/usr/include/libphylo/gtrModel.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
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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 52 53 54 55 56 | #ifndef _GTR_MODEL
#define _GTR_MODEL
#include "replacementModel.h"
#include "fromQtoPt.h"
class gtrModel : public replacementModel {
public:
enum modelElements {a = 0,c,g,t};
explicit gtrModel(const Vdouble& freq,
const MDOUBLE a2c = 0.25,
const MDOUBLE a2g = 0.25,
const MDOUBLE a2t = 0.25,
const MDOUBLE c2g = 0.25,
const MDOUBLE c2t = 0.25,
const MDOUBLE g2t = 0.25);
virtual replacementModel* clone() const { return new gtrModel(*this); }
virtual gtrModel& operator=(const gtrModel &other);
explicit gtrModel(const gtrModel &other);
const int alphabetSize() const {return _freq.size();}
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {return _q2pt.Pij_t(i,j,d);}
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{return _q2pt.dPij_dt(i,j,d);}
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{return _q2pt.d2Pij_dt2(i,j,d);}
const MDOUBLE freq(const int i) const {return _freq[i];};
void set_a2c(const MDOUBLE a2c);
void set_a2g(const MDOUBLE a2g);
void set_a2t(const MDOUBLE a2t);
void set_c2g(const MDOUBLE c2g);
void set_c2t(const MDOUBLE c2t);
void set_g2t(const MDOUBLE g2t);
MDOUBLE get_a2c() const;
MDOUBLE get_a2g() const;
MDOUBLE get_a2t() const;
MDOUBLE get_c2g() const;
MDOUBLE get_c2t() const;
MDOUBLE get_g2t() const;
const VVdouble& getQ() const {return _Q;}
private:
void updateQ(const MDOUBLE a2c,const MDOUBLE a2g,const MDOUBLE a2t,const MDOUBLE c2g,const MDOUBLE c2t,const MDOUBLE g2t);
void norm(const MDOUBLE scale);
MDOUBLE sumPijQij();
private:
VVdouble _Q;
Vdouble _freq;
q2pt _q2pt;
MDOUBLE _a2c;
MDOUBLE _a2g;
MDOUBLE _a2t;
MDOUBLE _c2g;
MDOUBLE _c2t;
MDOUBLE _g2t;
};
#endif
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