|
|
|
explicit pairwiseGammaDistance(stochasticProcess & sp,
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0)
|
|
: likeDist(sp,toll,maxPairwiseDistance) {}
|
|
|
|
const MDOUBLE giveDistance(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights = NULL,
|
|
MDOUBLE* score=NULL,
|
|
MDOUBLE* alpha=NULL) const;
|
|
|
|
virtual pairwiseGammaDistance* clone() const {return new pairwiseGammaDistance(*this);}
|
|
|
|
void setAlpha(MDOUBLE alpha) {
|
|
(static_cast<gammaDistribution*>(_sp.distr()))->setAlpha(alpha);
|
|
}
|
|
|
|
|
|
protected:
|
|
MDOUBLE giveInitialGuessOfDistance(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score) const;
|
|
MDOUBLE optimizeAlphaFixedDist(const sequence& s1,
|
|
const sequence& s2,
|
|
stochasticProcess & sp,
|
|
const MDOUBLE branchL,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score=NULL) const;
|
|
MDOUBLE optimizeAlphaFixedDist(stochasticProcess & sp,
|
|
const countTableComponentGam & ctc,
|
|
const MDOUBLE branchL,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score=NULL) const;
|
|
};
|
|
|
|
#endif
|