bpp::InMixedSubstitutionModel Member List

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

AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inline
AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
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::InMixedSubstitutionModel	inlinevirtual
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::InMixedSubstitutionModel	inlinevirtual
computeFrequencies() const override	bpp::InMixedSubstitutionModel	inlinevirtual
computeFrequencies(bool yn) override	bpp::InMixedSubstitutionModel	inlinevirtual
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::InMixedSubstitutionModel	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::InMixedSubstitutionModel	inlinevirtual
enableEigenDecomposition(bool yn) override	bpp::InMixedSubstitutionModel	inlinevirtual
enableEigenDecomposition() override	bpp::InMixedSubstitutionModel	inlinevirtual
exchangeabilityMatrix() const override	bpp::InMixedSubstitutionModel	inlinevirtual
fireParameterChanged(const ParameterList &parameters) override	bpp::InMixedSubstitutionModel	inlinevirtual
freq(size_t i) const override	bpp::InMixedSubstitutionModel	inlinevirtual
frequencySet() const override	bpp::AbstractWrappedTransitionModel	inlinevirtual
generator() const override	bpp::InMixedSubstitutionModel	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
getColumnRightEigenVectors() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getd2Pij_dt2(double t) const override	bpp::InMixedSubstitutionModel	inlinevirtual
getdPij_dt(double t) const override	bpp::InMixedSubstitutionModel	inlinevirtual
getEigenValues() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getFrequencies() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getFrequencies_() override	bpp::InMixedSubstitutionModel	inlineprotectedvirtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getIEigenValues() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getInitValue(size_t i, int state) const override	bpp::InMixedSubstitutionModel	inlinevirtual
getModelStates(int code) const override	bpp::AbstractWrappedModel	inlinevirtual
getModelStates(const std::string &code) const override	bpp::AbstractWrappedModel	inlinevirtual
getName() const override	bpp::InMixedSubstitutionModel	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
getPij_t(double t) const override	bpp::InMixedSubstitutionModel	inlinevirtual
getRate() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getRowLeftEigenVectors() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getScale() const override	bpp::InMixedSubstitutionModel	inlinevirtual
getStateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
getSubModelNumber() const	bpp::InMixedSubstitutionModel	inline
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
InMixedSubstitutionModel(std::unique_ptr< MixedTransitionModelInterface > mixedModel, const std::string &subModelName, const std::string &mixtDesc)	bpp::InMixedSubstitutionModel
InMixedSubstitutionModel(std::unique_ptr< MixedTransitionModelInterface > mixedModel, size_t subModelNumber, const std::string &mixtDesc)	bpp::InMixedSubstitutionModel
InMixedSubstitutionModel(const InMixedSubstitutionModel &fmsm)	bpp::InMixedSubstitutionModel
isDiagonalizable() const override	bpp::InMixedSubstitutionModel	inlinevirtual
isNonSingular() const override	bpp::InMixedSubstitutionModel	inlinevirtual
isScalable() const override	bpp::InMixedSubstitutionModel	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
matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
mixedModel() const	bpp::InMixedSubstitutionModel	inline
mixedModel_()	bpp::InMixedSubstitutionModel	inlineprotected
mixedModelPtr_	bpp::InMixedSubstitutionModel	private
mixtName_	bpp::InMixedSubstitutionModel	private
model() const override	bpp::AbstractWrappedTransitionModel	inlinevirtual
model_()	bpp::AbstractWrappedTransitionModel	inlineprotected
normalize() override	bpp::InMixedSubstitutionModel	inlinevirtual
operator=(const InMixedSubstitutionModel &fmsm)	bpp::InMixedSubstitutionModel
bpp::AbstractWrappedSubstitutionModel::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::InMixedSubstitutionModel	inlinevirtual
prefix_	bpp::AbstractParameterAliasable	private
Qij(size_t i, size_t j) const override	bpp::InMixedSubstitutionModel	inlinevirtual
removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setDiagonal() override	bpp::InMixedSubstitutionModel	inlinevirtual
setFreq(std::map< int, double > &frequencies) override	bpp::InMixedSubstitutionModel	inlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) override	bpp::InMixedSubstitutionModel	inlinevirtual
setNamespace(const std::string &name) override	bpp::InMixedSubstitutionModel	inlinevirtual
setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
setRate(double rate) override	bpp::InMixedSubstitutionModel	inlinevirtual
setScalable(bool scalable) override	bpp::InMixedSubstitutionModel	inlinevirtual
setScale(double scale) override	bpp::InMixedSubstitutionModel	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 override	bpp::InMixedSubstitutionModel	inlinevirtual
stateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
subModelNumber_	bpp::InMixedSubstitutionModel	private
substitutionModel() const override	bpp::InMixedSubstitutionModel	inlinevirtual
substitutionModel_() override	bpp::InMixedSubstitutionModel	inlineprotectedvirtual
SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inline
transitionModel() const	bpp::AbstractWrappedSubstitutionModel	inlinevirtual
transitionModel_()	bpp::AbstractWrappedSubstitutionModel	inlineprotectedvirtual
TransitionModelInterface()	bpp::TransitionModelInterface	inline
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
WrappedModelInterface()	bpp::WrappedModelInterface	inline
WrappedSubstitutionModelInterface()	bpp::WrappedSubstitutionModelInterface	inline
WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inline
~AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractWrappedModel()	bpp::AbstractWrappedModel	inlinevirtual
~AbstractWrappedSubstitutionModel()	bpp::AbstractWrappedSubstitutionModel	inlinevirtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SubstitutionModelInterface()	bpp::SubstitutionModelInterface	inlinevirtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual
~WrappedModelInterface()	bpp::WrappedModelInterface	inlinevirtual
~WrappedSubstitutionModelInterface()	bpp::WrappedSubstitutionModelInterface	inlinevirtual
~WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inlinevirtual