bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(DiscreteDistribution *rDist, bool verbose=true)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inline
AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inline
AbstractTreeLikelihood(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
clone() const =0	bpp::TreeLikelihood	pure virtual
computeFirstOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
computeSecondOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
data_	bpp::AbstractTreeLikelihood	protected
DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inline
displayLikelihoodArray(const VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
enableDerivatives(bool yn)	bpp::AbstractTreeLikelihood	inlinevirtual
enableFirstOrderDerivatives(bool yn)	bpp::AbstractTreeLikelihood	inline
enableFirstOrderDerivatives() const	bpp::AbstractTreeLikelihood	inline
enableSecondOrderDerivatives(bool yn)	bpp::AbstractTreeLikelihood	inline
enableSecondOrderDerivatives() const	bpp::AbstractTreeLikelihood	inline
getAlphabet() const	bpp::AbstractTreeLikelihood	inlinevirtual
getAlphabetStateAsChar(size_t i) const =0	bpp::TreeLikelihood	pure virtual
getAlphabetStateAsInt(size_t i) const =0	bpp::TreeLikelihood	pure virtual
getAlphabetStates() const =0	bpp::TreeLikelihood	pure virtual
getBranchLengthsParameters() const =0	bpp::TreeLikelihood	pure virtual
getData() const	bpp::AbstractTreeLikelihood	inlinevirtual
getDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLikelihood() const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodData()=0	bpp::TreeLikelihood	pure virtual
getLikelihoodData() const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLikelihoodForASiteForAState(size_t site, int state) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	virtual
getLikelihoodForEachSiteForEachRateClass() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLikelihoodForEachSiteForEachRateClassForEachState() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLikelihoodForEachSiteForEachState() const	bpp::AbstractTreeLikelihood	virtual
getLogLikelihood() const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLogLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	virtual
getLogLikelihoodForEachSiteForEachRateClass() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLogLikelihoodForEachSiteForEachState() const	bpp::AbstractTreeLikelihood	virtual
getNewBranchModelIterator(int nodeId) const =0	bpp::TreeLikelihood	pure virtual
getNewSiteModelIterator(size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getNonDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getNumberOfClasses() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
getNumberOfSites() const	bpp::AbstractTreeLikelihood	inlinevirtual
getNumberOfStates() const =0	bpp::TreeLikelihood	pure virtual
getPosteriorProbabilitiesOfEachRate() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getPosteriorRateOfEachSite() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getRateClassWithMaxPostProbOfEachSite() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getRateDistribution() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
getRateDistribution()	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
getRateDistributionParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getRateWithMaxPostProbOfEachSite() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getRootFrequencies(size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getSiteIndex(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getSubstitutionModel(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
getSubstitutionModel(int nodeId, size_t siteIndex)=0	bpp::TreeLikelihood	pure virtual
getSubstitutionModelParameters() const =0	bpp::TreeLikelihood	pure virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0	bpp::DiscreteRatesAcrossSitesTreeLikelihood	pure virtual
getTree() const	bpp::AbstractTreeLikelihood	inlinevirtual
initialize()	bpp::AbstractTreeLikelihood	inlinevirtual
initialized_	bpp::AbstractTreeLikelihood	protected
isInitialized() const	bpp::AbstractTreeLikelihood	inlinevirtual
operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
rateDistribution_	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	protected
resetLikelihoodArray(VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
setData(const SiteContainer &sites)=0	bpp::TreeLikelihood	pure virtual
tree_	bpp::AbstractTreeLikelihood	mutableprotected
TreeLikelihood()	bpp::TreeLikelihood	inline
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inlinevirtual
~DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~TreeLikelihood()	bpp::TreeLikelihood	inlinevirtual