mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:10:24 +08:00
60 lines
1.7 KiB
C++
60 lines
1.7 KiB
C++
#ifndef _W_YANG_MODEL
|
|
#define _W_YANG_MODEL
|
|
|
|
#include "replacementModel.h"
|
|
#include "fromQtoPt.h"
|
|
#include "codon.h"
|
|
|
|
|
|
class wYangModel : public replacementModel {
|
|
public:
|
|
explicit wYangModel(const MDOUBLE inW, const MDOUBLE inK,bool globalW, codon * coAlpha);
|
|
explicit wYangModel(const MDOUBLE inW, const MDOUBLE inK, const Vdouble& freq,bool globalW, codon *coAlpha);
|
|
explicit wYangModel(const wYangModel &other): _coAlpha(NULL) {(*this) = other;}
|
|
virtual wYangModel& operator=(const wYangModel &other);
|
|
virtual wYangModel* clone() const { return new wYangModel(*this); }
|
|
virtual ~wYangModel() {
|
|
if (_coAlpha)
|
|
delete _coAlpha;
|
|
}
|
|
|
|
const int alphabetSize() const {return _freq.size();}
|
|
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
|
|
return _q2pt.Pij_t(i,j,d);
|
|
}
|
|
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
|
|
return _q2pt.dPij_dt(i,j,d);
|
|
}
|
|
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
|
|
return _q2pt.d2Pij_dt2(i,j,d);
|
|
}
|
|
const MDOUBLE freq(const int i) const {return _freq[i];};
|
|
void setK(const MDOUBLE newK) { _k = newK; updateQ();}
|
|
void setW(const MDOUBLE newW) { _w = newW;updateQ();}
|
|
void homogenousFreq(){ _freq.erase(_freq.begin(),_freq.end()),_freq.resize(alphabetSize(),1.0/alphabetSize());}
|
|
|
|
MDOUBLE getK() const {return _k;}
|
|
MDOUBLE getW() const {return _w;}
|
|
|
|
MDOUBLE getQij(const int i,const int j)const {return _Q[i][j];}
|
|
void setGlobalW(bool globalW){_globalW = globalW;}
|
|
void norm(MDOUBLE scale);
|
|
MDOUBLE sumPijQij();
|
|
private:
|
|
void updateQ();
|
|
|
|
|
|
private:
|
|
|
|
MDOUBLE _w; //selection factor.
|
|
MDOUBLE _k; // Tr/Tv ratio.
|
|
q2pt _q2pt;
|
|
VVdouble _Q;
|
|
bool _globalW; //false when compute w per site
|
|
Vdouble _freq;
|
|
codon *_coAlpha;
|
|
};
|
|
|
|
|
|
#endif
|