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