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57 lines
1.8 KiB
C++
57 lines
1.8 KiB
C++
// $Id: goldmanYangModel.h 1841 2007-03-11 15:19:14Z adist $
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#ifndef ___GOLDMAN_YANG_MODEL
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#define ___GOLDMAN_YANG_MODEL
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#include "definitions.h"
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#include "replacementModel.h"
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#include "fromQtoPt.h"
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#include "granthamChemicalDistances.h"
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#include "codon.h"
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class goldmanYangModel : public replacementModel {
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public:
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explicit goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV=true);
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explicit goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const Vdouble& freq,const bool globalV=true);
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virtual replacementModel* clone() const { return new goldmanYangModel(*this); }
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const int alphabetSize() const {return _codonAlph.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 setV(const MDOUBLE newV) { _v = newV;updateQ();}
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void homogenousFreq(){ _freq.erase(_freq.begin(),_freq.end()),_freq.resize(_codonAlph.size(),1.0/_codonAlph.size());}
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MDOUBLE getK() {return _k;}
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MDOUBLE getV() {return _v;}
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void setGlobalV(const bool globalV){ _globalV=globalV;}
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const granthamChemicalDistances& getGCD(){return _gcd;}
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MDOUBLE getQij(const int i,const int j)const {return _Q[i][j];}
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VVdouble getQ() const { return _Q;}
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Vdouble getFreqs() const {return _freq;}
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private:
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Vdouble _freq;
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MDOUBLE _v; //selection factor.
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MDOUBLE _k; // Tr/Tv ratio.
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void updateQ();
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q2pt _q2pt;
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granthamChemicalDistances _gcd;
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bool _globalV; //false when compute v per site
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VVdouble _Q;
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codon & _codonAlph;
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};
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#endif
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