bpp::AbstractCodonAARateSubstitutionModel Member List

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

aaModel() const	bpp::AbstractCodonAARateSubstitutionModel	inline
AbstractCodonAARateSubstitutionModel(std::shared_ptr< ProteinSubstitutionModelInterface > pmodel, std::shared_ptr< const GeneticCode > pgencode, const std::string &prefix, bool paramSynRate=false)	bpp::AbstractCodonAARateSubstitutionModel
AbstractCodonAARateSubstitutionModel(const AbstractCodonAARateSubstitutionModel &model)	bpp::AbstractCodonAARateSubstitutionModel	inline
AbstractParameterAliasable(const std::string &prefix)	bpp::AbstractParameterAliasable
AbstractParameterAliasable(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
addParameter_(Parameter *parameter)	bpp::AbstractParameterAliasable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
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::AbstractParameterAliasable::aliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
bpp::AbstractParameterAliasable::aliasParameters(std::map< std::string, std::string > &unparsedParams, bool verbose)	bpp::AbstractParameterAliasable	virtual
beta_	bpp::AbstractCodonAARateSubstitutionModel	private
clone() const override	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
codonFrequencySet() const override	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inline
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
fireParameterChanged(const ParameterList &parameters) override	bpp::AbstractCodonAARateSubstitutionModel	virtual
gamma_	bpp::AbstractCodonAARateSubstitutionModel	private
getAAModel() const	bpp::AbstractCodonAARateSubstitutionModel	inline
bpp::getAlias(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::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::AbstractParameterAliasable::getAliases() const	bpp::AbstractParameterAliasable	virtual
getCodonsMulRate(size_t i, size_t j) const override	bpp::AbstractCodonAARateSubstitutionModel	virtual
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
bpp::getIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getNamespace() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::getNamespace() const override	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfIndependentParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
bpp::getNumberOfParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::getNumberOfParameters() const override	bpp::AbstractParameterAliasable	virtual
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::AbstractParameterAliasable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters() const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::getParameters() const override	bpp::AbstractParameterAliasable	virtual
bpp::getParameters_()=0	bpp::ParameterAliasable	protectedpure virtual
bpp::AbstractParameterAliasable::getParameters_() override	bpp::AbstractParameterAliasable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::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
hasCodonFrequencySet() const override	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
bpp::hasParameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
operator=(const AbstractCodonAARateSubstitutionModel &model)	bpp::AbstractCodonAARateSubstitutionModel	inline
bpp::AbstractParameterAliasable::operator=(const AbstractParameterAliasable &ap)	bpp::AbstractParameterAliasable
pAAmodel_	bpp::AbstractCodonAARateSubstitutionModel	private
bpp::parameter(const std::string &name) const=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::parameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
ParameterAliasable()	bpp::ParameterAliasable
parameters_	bpp::AbstractParameterAliasable	private
Parametrizable()	bpp::Parametrizable
pgencode_	bpp::AbstractCodonAARateSubstitutionModel	private
prefix_	bpp::AbstractParameterAliasable	private
bpp::removeConstraint(const std::string &name)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::removeConstraint(const std::string &name) override	bpp::AbstractParameterAliasable	virtual
resetParameters_()	bpp::AbstractParameterAliasable	protected
setAAModel(std::shared_ptr< ProteinSubstitutionModelInterface > model)	bpp::AbstractCodonAARateSubstitutionModel	inline
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::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::AbstractParameterAliasable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParameterAliasable	virtual
setFreq(std::map< int, double > &frequencies) override	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
setNamespace(const std::string &prefix) override	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
stateMap_	bpp::AbstractCodonAARateSubstitutionModel	private
bpp::unaliasParameters(const std::string &p1, const std::string &p2)=0	bpp::ParameterAliasable	pure virtual
bpp::AbstractParameterAliasable::unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
~AbstractCodonAARateSubstitutionModel()	bpp::AbstractCodonAARateSubstitutionModel	inlinevirtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~CoreCodonSubstitutionModelInterface()	bpp::CoreCodonSubstitutionModelInterface	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual