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63 lines
1.8 KiB
C++
63 lines
1.8 KiB
C++
#ifndef _GTR_MODEL
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#define _GTR_MODEL
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#include "replacementModel.h"
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#include "fromQtoPt.h"
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class gtrModel : public replacementModel {
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public:
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enum modelElements {a = 0,c,g,t};
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explicit gtrModel(const Vdouble& freq,
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const MDOUBLE a2c = 0.25,
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const MDOUBLE a2g = 0.25,
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const MDOUBLE a2t = 0.25,
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const MDOUBLE c2g = 0.25,
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const MDOUBLE c2t = 0.25,
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const MDOUBLE g2t = 0.25);
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virtual replacementModel* clone() const { return new gtrModel(*this); }
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virtual gtrModel& operator=(const gtrModel &other);
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explicit gtrModel(const gtrModel &other);
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const int alphabetSize() const {return _freq.size();}
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const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {return _q2pt.Pij_t(i,j,d);}
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const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{return _q2pt.dPij_dt(i,j,d);}
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const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{return _q2pt.d2Pij_dt2(i,j,d);}
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const MDOUBLE freq(const int i) const {return _freq[i];};
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void set_a2c(const MDOUBLE a2c);
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void set_a2g(const MDOUBLE a2g);
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void set_a2t(const MDOUBLE a2t);
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void set_c2g(const MDOUBLE c2g);
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void set_c2t(const MDOUBLE c2t);
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void set_g2t(const MDOUBLE g2t);
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MDOUBLE get_a2c() const;
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MDOUBLE get_a2g() const;
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MDOUBLE get_a2t() const;
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MDOUBLE get_c2g() const;
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MDOUBLE get_c2t() const;
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MDOUBLE get_g2t() const;
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const VVdouble& getQ() const {return _Q;}
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private:
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void updateQ(const MDOUBLE a2c,const MDOUBLE a2g,const MDOUBLE a2t,const MDOUBLE c2g,const MDOUBLE c2t,const MDOUBLE g2t);
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void norm(const MDOUBLE scale);
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MDOUBLE sumPijQij();
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private:
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VVdouble _Q;
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Vdouble _freq;
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q2pt _q2pt;
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MDOUBLE _a2c;
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MDOUBLE _a2g;
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MDOUBLE _a2t;
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MDOUBLE _c2g;
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MDOUBLE _c2t;
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MDOUBLE _g2t;
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};
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#endif
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