bpp::DRTreeLikelihoodInterface Member List

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

clone() const override=0	bpp::DRTreeLikelihoodInterface	pure virtual
computeLikelihoodAtNode(int nodeId, VVVdouble &likelihoodArray) const =0	bpp::DRTreeLikelihoodInterface	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
DiscreteRatesAcrossSitesTreeLikelihoodInterface()	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	inline
DRTreeLikelihoodInterface()	bpp::DRTreeLikelihoodInterface	inline
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
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodPerSite() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLikelihoodPerSitePerRateClass() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLikelihoodPerSitePerRateClassPerState() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	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
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSite() const =0	bpp::TreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSitePerRateClass() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSitePerRateClassPerState() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getLogLikelihoodPerSitePerState() const =0	bpp::TreeLikelihoodInterface	pure virtual
getModelForSite(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihoodInterface	pure virtual
getModelForSite(int nodeId, size_t siteIndex)=0	bpp::TreeLikelihoodInterface	pure virtual
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
getNumberOfClasses() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	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
getPosteriorProbabilitiesPerRate() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getPosteriorRatePerSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getRateClassWithMaxPostProbPerSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getRateDistribution() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getRateDistribution()=0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getRateDistributionParameters() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
getRateWithMaxPostProbPerSite() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	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
getSubstitutionModelParameters() const =0	bpp::TreeLikelihoodInterface	pure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihoodInterface	pure virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	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() override=0	bpp::DRTreeLikelihoodInterface	pure virtual
likelihoodData() const override=0	bpp::DRTreeLikelihoodInterface	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
rateDistribution() const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
rateDistribution()=0	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	pure virtual
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
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
~DiscreteRatesAcrossSitesTreeLikelihoodInterface()	bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface	inlinevirtual
~DRTreeLikelihoodInterface()	bpp::DRTreeLikelihoodInterface	inlinevirtual
~FirstOrderDerivable()	bpp::FirstOrderDerivable	virtual
~FunctionInterface()	bpp::FunctionInterface	virtual
~Parametrizable()	bpp::Parametrizable	virtual
~SecondOrderDerivable()	bpp::SecondOrderDerivable	virtual
~TreeLikelihoodInterface()	bpp::TreeLikelihoodInterface	inlinevirtual