bpp::YN98 Member List

This is the complete list of members for bpp::YN98, including all inherited members.

AbstractBiblioSubstitutionModel(const std::string &prefix)	bpp::AbstractBiblioSubstitutionModel	inline
AbstractBiblioSubstitutionModel(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel	inline
AbstractBiblioTransitionModel(const std::string &prefix)	bpp::AbstractBiblioTransitionModel
AbstractBiblioTransitionModel(const AbstractBiblioTransitionModel &model)	bpp::AbstractBiblioTransitionModel
AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inline
AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
AbstractTotallyWrappedSubstitutionModel(const std::string &prefix)	bpp::AbstractTotallyWrappedSubstitutionModel	inline
AbstractTotallyWrappedTransitionModel(const std::string &prefix)	bpp::AbstractTotallyWrappedTransitionModel	inline
AbstractWrappedModel(const std::string &prefix)	bpp::AbstractWrappedModel	inline
AbstractWrappedSubstitutionModel(const std::string &prefix)	bpp::AbstractWrappedSubstitutionModel	inline
AbstractWrappedTransitionModel(const std::string &prefix)	bpp::AbstractWrappedTransitionModel	inline
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
addRateParameter() override	bpp::AbstractBiblioTransitionModel	virtual
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
alphabet() const override	bpp::AbstractWrappedModel	inlinevirtual
BranchModelInterface()	bpp::BranchModelInterface	inline
clone() const override	bpp::YN98	inlinevirtual
codonFrequencySet() const override	bpp::YN98	inlinevirtual
CodonReversibleSubstitutionModelInterface()	bpp::CodonReversibleSubstitutionModelInterface	inline
CodonSubstitutionModelInterface()	bpp::CodonSubstitutionModelInterface	inline
computeFrequencies() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
computeFrequencies(bool yn) override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inline
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractLkTransitionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
d2Pij_dt2(size_t i, size_t j, double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::dLik_dt(const Eigen::VectorXd &values, double t) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractLkTransitionModel::dLik_dt(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
dPij_dt(size_t i, size_t j, double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
enableEigenDecomposition(bool yn)	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
enableEigenDecomposition()	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
exchangeabilityMatrix() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
fireParameterChanged(const ParameterList &parameters) override	bpp::AbstractBiblioTransitionModel	inlinevirtual
freq(size_t i) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
frequencySet() const override	bpp::YN98	inlinevirtual
generator() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getAliases() const	bpp::AbstractParameterAliasable	virtual
getAlphabet() const override	bpp::AbstractWrappedModel	inlinevirtual
getAlphabetStateAsChar(size_t i) const override	bpp::AbstractWrappedModel	inlinevirtual
getAlphabetStateAsInt(size_t i) const override	bpp::AbstractWrappedModel	inlinevirtual
getAlphabetStates() const override	bpp::AbstractWrappedModel	inlinevirtual
getCodonsMulRate(size_t i, size_t j) const override	bpp::YN98	inlinevirtual
getColumnRightEigenVectors() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getd2Pij_dt2(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getdPij_dt(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getEigenValues() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getFrequencies() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getFrequencies_() override	bpp::AbstractTotallyWrappedTransitionModel	inlineprotectedvirtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getGeneticCode() const override	bpp::YN98	inlinevirtual
getIEigenValues() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getInitValue(size_t i, int state) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getModelStates(int code) const override	bpp::AbstractWrappedModel	inlinevirtual
getModelStates(const std::string &code) const override	bpp::AbstractWrappedModel	inlinevirtual
getName() const override	bpp::YN98	inlinevirtual
getNamespace() const override	bpp::AbstractParameterAliasable	virtual
getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
getNumberOfStates() const override	bpp::AbstractWrappedModel	inlinevirtual
getParameter(const std::string &name) const	bpp::AbstractParameterAliasable
getParameter(size_t i) const	bpp::AbstractParameterAliasable	protected
getParameter(size_t i)	bpp::AbstractParameterAliasable	protected
getParameter_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index)	bpp::AbstractParameterAliasable	protected
getParameter_(size_t index) const	bpp::AbstractParameterAliasable	protected
getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameters() const override	bpp::AbstractParameterAliasable	virtual
getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
getParameterValue(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParameterAliasable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParameterAliasable	protected
getParNameFromPmodel(const std::string &name) const	bpp::AbstractBiblioTransitionModel
getPij_t(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getPmodelParName(const std::string &name) const	bpp::AbstractBiblioTransitionModel
getRate() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getRowLeftEigenVectors() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getScale() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
getStateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
hasCodonFrequencySet() const override	bpp::YN98	inlinevirtual
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
isDiagonalizable() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
isNonSingular() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
isScalable() const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
lik_	bpp::AbstractLkTransitionModel	mutableprivate
bpp::Lik_t(const Eigen::VectorXd &values, double t) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractLkTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
lParPmodel_	bpp::AbstractBiblioTransitionModel	protected
mapParNamesFromPmodel_	bpp::AbstractBiblioTransitionModel	protected
matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
model() const override	bpp::AbstractWrappedTransitionModel	inlinevirtual
model_()	bpp::AbstractWrappedTransitionModel	inlineprotected
normalize()	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
operator=(const YN98 &)	bpp::YN98
bpp::AbstractBiblioSubstitutionModel::operator=(const AbstractBiblioSubstitutionModel &model)	bpp::AbstractBiblioSubstitutionModel	inline
bpp::AbstractBiblioTransitionModel::operator=(const AbstractBiblioTransitionModel &model)	bpp::AbstractBiblioTransitionModel
bpp::AbstractTotallyWrappedTransitionModel::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
Pij_t(size_t i, size_t j, double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
pmodel_	bpp::YN98	private
prefix_	bpp::AbstractParameterAliasable	private
Qij(size_t i, size_t j) const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
ReversibleSubstitutionModelInterface()	bpp::ReversibleSubstitutionModelInterface	inline
setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setDiagonal()	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
setFreq(std::map< int, double > &frequencies) override	bpp::YN98	inlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) override	bpp::AbstractBiblioTransitionModel	virtual
setNamespace(const std::string &name) override	bpp::AbstractBiblioTransitionModel	virtual
setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
setRate(double rate) override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
setScalable(bool scalable)	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
setScale(double scale)	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
Sij(size_t i, size_t j) const	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
stateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
substitutionModel() const override	bpp::YN98	inlinevirtual
substitutionModel_() override	bpp::YN98	inlineprotectedvirtual
SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inline
bpp::transitionModel() const =0	bpp::WrappedTransitionModelInterface	pure virtual
bpp::AbstractTotallyWrappedSubstitutionModel::bpp::AbstractWrappedSubstitutionModel::transitionModel() const	bpp::AbstractWrappedSubstitutionModel	inlinevirtual
bpp::transitionModel_()=0	bpp::AbstractWrappedTransitionModel	protectedpure virtual
bpp::AbstractTotallyWrappedSubstitutionModel::bpp::AbstractWrappedSubstitutionModel::transitionModel_()	bpp::AbstractWrappedSubstitutionModel	inlineprotectedvirtual
TransitionModelInterface()	bpp::TransitionModelInterface	inline
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateMatrices_() override	bpp::AbstractBiblioSubstitutionModel	inlineprotectedvirtual
WrappedModelInterface()	bpp::WrappedModelInterface	inline
WrappedSubstitutionModelInterface()	bpp::WrappedSubstitutionModelInterface	inline
WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inline
YN98(std::shared_ptr< const GeneticCode > gc, std::unique_ptr< CodonFrequencySetInterface > codonFreqs)	bpp::YN98
YN98(const YN98 &yn98)	bpp::YN98
~AbstractBiblioSubstitutionModel()	bpp::AbstractBiblioSubstitutionModel	inlinevirtual
~AbstractBiblioTransitionModel()	bpp::AbstractBiblioTransitionModel	inlinevirtual
~AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractTotallyWrappedSubstitutionModel()	bpp::AbstractTotallyWrappedSubstitutionModel	inlinevirtual
~AbstractTotallyWrappedTransitionModel()	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
~AbstractWrappedModel()	bpp::AbstractWrappedModel	inlinevirtual
~AbstractWrappedSubstitutionModel()	bpp::AbstractWrappedSubstitutionModel	inlinevirtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~CodonReversibleSubstitutionModelInterface()	bpp::CodonReversibleSubstitutionModelInterface	inlinevirtual
~CodonSubstitutionModelInterface()	bpp::CodonSubstitutionModelInterface	inlinevirtual
~CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~ReversibleSubstitutionModelInterface()	bpp::ReversibleSubstitutionModelInterface	inlinevirtual
~SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inlinevirtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual
~WrappedModelInterface()	bpp::WrappedModelInterface	inlinevirtual
~WrappedSubstitutionModelInterface()	bpp::WrappedSubstitutionModelInterface	inlinevirtual
~WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inlinevirtual
~YN98()	bpp::YN98	inlinevirtual