bpp::OneChangeRegisterTransitionModel Member List

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

AbstractFromSubstitutionModelTransitionModel(std::unique_ptr< SubstitutionModelInterface > subModel, const std::string &prefix)	bpp::AbstractFromSubstitutionModelTransitionModel
AbstractFromSubstitutionModelTransitionModel(const AbstractFromSubstitutionModelTransitionModel &fmsm)	bpp::AbstractFromSubstitutionModelTransitionModel
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
AbstractWrappedTransitionModel(const std::string &prefix)	bpp::AbstractWrappedTransitionModel	inline
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
addRateParameter() override	bpp::AbstractFromSubstitutionModelTransitionModel	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::OneChangeRegisterTransitionModel	inlinevirtual
computeFrequencies() const override	bpp::AbstractFromSubstitutionModelTransitionModel	inlinevirtual
computeFrequencies(bool yn) override	bpp::AbstractFromSubstitutionModelTransitionModel	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::OneChangeRegisterTransitionModel	virtual
d2pij_t	bpp::AbstractFromSubstitutionModelTransitionModel	mutableprotected
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::OneChangeRegisterTransitionModel	virtual
dpij_t	bpp::AbstractFromSubstitutionModelTransitionModel	mutableprotected
fireParameterChanged(const ParameterList &parameters) override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
freq(size_t i) const override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
frequencySet() const override	bpp::OneChangeRegisterTransitionModel	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
getd2Pij_dt2(double t) const override	bpp::OneChangeRegisterTransitionModel	virtual
getdPij_dt(double t) const override	bpp::OneChangeRegisterTransitionModel	virtual
getFrequencies() const override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
getFrequencies_() override	bpp::AbstractFromSubstitutionModelTransitionModel	inlineprotectedvirtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getInitValue(size_t i, int state) const override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
getModelStates(int code) const override	bpp::AbstractWrappedModel	inlinevirtual
getModelStates(const std::string &code) const override	bpp::AbstractWrappedModel	inlinevirtual
getName() const override	bpp::OneChangeRegisterTransitionModel	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::OneChangeRegisterTransitionModel	virtual
getRate() const override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
getRegisterName() const	bpp::OneChangeRegisterTransitionModel	inline
getRegisterNumbers() const	bpp::OneChangeRegisterTransitionModel	inline
getStateMap() const override	bpp::AbstractWrappedModel	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
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
model() const override	bpp::AbstractFromSubstitutionModelTransitionModel	inlinevirtual
model_()	bpp::AbstractFromSubstitutionModelTransitionModel	inlineprotected
modelChanged_	bpp::OneChangeRegisterTransitionModel	private
nestedPrefix_	bpp::AbstractFromSubstitutionModelTransitionModel	protected
noChangedStates_	bpp::OneChangeRegisterTransitionModel	private
OneChangeRegisterTransitionModel(std::unique_ptr< SubstitutionModelInterface > originalModel, const SubstitutionRegisterInterface &reg, size_t numReg)	bpp::OneChangeRegisterTransitionModel
OneChangeRegisterTransitionModel(std::unique_ptr< SubstitutionModelInterface > originalModel, const SubstitutionRegisterInterface &reg, std::vector< size_t > vNumRegs)	bpp::OneChangeRegisterTransitionModel
OneChangeRegisterTransitionModel(const OneChangeRegisterTransitionModel &fmsm)	bpp::OneChangeRegisterTransitionModel	inline
operator=(const OneChangeRegisterTransitionModel &fmsm)	bpp::OneChangeRegisterTransitionModel	inline
bpp::AbstractFromSubstitutionModelTransitionModel::operator=(const AbstractFromSubstitutionModelTransitionModel &fmsm)	bpp::AbstractFromSubstitutionModelTransitionModel
bpp::AbstractWrappedTransitionModel::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	bpp::AbstractFromSubstitutionModelTransitionModel	mutableprotected
Pij_t(size_t i, size_t j, double t) const override	bpp::OneChangeRegisterTransitionModel	virtual
prefix_	bpp::AbstractParameterAliasable	private
registerName_	bpp::OneChangeRegisterTransitionModel	private
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
setFreq(std::map< int, double > &m) override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
setFreqFromData(const SequenceDataInterface &data, double pseudoCount) override	bpp::OneChangeRegisterTransitionModel	inlinevirtual
setNamespace(const std::string &prefix) override	bpp::AbstractFromSubstitutionModelTransitionModel	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::OneChangeRegisterTransitionModel	inlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
size_	bpp::AbstractFromSubstitutionModelTransitionModel	protected
stateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
subModel_	bpp::AbstractFromSubstitutionModelTransitionModel	protected
substitutionModel() const	bpp::AbstractFromSubstitutionModelTransitionModel	inline
substitutionModel_()	bpp::AbstractFromSubstitutionModelTransitionModel	inlineprotected
transitionModel() const override	bpp::AbstractFromSubstitutionModelTransitionModel	inlinevirtual
transitionModel_() override	bpp::AbstractFromSubstitutionModelTransitionModel	inlineprotectedvirtual
TransitionModelInterface()	bpp::TransitionModelInterface	inline
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateMatrices_()	bpp::OneChangeRegisterTransitionModel	protected
vNumRegs_	bpp::OneChangeRegisterTransitionModel	private
WrappedModelInterface()	bpp::WrappedModelInterface	inline
WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inline
~AbstractFromSubstitutionModelTransitionModel()	bpp::AbstractFromSubstitutionModelTransitionModel	inlinevirtual
~AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractWrappedModel()	bpp::AbstractWrappedModel	inlinevirtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~OneChangeRegisterTransitionModel()	bpp::OneChangeRegisterTransitionModel	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual
~WrappedModelInterface()	bpp::WrappedModelInterface	inlinevirtual
~WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inlinevirtual