bpp::HmmLikelihood_DF Member List

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

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
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
AlignedLikelihoodCalculation(Context &context)	bpp::AlignedLikelihoodCalculation	inline
AlignedLikelihoodCalculation(const AlignedLikelihoodCalculation &lik)	bpp::AlignedLikelihoodCalculation	inline
backwardLik_	bpp::HmmLikelihood_DF	protected
cleanAllLikelihoods()	bpp::AlignedLikelihoodCalculation	inlinevirtual
clone() const	bpp::HmmLikelihood_DF	inlinevirtual
context_	bpp::HmmLikelihood_DF	private
deleteParameter_(size_t index)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameter_(std::string &name)	bpp::AbstractParameterAliasable	protectedvirtual
deleteParameters_(const std::vector< std::string > &names)	bpp::AbstractParameterAliasable	protectedvirtual
emissionProbabilities_	bpp::HmmLikelihood_DF	protected
fireParameterChanged(const ParameterList &parameters)	bpp::AbstractParameterAliasable	virtual
forwardLik_	bpp::HmmLikelihood_DF	protected
getAlias(const std::string &name) const	bpp::AbstractParameterAliasable	virtual
getAliasedParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getAliases() const	bpp::AbstractParameterAliasable	virtual
getContext() const	bpp::LikelihoodCalculation	inline
getContext_()	bpp::LikelihoodCalculation	inlineprotected
getFrom(const std::string &name) const	bpp::AbstractParameterAliasable
getFromParameters(const ParameterList &pl) const	bpp::AbstractParameterAliasable
getHiddenStatesPosteriorProbabilities() const	bpp::HmmLikelihood_DF	inline
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const	bpp::HmmLikelihood_DF	inline
getHmmEmissionProbabilities() const	bpp::HmmLikelihood_DF	inline
getHmmEmissionProbabilities()	bpp::HmmLikelihood_DF	inline
getHmmTransitionMatrix() const	bpp::HmmLikelihood_DF	inline
getIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
getLikelihoodForASite(size_t site) const	bpp::HmmLikelihood_DF	inline
bpp::AlignedLikelihoodCalculation::getLikelihoodForASite(size_t pos, bool shrunk=false)	bpp::AlignedLikelihoodCalculation	inline
getLikelihoodNode()	bpp::LikelihoodCalculation	inline
getLikelihoodNode_()	bpp::LikelihoodCalculation	inlineprotected
getLikelihoodPerSite()	bpp::AlignedLikelihoodCalculation	inline
getLogLikelihoodForASite(size_t pos, bool shrunk=false)	bpp::AlignedLikelihoodCalculation	inline
getNamespace() const override	bpp::AbstractParameterAliasable	virtual
getNumberOfIndependentParameters() const	bpp::AbstractParameterAliasable	virtual
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
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
getSiteLikelihoods(bool shrunk=false)	bpp::AlignedLikelihoodCalculation	inline
hasIndependentParameter(const std::string &name) const	bpp::AbstractParameterAliasable
hasParameter(const std::string &name) const override	bpp::AbstractParameterAliasable	virtual
hiddenAlphabet_	bpp::HmmLikelihood_DF	protected
hiddenPostProb_	bpp::HmmLikelihood_DF	protected
hmmEmis_	bpp::HmmLikelihood_DF	protected
hmmEq_	bpp::HmmLikelihood_DF	protected
HmmLikelihood_DF(Context &context, std::shared_ptr< HmmStateAlphabet > hiddenAlphabet, std::shared_ptr< HmmTransitionMatrix > transitionMatrix, std::shared_ptr< HmmPhyloEmissionProbabilities > emissionProbabilities, const std::string &prefix="")	bpp::HmmLikelihood_DF
HmmLikelihood_DF(const HmmLikelihood_DF &lik)	bpp::HmmLikelihood_DF	inline
hmmStateAlphabet() const	bpp::HmmLikelihood_DF	inline
hmmStateAlphabet()	bpp::HmmLikelihood_DF	inline
hmmTrans_	bpp::HmmLikelihood_DF	protected
includeParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
independentParameters_	bpp::AbstractParameterAliasable	private
isInitialized() const	bpp::LikelihoodCalculation	inlinevirtual
likelihood_	bpp::LikelihoodCalculation	mutableprotected
LikelihoodCalculation(Context &context)	bpp::LikelihoodCalculation	inline
LikelihoodCalculation(Context &context, ParameterList &paramList)	bpp::LikelihoodCalculation	inline
LikelihoodCalculation(const LikelihoodCalculation &lik)	bpp::LikelihoodCalculation	inline
makeLikelihoods()	bpp::HmmLikelihood_DF	inlinevirtual
matchParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
matrix_	bpp::HmmLikelihood_DF	protected
nbSites_	bpp::HmmLikelihood_DF	protected
nbStates_	bpp::HmmLikelihood_DF	protected
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
patternedSiteLikelihoods_	bpp::AlignedLikelihoodCalculation	mutableprotected
prefix_	bpp::AbstractParameterAliasable	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
setLikelihoodNode(ValueRef< DataLik > ll)	bpp::LikelihoodCalculation	inline
setNamespace(const std::string &nameSpace)	bpp::HmmLikelihood_DF	virtual
setParameters(const ParameterList &pl)	bpp::HmmLikelihood_DF	inline
setParametersValues(const ParameterList &parameters) override	bpp::AbstractParameterAliasable	virtual
setParameterValue(const std::string &name, double value) override	bpp::AbstractParameterAliasable	virtual
setSiteLikelihoods(SiteLikelihoodsRef ll, bool shrunk=false)	bpp::AlignedLikelihoodCalculation	inline
shareParameter_(const std::shared_ptr< Parameter > &parameter)	bpp::AbstractParameterAliasable	protectedvirtual
shareParameters_(const ParameterList &parameters)	bpp::AbstractParameterAliasable	protectedvirtual
siteLikelihoods_	bpp::AlignedLikelihoodCalculation	mutableprotected
unaliasParameters(const std::string &p1, const std::string &p2)	bpp::AbstractParameterAliasable	virtual
~AbstractParameterAliasable()	bpp::AbstractParameterAliasable	virtual
~AbstractParametrizable()	bpp::AbstractParametrizable	virtual
~Clonable()=default	bpp::Clonable	virtual
~HmmLikelihood_DF()	bpp::HmmLikelihood_DF	inlinevirtual
~ParameterAliasable()	bpp::ParameterAliasable	virtual
~Parametrizable()	bpp::Parametrizable	virtual