/usr/include/libphylo/nucJC.h is in rate4site 3.0.0-5.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 | // $Id: nucJC.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___NUC_JC
#define ___NUC_JC
#include <cmath>
#include "replacementModel.h"
namespace nucDef {
const MDOUBLE Alp = 4.0;
const MDOUBLE odAl = 1.0/Alp; // one divided by alphabet
const MDOUBLE om_odAl = 1.0-odAl; // one minus odAl;
const MDOUBLE alDiv_omalp = Alp/(Alp-1.0);
const MDOUBLE m_alDiv_omalp = -alDiv_omalp;
}
class nucJC : public replacementModel {
public:
const int alphabetSize() const {return 4;}
virtual replacementModel* clone() const { return new nucJC(*this); }
explicit nucJC(){};
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
// return ((i==j) ? 0.25+0.75*exp(-4.0/3.0*d): 0.25-0.25*exp(-4.0/3.0*d));
return ((i==j) ? nucDef::odAl+nucDef::om_odAl*exp(nucDef::m_alDiv_omalp*d): nucDef::odAl-nucDef::odAl*exp(nucDef::m_alDiv_omalp*d));
}
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
// return ((i==j) ? -exp(-4.0/3.0*d): exp(-4.0/3.0*d)/3.0);
return ((i==j) ? -exp(nucDef::m_alDiv_omalp*d): exp(nucDef::m_alDiv_omalp*d)/(nucDef::Alp-1));
}
const MDOUBLE freq(const int i) const {return 0.25;};
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
// return ((i==j) ? 4.0/3.0*exp(-4.0/3.0*d): -4.0/3.0*exp(-4.0/3.0*d));
return ((i==j) ? nucDef::alDiv_omalp*exp(nucDef::m_alDiv_omalp*d): nucDef::m_alDiv_omalp*exp(nucDef::m_alDiv_omalp*d));
}
const MDOUBLE Q(const int i, const int j) const {
return ((i == j) ? ( - 1.0) : (1.0 / 3.0));
}
};
#endif
// note: according to the new C++ rules, the clone function should be like this:
// virtual nucJC* clone() const { return new nucJC(*this); }
// however, not all compiler support it yet. look at More Effective C++ page 126.
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