bpp::L95 Member List

This is the complete list of members for bpp::L95, including all inherited members.

AbstractSubstitutionModel(const Alphabet *alpha, StateMap *stateMap, const std::string &prefix)	bpp::AbstractSubstitutionModel
AbstractSubstitutionModel(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
bpp::addRateParameter()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::addRateParameter()	bpp::AbstractSubstitutionModel	virtual
alpha_	bpp::L95	private
alphabet_	bpp::AbstractSubstitutionModel	protected
beta_	bpp::L95	private
clone() const	bpp::L95	inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::d2Pij_dt2(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
d2pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::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
bpp::enableEigenDecomposition(bool yn)=0	bpp::SubstitutionModel	pure virtual
bpp::enableEigenDecomposition()=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition(bool yn)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractSubstitutionModel::enableEigenDecomposition()	bpp::AbstractSubstitutionModel	inlinevirtual
exchangeability_	bpp::AbstractSubstitutionModel	protected
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::freq(size_t i) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::freq(size_t i) const	bpp::AbstractSubstitutionModel	inlinevirtual
freq_	bpp::AbstractSubstitutionModel	protected
gamma_	bpp::L95	private
generator_	bpp::AbstractSubstitutionModel	protected
bpp::getAlphabet() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getAlphabet() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getAlphabetStateAsChar(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getAlphabetStateAsInt(size_t index) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getAlphabetStates() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getColumnRightEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getColumnRightEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getd2Pij_dt2(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getdPij_dt(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getdPij_dt(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getExchangeabilityMatrix() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getExchangeabilityMatrix() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getFrequencies() const	bpp::AbstractSubstitutionModel	inlinevirtual
getFrequenciesSet() const	bpp::SubstitutionModel	inlinevirtual
bpp::getGenerator() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getGenerator() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getIEigenValues() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getIEigenValues() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getInitValue(size_t i, int state) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getInitValue(size_t i, int state) const	bpp::AbstractSubstitutionModel	virtual
bpp::getModelStates(int code) const =0	bpp::SubstitutionModel	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getModelStates(int code) const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::AbstractSubstitutionModel::getModelStates(const std::string &code) const	bpp::AbstractSubstitutionModel	inlinevirtual
getName() const	bpp::L95	inlinevirtual
getNumberOfStates() const	bpp::NucleotideSubstitutionModel	inlinevirtual
bpp::getPij_t(double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getPij_t(double t) const	bpp::AbstractSubstitutionModel	virtual
bpp::getRate() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getRate() const	bpp::AbstractSubstitutionModel	virtual
bpp::getRowLeftEigenVectors() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getRowLeftEigenVectors() const	bpp::AbstractSubstitutionModel	inlinevirtual
bpp::getScale() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getScale() const	bpp::AbstractSubstitutionModel	virtual
bpp::getStateMap() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::getStateMap() const	bpp::AbstractSubstitutionModel	inlinevirtual
iEigenValues_	bpp::AbstractSubstitutionModel	protected
bpp::isDiagonalizable() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::isDiagonalizable() const	bpp::AbstractSubstitutionModel	inlinevirtual
isDiagonalizable_	bpp::AbstractSubstitutionModel	protected
bpp::isNonSingular() const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::isNonSingular() const	bpp::AbstractSubstitutionModel	inlinevirtual
isNonSingular_	bpp::AbstractSubstitutionModel	protected
kappa_	bpp::L95	private
L95(const NucleicAlphabet *alphabet, double alpha=0.5, double beta=0.5, double gamma=0.5, double kappa=1., double theta=0.5)	bpp::L95
leftEigenVectors_	bpp::AbstractSubstitutionModel	protected
operator=(const AbstractSubstitutionModel &model)	bpp::AbstractSubstitutionModel	inline
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::Pij_t(size_t i, size_t j, double t) const	bpp::AbstractSubstitutionModel	inlinevirtual
pijt_	bpp::AbstractSubstitutionModel	mutableprotected
bpp::Qij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::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::L95	virtual
bpp::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::setFreqFromData(const SequenceContainer &data, double pseudoCount=0)	bpp::AbstractSubstitutionModel	virtual
bpp::setRate(double rate)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::setRate(double rate)	bpp::AbstractSubstitutionModel	virtual
bpp::setScale(double scale)=0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::setScale(double scale)	bpp::AbstractSubstitutionModel	virtual
bpp::Sij(size_t i, size_t j) const =0	bpp::SubstitutionModel	pure virtual
bpp::AbstractSubstitutionModel::Sij(size_t i, size_t j) const	bpp::AbstractSubstitutionModel	inlinevirtual
size_	bpp::AbstractSubstitutionModel	protected
stateMap_	bpp::AbstractSubstitutionModel	protected
SubstitutionModel()	bpp::SubstitutionModel	inline
theta_	bpp::L95	private
tmpMat_	bpp::AbstractSubstitutionModel	mutableprotected
updateMatrices()	bpp::L95	virtual
vPowGen_	bpp::AbstractSubstitutionModel	protected
~AbstractSubstitutionModel()	bpp::AbstractSubstitutionModel	inlinevirtual
~L95()	bpp::L95	inlinevirtual
~NucleotideSubstitutionModel()	bpp::NucleotideSubstitutionModel	inlinevirtual
~SubstitutionModel()	bpp::SubstitutionModel	inlinevirtual