bpp::WordSubstitutionModel Member List

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

AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
AbstractWordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(SubstitutionModel *pmodel, unsigned int num, const std::string &prefix)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
AbstractWordSubstitutionModel(const Alphabet *alph, StateMap *stateMap, const std::string &prefix)	bpp::AbstractWordSubstitutionModel	protected
addRateParameter()	bpp::AbstractSubstitutionModel	virtual
alphabet_	bpp::AbstractSubstitutionModel	protected
clone() const	bpp::WordSubstitutionModel	inlinevirtual
completeMatrices()	bpp::WordSubstitutionModel	protectedvirtual
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
extractAlph(const std::vector< SubstitutionModel *> &modelVector)	bpp::AbstractWordSubstitutionModel	protectedstatic
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractSubstitutionModel	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 d) const	bpp::WordSubstitutionModel	virtual
getdPij_dt(double d) const	bpp::WordSubstitutionModel	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	bpp::WordSubstitutionModel	virtual
getNModel(size_t i) const	bpp::AbstractWordSubstitutionModel	inline
getNumberOfModels() const	bpp::AbstractWordSubstitutionModel	inline
getNumberOfStates() const	bpp::AbstractWordSubstitutionModel	virtual
getPij_t(double d) const	bpp::WordSubstitutionModel	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 AbstractWordSubstitutionModel &)	bpp::AbstractWordSubstitutionModel
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
Qij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
rate_	bpp::AbstractSubstitutionModel	protected
rightEigenVectors_	bpp::AbstractSubstitutionModel	protected
setFreq(std::map< int, double > &freqs)	bpp::AbstractWordSubstitutionModel	virtual
setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractSubstitutionModel	virtual
setNamespace(const std::string &prefix)	bpp::AbstractWordSubstitutionModel
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()	bpp::WordSubstitutionModel	protectedvirtual
VnestedPrefix_	bpp::AbstractWordSubstitutionModel	protected
vPowGen_	bpp::AbstractSubstitutionModel	protected
Vrate_	bpp::AbstractWordSubstitutionModel	protected
VSubMod_	bpp::AbstractWordSubstitutionModel	protected
WordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix="")	bpp::WordSubstitutionModel
WordSubstitutionModel(SubstitutionModel *pmodel, unsigned int num, const std::string &prefix="")	bpp::WordSubstitutionModel
WordSubstitutionModel(const Alphabet *alph, StateMap *stateMap, const std::string &prefix="")	bpp::WordSubstitutionModel	protected
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~AbstractWordSubstitutionModel()	bpp::AbstractWordSubstitutionModel	virtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual
~WordSubstitutionModel()	bpp::WordSubstitutionModel	inlinevirtual