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48 lines
1.5 KiB
C++
48 lines
1.5 KiB
C++
// $Id: codonJC.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___CODON_JC
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#define ___CODON_JC
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#include "replacementModel.h"
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#include <cmath>
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using namespace std;
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namespace codonDef {
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const MDOUBLE Alp = 61.0;
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const MDOUBLE odAl = 1.0/Alp; // one divided by alphabet
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const MDOUBLE om_odAl = 1.0-odAl; // one minus odAl;
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const MDOUBLE alDiv_omalp = Alp/(Alp-1.0);
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const MDOUBLE m_alDiv_omalp = -alDiv_omalp;
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}
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class codonJC : public replacementModel {
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public:
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virtual replacementModel* clone() const { return new codonJC(*this); }// see note down:
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const int alphabetSize() const {return 61;}
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explicit codonJC(){};
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const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
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return ((i==j) ? codonDef::odAl+codonDef::om_odAl*exp(codonDef::m_alDiv_omalp*d): codonDef::odAl-codonDef::odAl*exp(codonDef::m_alDiv_omalp*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 ((i==j) ? -exp(codonDef::m_alDiv_omalp*d): exp(codonDef::m_alDiv_omalp*d)/(codonDef::Alp-1));
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}
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const MDOUBLE freq(const int i) const {return codonDef::odAl;};
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const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
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return ((i==j) ? codonDef::alDiv_omalp*exp(codonDef::m_alDiv_omalp*d): codonDef::m_alDiv_omalp*exp(codonDef::m_alDiv_omalp*d));
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}
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};
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#endif
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// note: according to the new C++ rules, the clone function should be like this:
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// virtual aaJC* clone() const { return new aaJC(*this); }
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// however, not all compiler support it yet. look at More Effective C++ page 126.
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