mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:20:25 +08:00
52 lines
2.5 KiB
C++
52 lines
2.5 KiB
C++
#ifndef __GENERAL_GAMMA_DIST_PLUSINV
|
|
#define __GENERAL_GAMMA_DIST_PLUSINV
|
|
/************************************************************
|
|
This class describes a combination of a predefined dsitrubtion ,
|
|
with an additional invariant category of probability _Pinv
|
|
This category is always the last rate category (i.e., rate(categories()) == 0)
|
|
************************************************************/
|
|
#include "definitions.h"
|
|
#include "distributionPlusInvariant.h"
|
|
#include "distribution.h"
|
|
#include "generalGammaDistribution.h"
|
|
#include "errorMsg.h"
|
|
#include "gammaUtilities.h"
|
|
#include "logFile.h"
|
|
#include <cmath>
|
|
|
|
|
|
|
|
class generalGammaDistributionPlusInvariant : public distributionPlusInvariant {
|
|
public:
|
|
explicit generalGammaDistributionPlusInvariant(distribution* pDist, const MDOUBLE pInv, const MDOUBLE globalRate=1, MDOUBLE rateInvariantVal=1e-10): distributionPlusInvariant(pDist,pInv,globalRate,rateInvariantVal){}
|
|
explicit generalGammaDistributionPlusInvariant();
|
|
generalGammaDistributionPlusInvariant(const generalGammaDistributionPlusInvariant& other) {(*this) = other;}
|
|
//virtual generalGammaDistributionPlusInvariant& operator=(const generalGammaDistributionPlusInvariant& other);
|
|
generalGammaDistributionPlusInvariant* clone() const {return new generalGammaDistributionPlusInvariant(*this);}
|
|
virtual ~generalGammaDistributionPlusInvariant(){}
|
|
|
|
// distribution* getBaseDistribution(){return _pBaseDist;}
|
|
////get/set the parameters of the mixture
|
|
// const int categories() const;
|
|
// void setGlobalRate(const MDOUBLE r) {_globalRate = r;}
|
|
// MDOUBLE getGlobalRate() const {return _globalRate;}
|
|
// virtual void setInvProb(const MDOUBLE p) {_Pinv = p;}
|
|
// const MDOUBLE getInvProb() const {return _Pinv;}
|
|
//
|
|
////get distribution statistics
|
|
// virtual const MDOUBLE getCumulativeProb(const MDOUBLE x) const;
|
|
// virtual const MDOUBLE rates(const int category) const;
|
|
// virtual const MDOUBLE ratesProb(const int i) const;
|
|
|
|
// get generalGammaDistribution params
|
|
virtual void setAlpha(MDOUBLE newAlpha) {return static_cast<generalGammaDistribution*>(_pBaseDist)->setAlpha(newAlpha);};
|
|
virtual MDOUBLE getAlpha() const {return static_cast<generalGammaDistribution*>(_pBaseDist)->getAlpha();}
|
|
virtual void setBeta(MDOUBLE newBeta) {return static_cast<generalGammaDistribution*>(_pBaseDist)->setBeta(newBeta);};
|
|
virtual MDOUBLE getBeta() const {return static_cast<generalGammaDistribution*>(_pBaseDist)->getBeta();}
|
|
//protected:
|
|
//MDOUBLE _globalRate;
|
|
//MDOUBLE _Pinv;
|
|
//distribution* _pBaseDist;
|
|
};
|
|
#endif
|