/usr/include/libphylo/hky.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 | // $Id: hky.h 4291 2008-06-23 10:23:10Z itaymay $
#ifndef ___HKY
#define ___HKY
#include "replacementModel.h"
#include <cmath>
class hky : public replacementModel {
public:
explicit hky(const MDOUBLE inProb_a,
const MDOUBLE inProb_c,
const MDOUBLE inProb_g,
const MDOUBLE inProb_t,
const MDOUBLE TrTv);
explicit hky(vector<MDOUBLE> inProbs, const MDOUBLE TrTv);
virtual replacementModel* clone() const { return new hky(*this); }
// virtual nucJC* clone() const { return new nucJC(*this); } // see note down:
const int alphabetSize() const {return 4;}
void changeTrTv(const MDOUBLE In_TrTv);
MDOUBLE getTrTv() const;
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:
void initParams(MDOUBLE TrTv); // init _a, _b, _c, and _y by using _freq and TrTv
private:
Vdouble _freq;
MDOUBLE _a; //
MDOUBLE _b; //
MDOUBLE _c,_y; // relationship between probA, probC, prob G, prob T.
};
#endif
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