bpp::RELAX Member List

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

AbstractBiblioMixedTransitionModel(const std::string &prefix)	bpp::AbstractBiblioMixedTransitionModel
AbstractBiblioMixedTransitionModel(const AbstractBiblioMixedTransitionModel &model)	bpp::AbstractBiblioMixedTransitionModel
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
AbstractTotallyWrappedTransitionModel(const std::string &prefix)	bpp::AbstractTotallyWrappedTransitionModel	inline
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
bpp::addRateParameter()=0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::addRateParameter() override	bpp::AbstractBiblioTransitionModel	virtual
aliasListenersRegister_	bpp::AbstractParameterAliasable	private
bpp::aliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
bpp::AbstractBiblioTransitionModel::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
bpp::alphabet() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::alphabet() const override	bpp::AbstractWrappedModel	inlinevirtual
BranchModelInterface()	bpp::BranchModelInterface	inline
clone() const override	bpp::RELAX	inlinevirtual
bpp::computeFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
bpp::computeFrequencies(bool yn)=0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::computeFrequencies() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::AbstractBiblioTransitionModel::computeFrequencies(bool yn) override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::d2Lik_dt2(const Eigen::VectorXd &values, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::bpp::AbstractLkTransitionModel::d2Lik_dt2(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
bpp::d2Pij_dt2(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::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::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::bpp::AbstractLkTransitionModel::dLik_dt(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
bpp::dPij_dt(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::dPij_dt(size_t i, size_t j, double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
fireParameterChanged(const ParameterList &parameters) override	bpp::AbstractBiblioTransitionModel	inlinevirtual
bpp::freq(size_t i) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::freq(size_t i) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
frequencySet() const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getAliases() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getAliases() const	bpp::AbstractParameterAliasable	virtual
bpp::getAlphabet() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getAlphabet() const override	bpp::AbstractWrappedModel	inlinevirtual
bpp::getAlphabetStateAsChar(size_t index) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getAlphabetStateAsChar(size_t i) const override	bpp::AbstractWrappedModel	inlinevirtual
bpp::getAlphabetStateAsInt(size_t index) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getAlphabetStateAsInt(size_t i) const override	bpp::AbstractWrappedModel	inlinevirtual
bpp::getAlphabetStates() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getAlphabetStates() const override	bpp::AbstractWrappedModel	inlinevirtual
bpp::getd2Pij_dt2(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getd2Pij_dt2(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::getdPij_dt(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getdPij_dt(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::getFrequencies() const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getFrequencies() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::getFrequencies_()=0	bpp::TransitionModelInterface	protectedpure virtual
bpp::AbstractBiblioTransitionModel::getFrequencies_() override	bpp::AbstractTotallyWrappedTransitionModel	inlineprotectedvirtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getInitValue(size_t i, int state) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getInitValue(size_t i, int state) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::getModelStates(int code) const =0	bpp::BranchModelInterface	pure virtual
bpp::getModelStates(const std::string &code) const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getModelStates(int code) const override	bpp::AbstractWrappedModel	inlinevirtual
bpp::AbstractBiblioTransitionModel::getModelStates(const std::string &code) const override	bpp::AbstractWrappedModel	inlinevirtual
getName() const override	bpp::RELAX	inlinevirtual
bpp::getNamespace() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getNamespace() const override	bpp::AbstractParameterAliasable	virtual
getNModel(size_t i) const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
getNProbability(size_t i) const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
getNRate(size_t i) const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getNumberOfModels() const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfStates() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::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
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::getParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
bpp::AbstractBiblioTransitionModel::getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::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
bpp::getPij_t(double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getPij_t(double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
getPmodelParName(const std::string &name) const	bpp::AbstractBiblioTransitionModel
getProbabilities() const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::getRate() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getRate() const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
bpp::getStateMap() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::getStateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
getSubmodelNumbers(const std::string &desc) const override	bpp::AbstractBiblioMixedTransitionModel	virtual
getVRates() const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::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::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::bpp::AbstractLkTransitionModel::Lik_t(const Eigen::VectorXd &values, double t) const override	bpp::AbstractLkTransitionModel	inlinevirtual
lParPmodel_	bpp::AbstractBiblioTransitionModel	protected
mapParNamesFromPmodel_	bpp::AbstractBiblioTransitionModel	protected
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
mixedModel() const	bpp::AbstractBiblioMixedTransitionModel	inline
mixedModel_()	bpp::AbstractBiblioMixedTransitionModel	inlineprotected
mixedModelPtr_	bpp::AbstractBiblioMixedTransitionModel	protected
mixedSubModelPtr_	bpp::YNGP_M	protected
MixedTransitionModelInterface()	bpp::MixedTransitionModelInterface	inline
model(const std::string &name) const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::AbstractBiblioTransitionModel::model() const override	bpp::AbstractWrappedTransitionModel	inlinevirtual
model_()	bpp::AbstractWrappedTransitionModel	inlineprotected
nModel(size_t i) const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
nModel_(size_t i) override	bpp::AbstractBiblioMixedTransitionModel	inlineprotectedvirtual
normalizeVRates() override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
operator=(const YNGP_M &mod2)	bpp::YNGP_M	inline
bpp::AbstractBiblioMixedTransitionModel::operator=(const AbstractBiblioMixedTransitionModel &model)	bpp::AbstractBiblioMixedTransitionModel
bpp::AbstractBiblioTransitionModel::operator=(const AbstractBiblioTransitionModel &model)	bpp::AbstractBiblioTransitionModel
bpp::AbstractTotallyWrappedTransitionModel::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
bpp::parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
bpp::Pij_t(size_t i, size_t j, double t) const =0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::Pij_t(size_t i, size_t j, double t) const override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
prefix_	bpp::AbstractParameterAliasable	private
RELAX(std::shared_ptr< const GeneticCode > gc, std::unique_ptr< CodonFrequencySetInterface > codonFreqs)	bpp::RELAX
bpp::removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
bpp::setFreq(std::map< int, double > &frequencies)=0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::setFreq(std::map< int, double > &frequ) override	bpp::AbstractBiblioTransitionModel	virtual
bpp::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0)=0	bpp::TransitionModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::setFreqFromData(const SequenceDataInterface &data, double pseudoCount=0) override	bpp::AbstractBiblioTransitionModel	virtual
bpp::setNamespace(const std::string &prefix)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::setNamespace(const std::string &name) override	bpp::AbstractBiblioTransitionModel	virtual
setNProbability(size_t i, double prob) override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
bpp::setRate(double rate)=0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::setRate(double rate) override	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
setVRates(const Vdouble &vd) override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
bpp::stateMap() const =0	bpp::BranchModelInterface	pure virtual
bpp::AbstractBiblioTransitionModel::stateMap() const override	bpp::AbstractWrappedModel	inlinevirtual
synfrom_	bpp::YNGP_M	protected
synto_	bpp::YNGP_M	protected
transitionModel() const override	bpp::AbstractBiblioMixedTransitionModel	inlinevirtual
transitionModel_() override	bpp::AbstractBiblioMixedTransitionModel	inlineprotectedvirtual
bpp::TransitionModelInterface()	bpp::TransitionModelInterface	inline
bpp::TransitionModelInterface::TransitionModelInterface()	bpp::TransitionModelInterface	inline
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractBiblioTransitionModel::unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
updateMatrices_() override	bpp::RELAX	protectedvirtual
WrappedModelInterface()	bpp::WrappedModelInterface	inline
WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inline
YNGP_M(const std::string &name)	bpp::YNGP_M	inline
YNGP_M(const YNGP_M &mod2)	bpp::YNGP_M	inline
~AbstractBiblioMixedTransitionModel()	bpp::AbstractBiblioMixedTransitionModel	virtual
~AbstractBiblioTransitionModel()	bpp::AbstractBiblioTransitionModel	inlinevirtual
~AbstractLkTransitionModel()	bpp::AbstractLkTransitionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~AbstractTotallyWrappedTransitionModel()	bpp::AbstractTotallyWrappedTransitionModel	inlinevirtual
~AbstractWrappedModel()	bpp::AbstractWrappedModel	inlinevirtual
~BranchModelInterface()	bpp::BranchModelInterface	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~MixedTransitionModelInterface()	bpp::MixedTransitionModelInterface	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~TransitionModelInterface()	bpp::TransitionModelInterface	inlinevirtual
~WrappedModelInterface()	bpp::WrappedModelInterface	inlinevirtual
~WrappedTransitionModelInterface()	bpp::WrappedTransitionModelInterface	inlinevirtual