/usr/include/libphylo/aaJC.h is in rate4site 3.0.0-2.
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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 | // $Id: aaJC.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___AA_JC
#define ___AA_JC
#include "replacementModel.h"
#include <cmath>
using namespace std;
namespace aaDef {
const MDOUBLE Alp = 20.0;
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 aaJC : public replacementModel {
public:
virtual replacementModel* clone() const { return new aaJC(*this); }// see note down:
// virtual aaJC* clone() const { return new aaJC(*this); }
const int alphabetSize() const {return 20;}
explicit aaJC(){};
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
//(wrong!) return ((i==j) ? 0.05+0.95*exp(-20.0*d): 0.05-0.05*exp(-20.0*d));
return ((i==j) ? aaDef::odAl+aaDef::om_odAl*exp(aaDef::m_alDiv_omalp*d): aaDef::odAl-aaDef::odAl*exp(aaDef::m_alDiv_omalp*d));
}
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
//(worng!)return ((i==j) ? -19.0*exp(-20.0*d): exp(-20.0*d));
return ((i==j) ? -exp(aaDef::m_alDiv_omalp*d): exp(aaDef::m_alDiv_omalp*d)/(aaDef::Alp-1));
}
const MDOUBLE freq(const int i) const {return aaDef::odAl;};
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
//(wrong!) return ((i==j) ? 19.0*20.0*exp(-20.0*d): 0.0-20.0*exp(-20.0*d));
return ((i==j) ? aaDef::alDiv_omalp*exp(aaDef::m_alDiv_omalp*d): aaDef::m_alDiv_omalp*exp(aaDef::m_alDiv_omalp*d));
}
};
#endif
// note: according to the new C++ rules, the clone function should be like this:
// virtual aaJC* clone() const { return new aaJC(*this); }
// however, not all compiler support it yet. look at More Effective C++ page 126.
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