bpp::HmmPhyloAlphabet Member List

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

AbstractParametrizable(const std::string &prefix)	bpp::AbstractParametrizable
addParameter_(Parameter *parameter)	bpp::AbstractParametrizable	protectedvirtual
addParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
alignedPhyloLikelihood(size_t stateIndex) const	bpp::HmmPhyloAlphabet	inline
clone() const override	bpp::HmmPhyloAlphabet	inlinevirtual
context_	bpp::HmmPhyloAlphabet	private
deleteParameter_(size_t index)	bpp::AbstractParametrizable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParametrizable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParametrizable	protectedvirtual
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractParametrizable	virtual
getAlignedPhyloLikelihood(size_t stateIndex) const	bpp::HmmPhyloAlphabet	inline
getContext()	bpp::HmmPhyloAlphabet	inline
bpp::getNamespace() const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::getNamespace() const override	bpp::AbstractParametrizable	virtual
bpp::getNumberOfParameters() const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::getNumberOfParameters() const override	bpp::AbstractParametrizable	virtual
getNumberOfSites() const	bpp::HmmPhyloAlphabet	inline
getNumberOfStates() const override	bpp::HmmPhyloAlphabet	inlinevirtual
getParameter(const std::string &name) const	bpp::AbstractParametrizable
getParameter(size_t i) const	bpp::AbstractParametrizable	protected
getParameter(size_t i)	bpp::AbstractParametrizable	protected
getParameter_(const std::string &name)	bpp::AbstractParametrizable	protected
getParameter_(size_t index)	bpp::AbstractParametrizable	protected
getParameter_(size_t index) const	bpp::AbstractParametrizable	protected
bpp::getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::getParameterNameWithoutNamespace(const std::string &name) const override	bpp::AbstractParametrizable	virtual
bpp::getParameters() const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::getParameters() const override	bpp::AbstractParametrizable	virtual
bpp::getParameters_()=0	bpp::HmmStateAlphabet	protectedpure virtual
bpp::AbstractParametrizable::getParameters_() override	bpp::AbstractParametrizable	protectedvirtual
bpp::getParameterValue(const std::string &name) const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::getParameterValue(const std::string &name) const override	bpp::AbstractParametrizable	virtual
getParameterWithNamespace_(const std::string &name)	bpp::AbstractParametrizable	protected
getParameterWithNamespace_(const std::string &name) const	bpp::AbstractParametrizable	protected
getState(size_t stateIndex) const override	bpp::HmmPhyloAlphabet	inlinevirtual
bpp::hasParameter(const std::string &name) const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::hasParameter(const std::string &name) const override	bpp::AbstractParametrizable	virtual
HmmPhyloAlphabet(AlignedPhyloLikelihoodSetInterface &soap)	bpp::HmmPhyloAlphabet	inline
HmmPhyloAlphabet(MultiProcessSequencePhyloLikelihood &mpsp)	bpp::HmmPhyloAlphabet	inline
HmmPhyloAlphabet(const HmmPhyloAlphabet &hpa)	bpp::HmmPhyloAlphabet	inline
HmmStateAlphabet()	bpp::HmmStateAlphabet
includeParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
bpp::matchParametersValues(const ParameterList &parameters)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
nbSites_	bpp::HmmPhyloAlphabet	private
bpp::parameter(const std::string &name) const=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::parameter(const std::string &name) const override	bpp::AbstractParametrizable	virtual
parameters_	bpp::AbstractParametrizable	private
Parametrizable()	bpp::Parametrizable
prefix_	bpp::AbstractParametrizable	private
bpp::removeConstraint(const std::string &name)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::removeConstraint(const std::string &name) override	bpp::AbstractParametrizable	virtual
resetParameters_()	bpp::AbstractParametrizable	protected
bpp::setAllParametersValues(const ParameterList &parameters)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::setAllParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
bpp::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override	bpp::AbstractParametrizable	virtual
bpp::setNamespace(const std::string &prefix)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::setNamespace(const std::string &prefix) override	bpp::AbstractParametrizable	virtual
bpp::setParametersValues(const ParameterList &parameters)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::setParametersValues(const ParameterList &parameters) override	bpp::AbstractParametrizable	virtual
bpp::setParameterValue(const std::string &name, double value)=0	bpp::HmmStateAlphabet	pure virtual
bpp::AbstractParametrizable::setParameterValue(const std::string &name, double value) override	bpp::AbstractParametrizable	virtual
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParametrizable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParametrizable	protectedvirtual
vAP_	bpp::HmmPhyloAlphabet	private
worksWith(const HmmStateAlphabet &stateAlphabet) const override	bpp::HmmPhyloAlphabet	inlinevirtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~HmmPhyloAlphabet()	bpp::HmmPhyloAlphabet	inlinevirtual
~HmmStateAlphabet()	bpp::HmmStateAlphabet	virtual
~Parametrizable()	bpp::Parametrizable	virtual