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59 lines
2.1 KiB
C++
59 lines
2.1 KiB
C++
// $Id: stochasticProcess.h 2511 2007-11-04 12:08:50Z cohenofi $
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#ifndef ___STOCHASTIC_PROCESS
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#define ___STOCHASTIC_PROCESS
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#include "pijAccelerator.h"
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#include "distribution.h"
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#include <cassert>
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class stochasticProcess{
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public:
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explicit stochasticProcess(const distribution *in_distr,const pijAccelerator *pijAccelerator, bool isReversible = true);
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explicit stochasticProcess() {
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_distr=NULL; _pijAccelerator=NULL; _isReversible=true;
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}
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stochasticProcess(const stochasticProcess& other);
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virtual stochasticProcess* clone() const {return new stochasticProcess(*this);}
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const int alphabetSize() const {return _pijAccelerator->alphabetSize();} // The alphabet size is the same as the matrix Pij size
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virtual const int categories() const {return _distr->categories();}
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virtual const MDOUBLE rates(const int i) const {return _distr->rates(i);}
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virtual const MDOUBLE ratesProb(const int i) const {return _distr->ratesProb(i);}
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virtual const MDOUBLE Pij_t(const int i, const int j, const MDOUBLE t) const {
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if (t!=0) return _pijAccelerator->Pij_t(i,j,t);
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return (i==j)? 1 : 0;
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}
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const MDOUBLE freq(const int i) const {assert(i>=0);return _pijAccelerator->freq(i);} // P(i)
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const MDOUBLE dPij_dt(const int i,const int j,const MDOUBLE t) const { return _pijAccelerator->dPij_dt(i,j,t);}
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const MDOUBLE d2Pij_dt2(const int i, const int j, const MDOUBLE t) const { return _pijAccelerator->d2Pij_dt2(i,j,t);}
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virtual distribution* distr() const {return _distr;} // @@@@ this const is a lie !!!
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virtual const pijAccelerator* getPijAccelerator() const {return _pijAccelerator;}
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virtual void setDistribution(const distribution* in_distr);
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stochasticProcess& operator=(const stochasticProcess &otherStoc);
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virtual ~stochasticProcess();
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virtual void setGlobalRate(const MDOUBLE x) {_distr->setGlobalRate(x);}
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virtual MDOUBLE getGlobalRate() const {return _distr->getGlobalRate();}
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const bool isReversible() const {return _isReversible;}
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protected:
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distribution *_distr;
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pijAccelerator *_pijAccelerator;
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bool _isReversible;
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};
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#endif
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// Stochastic process is composed of two objects: a distribution of rates and a Pij accelerator.
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