bpp::YpR Member List

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

_nestedPrefix	bpp::YpR	protected
AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
addRateParameter()	bpp::AbstractSubstitutionModel	virtual
alphabet_	bpp::AbstractSubstitutionModel	protected
check_model(SubstitutionModel *const) const	bpp::YpR	protected
clone() const =0	bpp::AbstractSubstitutionModel	pure virtual
d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
d2pijt_	bpp::AbstractSubstitutionModel	mutableprotected
dPij_dt(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
dpijt_	bpp::AbstractSubstitutionModel	mutableprotected
eigenDecompose_	bpp::AbstractSubstitutionModel	protected
eigenValues_	bpp::AbstractSubstitutionModel	protected
enableEigenDecomposition(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
enableEigenDecomposition()	bpp::AbstractSubstitutionModel	inlinevirtual
exchangeability_	bpp::AbstractSubstitutionModel	protected
fireParameterChanged(const ParameterList &parameters)	bpp::YpR	inlinevirtual
freq(size_t i) const	bpp::AbstractSubstitutionModel	inlinevirtual
freq_	bpp::AbstractSubstitutionModel	protected
generator_	bpp::AbstractSubstitutionModel	protected
getAlphabet() const	bpp::AbstractSubstitutionModel	inlinevirtual
getAlphabetStateAsChar(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
getAlphabetStateAsInt(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
getAlphabetStates() const	bpp::AbstractSubstitutionModel	inlinevirtual
getColumnRightEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
getd2Pij_dt2(double t) const	bpp::AbstractSubstitutionModel	virtual
getdPij_dt(double t) const	bpp::AbstractSubstitutionModel	virtual
getEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
getExchangeabilityMatrix() const	bpp::AbstractSubstitutionModel	inlinevirtual
getFrequencies() const	bpp::AbstractSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::SubstitutionModel	inlinevirtual
getGenerator() const	bpp::AbstractSubstitutionModel	inlinevirtual
getIEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
getInitValue(size_t i, int state) const	bpp::AbstractSubstitutionModel	virtual
getModelStates(int code) const	bpp::AbstractSubstitutionModel	inlinevirtual
getModelStates(const std::string &code) const	bpp::AbstractSubstitutionModel	inlinevirtual
getName() const =0	bpp::SubstitutionModel	pure virtual
getNestedModel() const	bpp::YpR	inline
getNestedPrefix() const	bpp::YpR	inlineprotected
getNumberOfStates() const	bpp::YpR	inlinevirtual
getPij_t(double t) const	bpp::AbstractSubstitutionModel	virtual
getRate() const	bpp::AbstractSubstitutionModel	virtual
getRowLeftEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
getScale() const	bpp::AbstractSubstitutionModel	virtual
getStateMap() const	bpp::AbstractSubstitutionModel	inlinevirtual
iEigenValues_	bpp::AbstractSubstitutionModel	protected
isDiagonalizable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isDiagonalizable_	bpp::AbstractSubstitutionModel	protected
isNonSingular() const	bpp::AbstractSubstitutionModel	inlinevirtual
isNonSingular_	bpp::AbstractSubstitutionModel	protected
leftEigenVectors_	bpp::AbstractSubstitutionModel	protected
operator=(const YpR &ypr)	bpp::YpR	inlineprotected
bpp::AbstractSubstitutionModel::operator=(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
Pij_t(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
pijt_	bpp::AbstractSubstitutionModel	mutableprotected
pmodel_	bpp::YpR	protected
Qij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
rate_	bpp::AbstractSubstitutionModel	protected
rightEigenVectors_	bpp::AbstractSubstitutionModel	protected
setFreq(std::map< int, double > &)	bpp::AbstractSubstitutionModel	virtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractSubstitutionModel	virtual
setNamespace(const std::string &)	bpp::YpR	virtual
setRate(double rate)	bpp::AbstractSubstitutionModel	virtual
setScale(double scale)	bpp::AbstractSubstitutionModel	virtual
Sij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
size_	bpp::AbstractSubstitutionModel	protected
stateMap_	bpp::AbstractSubstitutionModel	protected
SubstitutionModel()	bpp::SubstitutionModel	inline
tmpMat_	bpp::AbstractSubstitutionModel	mutableprotected
updateMatrices(double, double, double, double, double, double, double, double)	bpp::YpR	protected
updateMatrices()	bpp::YpR	virtual
vPowGen_	bpp::AbstractSubstitutionModel	protected
YpR(const RNY *, SubstitutionModel *const, const std::string &prefix)	bpp::YpR	protected
YpR(const YpR &, const std::string &prefix)	bpp::YpR	protected
YpR(const YpR &ypr)	bpp::YpR	protected
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual
~YpR()	bpp::YpR	inlinevirtual