mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 05:10:26 +08:00
73 lines
2.2 KiB
C++
73 lines
2.2 KiB
C++
// $Id: posteriorDistance.h 1752 2007-02-26 14:01:09Z itaymay $
|
|
|
|
|
|
#ifndef POSTERIOR_DISTANCE_H
|
|
#define POSTERIOR_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;
|
|
|
|
class posteriorDistance : public likeDist {
|
|
public:
|
|
explicit posteriorDistance(const stochasticProcess & sp,
|
|
const VVdoubleRep & posteriorProb, // pos * rate
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0);
|
|
|
|
explicit posteriorDistance(stochasticProcess & sp,
|
|
const VVdoubleRep & posteriorProb, // pos * rate
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0);
|
|
|
|
explicit posteriorDistance(const stochasticProcess & sp,
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0);
|
|
|
|
explicit posteriorDistance(stochasticProcess & sp,
|
|
const MDOUBLE toll =0.0001,
|
|
const MDOUBLE maxPairwiseDistance = 5.0);
|
|
posteriorDistance(const posteriorDistance& other);
|
|
virtual posteriorDistance* clone() const {return new posteriorDistance(*this);}
|
|
|
|
// distance is computed based on the posterior probability
|
|
const MDOUBLE giveDistance(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score=NULL) const;
|
|
|
|
MDOUBLE giveDistanceOptAlphaForEachPairOfSequences(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score=NULL,
|
|
MDOUBLE* alpha=NULL) const;
|
|
|
|
MDOUBLE giveDistanceOptAlphaForPairOfSequences(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score,
|
|
MDOUBLE* alpha) const;
|
|
|
|
void setPosterior(VVdoubleRep posteriorProb) {_posteriorProb = posteriorProb;}
|
|
void setAlpha(MDOUBLE alpha) {
|
|
(static_cast<gammaDistribution*>(_sp.distr()))->setAlpha(alpha);
|
|
}
|
|
|
|
private:
|
|
VVdoubleRep _posteriorProb;
|
|
MDOUBLE giveInitialGuessOfDistance(const sequence& s1,
|
|
const sequence& s2,
|
|
const vector<MDOUBLE> * weights,
|
|
MDOUBLE* score) const;
|
|
};
|
|
|
|
|
|
|
|
#endif
|