bpp::SequencePhyloLikelihoodInterface Member List

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

alignedLikelihoodCalculation() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
AlignedPhyloLikelihoodInterface()	bpp::AlignedPhyloLikelihoodInterface	inline
clone() const override=0	bpp::SequencePhyloLikelihoodInterface	protectedpure virtual
context() const =0	bpp::PhyloLikelihoodInterface	pure virtual
context()=0	bpp::PhyloLikelihoodInterface	pure virtual
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)=0	bpp::SecondOrderDerivable	pure virtual
enableFirstOrderDerivatives() const=0	bpp::SecondOrderDerivable	pure virtual
enableSecondOrderDerivatives(bool yn)=0	bpp::SecondOrderDerivable	pure virtual
enableSecondOrderDerivatives() const=0	bpp::SecondOrderDerivable	pure virtual
f(const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
FirstOrderDerivable()	bpp::FirstOrderDerivable
FunctionInterface()	bpp::FunctionInterface
getAlignedLikelihoodCalculation() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getAlphabet() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
getBranchLengthParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getData() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
getDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getFirstOrderDerivative(const std::string &variable) const=0	bpp::SecondOrderDerivable	pure virtual
getLikelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getLikelihoodNode() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getLikelihoodPerSite() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getLogLikelihood() const	bpp::PhyloLikelihoodInterface	inline
getLogLikelihoodForASite(size_t site) const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getNamespace() const=0	bpp::SecondOrderDerivable	pure virtual
getNData() const =0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
getNonDerivableParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getNumberOfParameters() const=0	bpp::SecondOrderDerivable	pure virtual
getNumberOfSites() const =0	bpp::AlignedPhyloLikelihoodInterface	pure virtual
getNumberOfStates() const =0	bpp::SingleDataPhyloLikelihoodInterface	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=0	bpp::SecondOrderDerivable	pure virtual
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const=0	bpp::SecondOrderDerivable	pure virtual
getSequenceEvolution() const =0	bpp::SequencePhyloLikelihoodInterface	pure virtual
getSequenceEvolutionNumber() const =0	bpp::SequencePhyloLikelihoodInterface	pure virtual
getSubstitutionModelParameters() const =0	bpp::PhyloLikelihoodInterface	pure virtual
getValue() const=0	bpp::SecondOrderDerivable	pure virtual
hasParameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
isInitialized() const =0	bpp::PhyloLikelihoodInterface	pure virtual
likelihoodCalculation() const =0	bpp::PhyloLikelihoodInterface	pure virtual
matchParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
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
sequenceEvolution() const =0	bpp::SequencePhyloLikelihoodInterface	pure virtual
setAllParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setConstraint(const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0	bpp::SecondOrderDerivable	pure virtual
setData(std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0)=0	bpp::SingleDataPhyloLikelihoodInterface	pure virtual
setNamespace(const std::string &prefix)=0	bpp::SecondOrderDerivable	pure virtual
setParameters(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setParametersValues(const ParameterList &parameters)=0	bpp::SecondOrderDerivable	pure virtual
setParameterValue(const std::string &name, double value)=0	bpp::SecondOrderDerivable	pure virtual
SingleDataPhyloLikelihoodInterface()	bpp::SingleDataPhyloLikelihoodInterface	inline
~AlignedPhyloLikelihoodInterface()	bpp::AlignedPhyloLikelihoodInterface	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
~SequencePhyloLikelihoodInterface()	bpp::SequencePhyloLikelihoodInterface	inlineprotectedvirtual
~SingleDataPhyloLikelihoodInterface()	bpp::SingleDataPhyloLikelihoodInterface	inlinevirtual