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62 lines
1.3 KiB
C++
62 lines
1.3 KiB
C++
// $Id: indelModel.h 962 2006-11-07 15:13:34Z privmane $
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#ifndef ___INDEL_MODEL
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#define ___INDEL_MODEL
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#include "replacementModel.h"
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#include <cmath>
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using namespace std;
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class indelModel : public replacementModel
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{
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public:
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explicit indelModel(const MDOUBLE freq_x, const MDOUBLE freq_g)
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{
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_alpha = 1/(2*freq_x*freq_g);
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_freq.push_back(freq_x);
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_freq.push_back(freq_g);
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}
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virtual const MDOUBLE Pij_t(const int i, const int j, const MDOUBLE t) const
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{
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if (i==j)
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return exp(-t*_alpha);
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return (1-exp(-t*_alpha));
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}
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virtual const MDOUBLE freq(const int i) const { return _freq[i];}
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virtual const MDOUBLE dPij_dt(const int i, const int j, const MDOUBLE t) const
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{
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// [e^(-t/2PxPg)] / 2PxPg
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return (exp(-t*_alpha)*_alpha);
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}
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virtual const MDOUBLE d2Pij_dt2(const int i, const int j, const MDOUBLE t) const
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{
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// [-e^(-t/2PxPg)] / [(2PxPg)^2]
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return ( -exp(-t*_alpha) * _alpha * _alpha);
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}
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virtual replacementModel* clone() const { return new indelModel(*this);}
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virtual const int alphabetSize() const {return 2;};
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void setFreqX(const MDOUBLE freq_x);
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void setFreqG(const MDOUBLE freq_g);
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private:
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Vdouble _freq; // [0] X [1] -
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// save _alpha to make things faster. _alpha depends on _freq
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MDOUBLE _alpha;
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};
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#endif
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