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132 lines
4.5 KiB
C++
132 lines
4.5 KiB
C++
#ifndef ___3STATE_MODEL
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#define ___3STATE_MODEL
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#include "definitions.h"
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#include "replacementModel.h"
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#include "fromQtoPt.h"
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#include "errorMsg.h"
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#include "matrixUtils.h"
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class threeStateModel : public replacementModel {
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public:
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explicit threeStateModel(const MDOUBLE m1, const MDOUBLE m2,
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const MDOUBLE m3, const MDOUBLE m4,const Vdouble &freq, bool useMarkovLimiting = true);
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threeStateModel(const threeStateModel& other) {*this = other;}
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virtual threeStateModel& operator=(const threeStateModel &other);
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virtual threeStateModel* clone() const { return new threeStateModel(*this); }
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virtual ~threeStateModel() {}
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const int alphabetSize() const {return 3;} // two states and an intermediate (both states at once)
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const MDOUBLE err_allow_for_pijt_function() const {return 1e-4;} // same as q2p definitions
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const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const ;
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const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
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if (d==0.0)
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return _Q[i][j];
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errorMsg::reportError("Error in threeStateModel, dPij_dt called");
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return 0.0; // not supposed to be here
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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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errorMsg::reportError("Error in threeStateModel, d2Pij_dt2 called");
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return 0.0; // not supposed to be here
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}
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const MDOUBLE freq(const int i) const {
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if (i >= _freq.size())
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errorMsg::reportError("Error in threeStateModel::freq, i > size of frequency vector");
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return _freq[i];
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}
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const Vdouble getFreqs() const {return _freq;}
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void setFreq(const Vdouble &freq);
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void setMu1(const MDOUBLE val) ;
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void setMu2(const MDOUBLE val) ;
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void setMu3(const MDOUBLE val) ;
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void setMu4(const MDOUBLE val) ;
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const MDOUBLE getMu1() const {return _gainState1;}
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const MDOUBLE getMu2() const {return _gainState0;}
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const MDOUBLE getMu3() const {return _lossState1;}
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const MDOUBLE getMu4() const {return _lossState0;}
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void computeMarkovLimitingDistribution(); // compute P(infinity), which specifies the stationary distribution
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private:
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virtual void updateQ();
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void setEpsilonForZeroParams();
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bool checkIsNullModel();
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bool pijt_is_prob_value(MDOUBLE val) const;
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bool areFreqsValid(Vdouble freq) const; // tests if frequencies are valid (>0, sum=1)
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private:
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MDOUBLE _gainState1; // _Q[0][2]
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MDOUBLE _gainState0; // _Q[1][2]
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MDOUBLE _lossState1; // _Q[2][0]
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MDOUBLE _lossState0; // _Q[2][1]
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VVdouble _Q;
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Vdouble _freq;
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bool _useMarkovLimiting; // should the markov limiting distribution be used to estimate the root frequencies
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mutable bool _bQchanged; //indicates whether the Q matrix was changed after the last Pij_t call
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mutable MDOUBLE _lastTcalculated;
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mutable VVdoubleRep _lastPtCalculated;
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};
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/*class gainLossModel : public replacementModel {
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public:
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explicit gainLossModel(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq);
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virtual replacementModel* clone() const { return new gainLossModel(*this); }
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gainLossModel(const gainLossModel& other): _q2pt(NULL) {*this = other;}
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virtual gainLossModel& operator=(const gainLossModel &other);
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virtual ~gainLossModel() {if (_q2pt) delete _q2pt;}
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const int alphabetSize() const {return 3;} // two states and an intermediate (both states at once)
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const MDOUBLE err_allow_for_pijt_function() const {return 1e-4;} // same as q2p definitions
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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 {
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if (i >= _freq.size())
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errorMsg::reportError("Error in gainLossModel::freq, i > size of frequency vector");
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return _freq[i];
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}
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void setMu1(const MDOUBLE val, bool isReversible=true) { _gainState1 = val; updateQ(isReversible);}
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void setMu2(const MDOUBLE val,bool isReversible=true) { _gainState0 = val; updateQ(isReversible);}
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const MDOUBLE getMu1() const {return _gainState1;}
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const MDOUBLE getMu2() const {return _gainState0;}
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protected:
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virtual void updateQ(bool isReversible=true);
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virtual void normalizeQ();
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protected:
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Vdouble _freq;
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MDOUBLE _gainState1;
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MDOUBLE _gainState0;
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VVdouble _Q;
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q2pt *_q2pt;
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};
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*/
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/*
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Q is a matrix of the following form:
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0 1 01
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0 1-m1 0 m1
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1 0 1-m2 m2
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01 (filled in assuming reversibility)
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i.e. no direct change from state 0 to state 1 is allowed
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*/
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#endif // ___3STATE_MODEL
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