bpp::AbstractPhyloLikelihood Member List

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

AbstractPhyloLikelihood(Context &context)	bpp::AbstractPhyloLikelihood	inline
AbstractPhyloLikelihood(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
accessVariableNode(const Parameter &param)	bpp::AbstractPhyloLikelihood	inlineprotectedstatic
accessVariableNode(const std::string &name) const	bpp::AbstractPhyloLikelihood	inlineprotected
clone() const =0	bpp::PhyloLikelihoodInterface	pure virtual
context() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
context() override	bpp::AbstractPhyloLikelihood	inlinevirtual
context_	bpp::AbstractPhyloLikelihood	protected
d2f(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
d2f(const std::string &variable1, const std::string &variable2, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
df(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
enableFirstOrderDerivatives(bool yn) override	bpp::AbstractPhyloLikelihood	inlinevirtual
enableFirstOrderDerivatives() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
enableSecondOrderDerivatives(bool yn) override	bpp::AbstractPhyloLikelihood	inlinevirtual
enableSecondOrderDerivatives() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
f(const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
FirstOrderDerivable()	bpp::FirstOrderDerivable
firstOrderDerivativeNode(const std::string &variable) const	bpp::AbstractPhyloLikelihood	inline
firstOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
FunctionInterface()	bpp::FunctionInterface
getBranchLengthParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getFirstOrderDerivative(const std::string &variable) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getLikelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getLikelihoodNode() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getLogLikelihood() const	bpp::PhyloLikelihoodInterface	inline
getNamespace() const=0	bpp::SecondOrderDerivable	pure virtual
getNonDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getNumberOfParameters() const=0	bpp::SecondOrderDerivable	pure virtual
getParameterNameWithoutNamespace(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
getParameters() const=0	bpp::SecondOrderDerivable	pure virtual
getParameters_()=0	bpp::SecondOrderDerivable	protectedpure virtual
getParameterValue(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
getRateDistributionParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getRootFrequenciesParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getSecondOrderDerivative(const std::string &variable) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const override	bpp::AbstractPhyloLikelihood	inlinevirtual
getSubstitutionModelParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getValue() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
hasParameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
isInitialized() const override	bpp::AbstractPhyloLikelihood	inlinevirtual
likelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
minusLogLik_	bpp::AbstractPhyloLikelihood	mutableprotected
operator=(const AbstractPhyloLikelihood &apl)	bpp::AbstractPhyloLikelihood	inline
parameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
Parametrizable()	bpp::Parametrizable
PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inline
removeConstraint(const std::string &name)=0	bpp::SecondOrderDerivable	pure virtual
SecondOrderDerivable()	bpp::SecondOrderDerivable
secondOrderDerivativeNode(const std::string &variable1, const std::string &variable2) const	bpp::AbstractPhyloLikelihood	inline
secondOrderDerivativeNodes_	bpp::AbstractPhyloLikelihood	mutableprotected
setAllParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::SecondOrderDerivable	pure virtual
setNamespace(const std::string &prefix)=0	bpp::SecondOrderDerivable	pure virtual
setParameters(const ParameterList &parameters) override	bpp::AbstractPhyloLikelihood	inlinevirtual
setParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::SecondOrderDerivable	pure virtual
shareParameters(const ParameterList &variableNodes)	bpp::AbstractPhyloLikelihood	inline
~AbstractPhyloLikelihood()	bpp::AbstractPhyloLikelihood	inlinevirtual
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	virtual
~FunctionInterface()	bpp::FunctionInterface	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~PhyloLikelihoodInterface()	bpp::PhyloLikelihoodInterface	inlinevirtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	virtual