/usr/include/libphylo/tamura92.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 | // $Id: tamura92.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___TAMURA92
#define ___TAMURA92
#include "replacementModel.h"
#include <cmath>
class tamura92 : public replacementModel {
public:
explicit tamura92(const MDOUBLE theta,
const MDOUBLE TrTv);
virtual replacementModel* clone() const { return new tamura92 (*this); }
const int alphabetSize() const {return 4;}
inline void changeTrTv(const MDOUBLE TrTv) { _TrTv = TrTv; }
void changeTheta(const MDOUBLE theta);
MDOUBLE getTrTv() const {return _TrTv;}
MDOUBLE getTheta() const {return _theta;}
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const;
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const;
const MDOUBLE freq(const int i) const {return _freq[i];};
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const;
const MDOUBLE dPij_tdBeta(const int i, const int j, const MDOUBLE t) const;
private:
Vdouble _freq;
MDOUBLE _theta;
MDOUBLE _TrTv;
};
#endif
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