bpp::MarkovModulatedSubstitutionModel Member List

This is the complete list of members for bpp::MarkovModulatedSubstitutionModel, including all inherited members.

addRateParameter()=0	bpp::SubstitutionModel	pure virtual
clone() const =0	bpp::MarkovModulatedSubstitutionModel	pure virtual
d2Pij_dt2(size_t i, size_t j, double t) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
d2pijt_	bpp::MarkovModulatedSubstitutionModel	mutableprotected
dPij_dt(size_t i, size_t j, double t) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
dpijt_	bpp::MarkovModulatedSubstitutionModel	mutableprotected
eigenDecompose_	bpp::MarkovModulatedSubstitutionModel	protected
eigenValues_	bpp::MarkovModulatedSubstitutionModel	protected
enableEigenDecomposition(bool yn)	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
enableEigenDecomposition()	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
exchangeability_	bpp::MarkovModulatedSubstitutionModel	protected
fireParameterChanged(const ParameterList &parameters)	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
freq(size_t i) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
freq_	bpp::MarkovModulatedSubstitutionModel	protected
generator_	bpp::MarkovModulatedSubstitutionModel	protected
getAlphabet() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getAlphabetStateAsChar(size_t index) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getAlphabetStateAsInt(size_t index) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getAlphabetStates() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getColumnRightEigenVectors() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getd2Pij_dt2(double t) const	bpp::MarkovModulatedSubstitutionModel	virtual
getdPij_dt(double t) const	bpp::MarkovModulatedSubstitutionModel	virtual
getEigenValues() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getExchangeabilityMatrix() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getFrequencies() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::SubstitutionModel	inlinevirtual
getGenerator() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getIEigenValues() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getInitValue(size_t i, int state) const	bpp::MarkovModulatedSubstitutionModel	virtual
getModelStates(int code) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getModelStates(const std::string &code) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getName() const =0	bpp::SubstitutionModel	pure virtual
getNestedModel() const	bpp::MarkovModulatedSubstitutionModel	inline
getNumberOfStates() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getPij_t(double t) const	bpp::MarkovModulatedSubstitutionModel	virtual
getRate(size_t i) const	bpp::MarkovModulatedSubstitutionModel	inline
getRate() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getRowLeftEigenVectors() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getScale() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
getStateMap() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
iEigenValues_	bpp::MarkovModulatedSubstitutionModel	protected
isDiagonalizable() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
isNonSingular() const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
leftEigenVectors_	bpp::MarkovModulatedSubstitutionModel	protected
MarkovModulatedSubstitutionModel(ReversibleSubstitutionModel *model, unsigned int nbRates, bool normalizeRateChanges, const std::string &prefix)	bpp::MarkovModulatedSubstitutionModel	inline
MarkovModulatedSubstitutionModel(const MarkovModulatedSubstitutionModel &model)	bpp::MarkovModulatedSubstitutionModel
model_	bpp::MarkovModulatedSubstitutionModel	protected
nbRates_	bpp::MarkovModulatedSubstitutionModel	protected
nbStates_	bpp::MarkovModulatedSubstitutionModel	protected
nestedPrefix_	bpp::MarkovModulatedSubstitutionModel	protected
normalizeRateChanges_	bpp::MarkovModulatedSubstitutionModel	protected
operator=(const MarkovModulatedSubstitutionModel &model)	bpp::MarkovModulatedSubstitutionModel
Pij_t(size_t i, size_t j, double t) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
pijt_	bpp::MarkovModulatedSubstitutionModel	mutableprotected
Qij(size_t i, size_t j) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
rates_	bpp::MarkovModulatedSubstitutionModel	protected
ratesExchangeability_	bpp::MarkovModulatedSubstitutionModel	protected
ratesFreq_	bpp::MarkovModulatedSubstitutionModel	protected
ratesGenerator_	bpp::MarkovModulatedSubstitutionModel	protected
ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inline
rightEigenVectors_	bpp::MarkovModulatedSubstitutionModel	protected
setFreq(std::map< int, double > &frequencies)	bpp::SubstitutionModel	inlinevirtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
setNamespace(const std::string &prefix)	bpp::MarkovModulatedSubstitutionModel
setRate(double rate)	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
setScale(double scale)	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
Sij(size_t i, size_t j) const	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
stateMap_	bpp::MarkovModulatedSubstitutionModel	protected
SubstitutionModel()	bpp::SubstitutionModel	inline
updateMatrices()	bpp::MarkovModulatedSubstitutionModel	protectedvirtual
updateRatesModel()=0	bpp::MarkovModulatedSubstitutionModel	protectedpure virtual
~MarkovModulatedSubstitutionModel()	bpp::MarkovModulatedSubstitutionModel	inlinevirtual
~ReversibleSubstitutionModel()	bpp::ReversibleSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual