bpp::AbstractTreeLikelihood Member List

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

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
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 =0	bpp::TreeLikelihood	pure 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
getLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
getLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	virtual
getLikelihoodForEachSiteForEachState() const	bpp::AbstractTreeLikelihood	virtual
getLogLikelihood() const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASite(size_t site) const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
getLogLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	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 =0	bpp::TreeLikelihood	pure virtual
getNumberOfSites() const	bpp::AbstractTreeLikelihood	inlinevirtual
getNumberOfStates() const =0	bpp::TreeLikelihood	pure 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 =0	bpp::TreeLikelihood	pure virtual
getTree() const	bpp::AbstractTreeLikelihood	inlinevirtual
initialize()	bpp::AbstractTreeLikelihood	inlinevirtual
initialized_	bpp::AbstractTreeLikelihood	protected
isInitialized() const	bpp::AbstractTreeLikelihood	inlinevirtual
operator=(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
setData(const SiteContainer &sites)=0	bpp::TreeLikelihood	pure virtual
tree_	bpp::AbstractTreeLikelihood	mutableprotected
TreeLikelihood()	bpp::TreeLikelihood	inline
~AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inlinevirtual
~TreeLikelihood()	bpp::TreeLikelihood	inlinevirtual