mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:20:25 +08:00
85 lines
2.6 KiB
C++
85 lines
2.6 KiB
C++
#ifndef ___BEST_ALPHA_AND_K
|
|
#define ___BEST_ALPHA_AND_K
|
|
|
|
#include "definitions.h"
|
|
#include "tree.h"
|
|
#include "likelihoodComputation.h"
|
|
#include "likelihoodComputation2Codon.h"
|
|
#include "sequenceContainer.h"
|
|
#include "stochasticProcess.h"
|
|
#include "generalGammaDistribution.h"
|
|
#include "logFile.h"
|
|
#include "wYangModel.h"
|
|
#include "bblEM2codon.h"
|
|
#include "computeUpAlg.h"
|
|
#include "numRec.h"
|
|
|
|
|
|
|
|
//evaluate best parameters
|
|
class optimizeSelectonParameters {
|
|
public:
|
|
explicit optimizeSelectonParameters(tree& et,
|
|
const sequenceContainer& sc,
|
|
vector<stochasticProcess>& spVec,
|
|
distribution * distr,
|
|
bool bblFlag = true,
|
|
bool isGamma = true, bool isBetaProbSet=false,bool isOmegaSet = false,
|
|
bool isKappaSet=false, bool isAlphaSet=false, bool isBetaSet=false,
|
|
const MDOUBLE upperBoundOnAlpha = 3.0, // changed from 20, Adi S. 2/7/07
|
|
const MDOUBLE upperBoundOnBeta = 3.0, // changed from 20, Adi S. 2/7/07
|
|
const MDOUBLE epsilonAlphaOptimization= 0.01,
|
|
const MDOUBLE epsilonKOptimization=0.01,
|
|
const MDOUBLE epsilonLikelihoodImprovment= 0.1,
|
|
const int maxBBLIterations=20,
|
|
const int maxTotalIterations=20);
|
|
const MDOUBLE getBestAlpha() const{return _bestAlpha;}
|
|
const MDOUBLE getBestBeta() const{return _bestBeta;}
|
|
const MDOUBLE getBestL() const {return _bestL;}
|
|
const MDOUBLE getBestK() const {return _bestK;}
|
|
const MDOUBLE getBestOmega() const {return _bestOmega;}
|
|
const MDOUBLE getBestBetaProb() const {return _bestBetaProb;}
|
|
private:
|
|
MDOUBLE _bestAlpha;
|
|
MDOUBLE _bestL;
|
|
MDOUBLE _bestK;
|
|
MDOUBLE _bestBeta;
|
|
MDOUBLE _bestOmega;
|
|
MDOUBLE _bestBetaProb;
|
|
};
|
|
|
|
|
|
//The functor to eval likelihood given a change in a parameters
|
|
class evalParam{
|
|
public:
|
|
explicit evalParam(const tree& et,
|
|
const sequenceContainer& sc,
|
|
vector<stochasticProcess> spVec,
|
|
int alphaOrKs,
|
|
const distribution * in_distr,
|
|
bool isGamma)
|
|
: _et(et),_sc(sc),_spVec(spVec),_alphaOrKs(alphaOrKs),_isGamma(isGamma){_distr=in_distr->clone();};
|
|
MDOUBLE operator()(MDOUBLE param);
|
|
|
|
virtual ~evalParam();
|
|
evalParam(const evalParam &other);
|
|
void updateAlpha(MDOUBLE param);
|
|
void updateK(MDOUBLE param);
|
|
void updateBeta(MDOUBLE param);
|
|
void updateOmega(MDOUBLE param);
|
|
void updateBetaProb(MDOUBLE param);
|
|
private:
|
|
const tree& _et;
|
|
const sequenceContainer& _sc;
|
|
|
|
vector<stochasticProcess> _spVec;
|
|
int _alphaOrKs; //flag to eval different parameters (alpha,beta or ks)
|
|
distribution *_distr;
|
|
bool _isGamma; //gamma = true/ beta=false
|
|
|
|
};
|
|
|
|
#endif
|
|
|
|
|