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74 lines
2.6 KiB
C++
74 lines
2.6 KiB
C++
// $Id: replacementModelSSRV.h 1914 2007-04-04 08:40:35Z osnatz $
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#ifndef ___REPLACEMENT_MODEL_SSRV
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#define ___REPLACEMENT_MODEL_SSRV
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#include <cmath>
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#include "replacementModel.h"
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#include "distribution.h"
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#include "fromQtoPt.h"
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#include "errorMsg.h"
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#include "definitions.h"
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class replacementModelSSRV : public replacementModel
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{
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public:
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explicit replacementModelSSRV(const distribution* dist, const replacementModel* baseRM, MDOUBLE rateOfRate = 1);
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explicit replacementModelSSRV(const replacementModelSSRV& other);
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~replacementModelSSRV();
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replacementModelSSRV& operator=(const replacementModelSSRV &other);
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const int alphabetSize() const;
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virtual replacementModel* clone() const {return new replacementModelSSRV(*this);}
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const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
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return _q2pt.Pij_t(i,j,d);
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}
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const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
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return _q2pt.dPij_dt(i,j,d);
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}
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const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
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return _q2pt.d2Pij_dt2(i,j,d);
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}
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const MDOUBLE freq(const int i) const {return _freq[i];}
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distribution* getDistribution() const { return _dist;} // @@@@ this const is a lie !!!
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void setDistribution(const distribution* dist); // it's important to call updateQ after changing the distribution parameters
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replacementModel* getBaseRM() const { return _baseRM;} // @@@@ this const is a lie (for the same reason as getDistribution()
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MDOUBLE getRateOfRate() const { return _rateOfRate;}
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void setRateOfRate(MDOUBLE rateOfRate) { _rateOfRate=rateOfRate; updateQ();}
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VVdouble getQ() const { return _Q;}
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Vdouble getFreqs() const {return _freq;}
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MDOUBLE sumPijQij() const;
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void updateQ();
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void updateFreq();
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q2pt getQ2pt() const {return _q2pt;} // used for debug only
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//void norm(MDOUBLE scale);
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private:
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distribution* _dist;
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replacementModel* _baseRM;
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MDOUBLE _rateOfRate;
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q2pt _q2pt;
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Vdouble _freq;
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VVdouble _Q;
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};
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#endif
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/* @@@@ When we want to optimize alpha, we usually get the distibution from the stochastic process and then
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convert it using static_cast, for example to gammaDistribution and use its method setAlpha.
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For this reason, the method distr() in replacmentModel and the method getDistribution here are both const, although
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they actually allow changing the distribution.
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A good solution for this is to add a setDistribution in the stochasticProcess.
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This will check if the distributions are of the same type and if so, will just update the alpha.
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*/
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// @@@@ Idea - maybe there is no need of replacementModelSSRV. This can be stochasticProcessSSRV - not good. the SP also has an accelerator.
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