bpp::HomogeneousTreeLikelihood Member List

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

clone() const =0	bpp::HomogeneousTreeLikelihood	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
data() const =0	bpp::TreeLikelihoodInterface	pure virtual
df(const std::string &variable, const ParameterList &parameters)	bpp::SecondOrderDerivable	virtual
enableDerivatives(bool yn)=0	bpp::TreeLikelihoodInterface	pure 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
getAlphabet() const =0	bpp::TreeLikelihoodInterface	pure virtual
getAlphabetStateAsChar(size_t i) const =0	bpp::TreeLikelihoodInterface	pure virtual
getAlphabetStateAsInt(size_t i) const =0	bpp::TreeLikelihoodInterface	pure virtual
getAlphabetStates() const =0	bpp::TreeLikelihoodInterface	pure virtual
getBranchLengthsParameters() const =0	bpp::TreeLikelihoodInterface	pure virtual
getDerivableParameters() const =0	bpp::TreeLikelihoodInterface	pure virtual
getFirstOrderDerivative(const std::string &variable) const=0	bpp::SecondOrderDerivable	pure virtual
getLikelihood() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodPerSite() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodPerSitePerState() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihood() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSite() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSitePerState() const =0	bpp::TreeLikelihoodInterface	pure virtual
getModel() const =0	bpp::HomogeneousTreeLikelihood	pure virtual
getModel()=0	bpp::HomogeneousTreeLikelihood	pure virtual
getModelForSite(int nodeId, size_t siteIndex) const	bpp::HomogeneousTreeLikelihood	inlinevirtual
getModelForSite(int nodeId, size_t siteIndex)	bpp::HomogeneousTreeLikelihood	inlinevirtual
getNamespace() const=0	bpp::SecondOrderDerivable	pure virtual
getNewBranchModelIterator(int nodeId) const =0	bpp::TreeLikelihoodInterface	pure virtual
getNewSiteModelIterator(size_t siteIndex) const =0	bpp::TreeLikelihoodInterface	pure virtual
getNonDerivableParameters() const =0	bpp::TreeLikelihoodInterface	pure virtual
getNumberOfParameters() const=0	bpp::SecondOrderDerivable	pure virtual
getNumberOfSites() const =0	bpp::TreeLikelihoodInterface	pure virtual
getNumberOfStates() const =0	bpp::TreeLikelihoodInterface	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
getRootFrequencies(size_t siteIndex) const =0	bpp::TreeLikelihoodInterface	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
getSiteIndex(size_t site) const =0	bpp::TreeLikelihoodInterface	pure virtual
getSubstitutionModel() const =0	bpp::HomogeneousTreeLikelihood	pure virtual
getSubstitutionModel(int nodeId, size_t siteIndex) const =0	bpp::HomogeneousTreeLikelihood	pure virtual
getSubstitutionModelParameters() const =0	bpp::TreeLikelihoodInterface	pure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihoodInterface	pure virtual
getValue() const=0	bpp::SecondOrderDerivable	pure virtual
hasLikelihoodData() const =0	bpp::TreeLikelihoodInterface	pure virtual
hasParameter(const std::string &name) const=0	bpp::SecondOrderDerivable	pure virtual
initialize()=0	bpp::TreeLikelihoodInterface	pure virtual
isInitialized() const =0	bpp::TreeLikelihoodInterface	pure virtual
likelihoodData()=0	bpp::TreeLikelihoodInterface	pure virtual
likelihoodData() const =0	bpp::TreeLikelihoodInterface	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
removeConstraint(const std::string &name)=0	bpp::SecondOrderDerivable	pure virtual
SecondOrderDerivable()	bpp::SecondOrderDerivable
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(const AlignmentDataInterface &sites)=0	bpp::TreeLikelihoodInterface	pure virtual
setModel(std::shared_ptr< TransitionModelInterface > model)=0	bpp::HomogeneousTreeLikelihood	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
tree() const =0	bpp::TreeLikelihoodInterface	pure virtual
TreeLikelihoodInterface()	bpp::TreeLikelihoodInterface	inline
~Clonable()=default	bpp::Clonable	virtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	virtual
~FunctionInterface()	bpp::FunctionInterface	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	virtual
~TreeLikelihoodInterface()	bpp::TreeLikelihoodInterface	inlinevirtual