bpp::AbstractHmmLikelihood Member List

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

AbstractHmmLikelihood()	bpp::AbstractHmmLikelihood
AbstractHmmLikelihood(const AbstractHmmLikelihood &adhlik)	bpp::AbstractHmmLikelihood
clone() const =0	bpp::HmmLikelihood	pure virtual
computeD2Likelihood_() const =0	bpp::HmmLikelihood	protectedpure virtual
computeDLikelihood_() const =0	bpp::HmmLikelihood	protectedpure virtual
d2f(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	inlinevirtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)	bpp::SecondOrderDerivable	inlinevirtual
d2LogLik_	bpp::AbstractHmmLikelihood	mutableprotected
d2Variable_	bpp::AbstractHmmLikelihood	mutableprotected
df(const std::string &variable, const ParameterList &parameters)	bpp::FirstOrderDerivable	inlinevirtual
dLogLik_	bpp::AbstractHmmLikelihood	mutableprotected
dVariable_	bpp::AbstractHmmLikelihood	mutableprotected
enableFirstOrderDerivatives(bool yn)	bpp::AbstractHmmLikelihood	inlinevirtual
enableFirstOrderDerivatives() const	bpp::AbstractHmmLikelihood	inlinevirtual
enableSecondOrderDerivatives(bool yn)	bpp::AbstractHmmLikelihood	inlinevirtual
enableSecondOrderDerivatives() const	bpp::AbstractHmmLikelihood	inlinevirtual
f(const ParameterList &parameters)	bpp::FunctionInterface	inlinevirtual
FirstOrderDerivable()	bpp::FirstOrderDerivable	inline
FunctionInterface()	bpp::FunctionInterface	inline
getBreakPoints() const =0	bpp::HmmLikelihood	pure virtual
getD2LogLikelihood() const	bpp::AbstractHmmLikelihood	inlinevirtual
getD2LogLikelihoodForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getDLogLikelihood() const	bpp::AbstractHmmLikelihood	inlinevirtual
getDLogLikelihoodForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getFirstOrderDerivative(const std::string &variable) const	bpp::AbstractHmmLikelihood	virtual
getHiddenStatesPosteriorProbabilities(std::vector< std::vector< double >> &probs, bool append) const =0	bpp::HmmLikelihood	pure virtual
getHiddenStatesPosteriorProbabilitiesForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getHmmEmissionProbabilities() const =0	bpp::HmmLikelihood	pure virtual
getHmmEmissionProbabilities()=0	bpp::HmmLikelihood	pure virtual
getHmmStateAlphabet() const =0	bpp::HmmLikelihood	pure virtual
getHmmStateAlphabet()=0	bpp::HmmLikelihood	pure virtual
getHmmTransitionMatrix() const =0	bpp::HmmLikelihood	pure virtual
getHmmTransitionMatrix()=0	bpp::HmmLikelihood	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::HmmLikelihood	pure virtual
getLikelihoodForEachSite() const =0	bpp::HmmLikelihood	pure virtual
getLogLikelihood() const =0	bpp::HmmLikelihood	pure virtual
getNamespace() const =0	bpp::Parametrizable	pure virtual
getNumberOfParameters() const =0	bpp::Parametrizable	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getParameters() const =0	bpp::Parametrizable	pure virtual
getParameters_()=0	bpp::Parametrizable	protectedpure virtual
getParameterValue(const std::string &name) const =0	bpp::Parametrizable	pure virtual
getSecondOrderDerivative(const std::string &variable) const	bpp::AbstractHmmLikelihood	virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const	bpp::AbstractHmmLikelihood	inlinevirtual
getValue() const =0	bpp::FunctionInterface	pure virtual
hasParameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
hmmEmissionProbabilities() const =0	bpp::HmmLikelihood	pure virtual
hmmEmissionProbabilities()=0	bpp::HmmLikelihood	pure virtual
hmmStateAlphabet() const =0	bpp::HmmLikelihood	pure virtual
hmmStateAlphabet()=0	bpp::HmmLikelihood	pure virtual
hmmTransitionMatrix() const =0	bpp::HmmLikelihood	pure virtual
hmmTransitionMatrix()=0	bpp::HmmLikelihood	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
operator=(const AbstractHmmLikelihood &adhlik)	bpp::AbstractHmmLikelihood
parameter(const std::string &name) const =0	bpp::Parametrizable	pure virtual
Parametrizable()	bpp::Parametrizable	inline
removeConstraint(const std::string &name)=0	bpp::Parametrizable	pure virtual
SecondOrderDerivable()	bpp::SecondOrderDerivable	inline
setAllParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setBreakPoints(const std::vector< size_t > &breakPoints)=0	bpp::HmmLikelihood	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::Parametrizable	pure virtual
setNamespace(const std::string &prefix)=0	bpp::Parametrizable	pure virtual
setParameters(const ParameterList &parameters)=0	bpp::FunctionInterface	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::Parametrizable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::Parametrizable	pure virtual
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	inlinevirtual
~FunctionInterface()	bpp::FunctionInterface	inlinevirtual
~Parametrizable()	bpp::Parametrizable	inlinevirtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	inlinevirtual