bpp::TwoTreeLikelihood Member List

This is the complete list of members for bpp::TwoTreeLikelihood, 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
applyParameters()	bpp::TwoTreeLikelihood	protectedvirtual
brLen_	bpp::TwoTreeLikelihood	private
brLenConstraint_	bpp::TwoTreeLikelihood	private
brLenParameters_	bpp::TwoTreeLikelihood	private
clone() const	bpp::TwoTreeLikelihood	inlinevirtual
computeFirstOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
computeSecondOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
computeTreeD2Likelihood()	bpp::TwoTreeLikelihood	protectedvirtual
computeTreeDLikelihood()	bpp::TwoTreeLikelihood	protectedvirtual
computeTreeLikelihood()	bpp::TwoTreeLikelihood	protectedvirtual
d2Likelihoods_	bpp::TwoTreeLikelihood	mutableprivate
d2pxy_	bpp::TwoTreeLikelihood	mutableprivate
data_	bpp::AbstractTreeLikelihood	protected
DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inline
displayLikelihoodArray(const VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
dLikelihoods_	bpp::TwoTreeLikelihood	mutableprivate
dpxy_	bpp::TwoTreeLikelihood	mutableprivate
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
fireParameterChanged(const ParameterList &params)	bpp::TwoTreeLikelihood	protected
getAlphabet() const	bpp::AbstractTreeLikelihood	inlinevirtual
getAlphabetStateAsChar(size_t i) const	bpp::TwoTreeLikelihood	inlinevirtual
getAlphabetStateAsInt(size_t i) const	bpp::TwoTreeLikelihood	inlinevirtual
getAlphabetStates() const	bpp::TwoTreeLikelihood	inlinevirtual
getBranchLengthsParameters() const	bpp::TwoTreeLikelihood	virtual
getData() const	bpp::AbstractTreeLikelihood	inlinevirtual
getDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getFirstOrderDerivative(const std::string &variable) const	bpp::TwoTreeLikelihood
getLikelihood() const	bpp::TwoTreeLikelihood	virtual
getLikelihoodData()	bpp::TwoTreeLikelihood	inlinevirtual
getLikelihoodData() const	bpp::TwoTreeLikelihood	inlinevirtual
getLikelihoodForASite(size_t site) const	bpp::TwoTreeLikelihood	virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const	bpp::TwoTreeLikelihood	virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const	bpp::TwoTreeLikelihood	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	bpp::TwoTreeLikelihood	virtual
getLogLikelihoodForASite(size_t site) const	bpp::TwoTreeLikelihood	virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const	bpp::TwoTreeLikelihood	virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const	bpp::TwoTreeLikelihood	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
getMinimumBranchLength() const	bpp::TwoTreeLikelihood	inlinevirtual
getNewBranchModelIterator(int nodeId) const	bpp::TwoTreeLikelihood	inlinevirtual
getNewSiteModelIterator(size_t siteIndex) const	bpp::TwoTreeLikelihood	inlinevirtual
getNonDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getNumberOfClasses() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
getNumberOfSites() const	bpp::AbstractTreeLikelihood	inlinevirtual
getNumberOfStates() const	bpp::TwoTreeLikelihood	inlinevirtual
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	bpp::TwoTreeLikelihood	inlinevirtual
getSecondOrderDerivative(const std::string &variable) const	bpp::TwoTreeLikelihood
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const	bpp::TwoTreeLikelihood	inline
getSiteIndex(size_t site) const	bpp::TwoTreeLikelihood	inlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex)	bpp::TwoTreeLikelihood	inlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) const	bpp::TwoTreeLikelihood	inlinevirtual
getSubstitutionModel() const	bpp::TwoTreeLikelihood	inline
getSubstitutionModel()	bpp::TwoTreeLikelihood	inline
getSubstitutionModelParameters() const	bpp::TwoTreeLikelihood	virtual
getTransitionProbabilities(int nodeId, size_t siteIndex) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const	bpp::TwoTreeLikelihood	inlinevirtual
getTree() const	bpp::AbstractTreeLikelihood	inlinevirtual
getValue() const	bpp::TwoTreeLikelihood
initBranchLengthsParameters()	bpp::TwoTreeLikelihood	virtual
initialize()	bpp::TwoTreeLikelihood	virtual
initialized_	bpp::AbstractTreeLikelihood	protected
initParameters()	bpp::TwoTreeLikelihood	protectedvirtual
initTreeLikelihoods(const SequenceContainer &sequences)	bpp::TwoTreeLikelihood	protectedvirtual
isInitialized() const	bpp::AbstractTreeLikelihood	inlinevirtual
leafLikelihoods1_	bpp::TwoTreeLikelihood	mutableprivate
leafLikelihoods2_	bpp::TwoTreeLikelihood	mutableprivate
minimumBrLen_	bpp::TwoTreeLikelihood	private
model_	bpp::TwoTreeLikelihood	private
nbClasses_	bpp::TwoTreeLikelihood	private
nbDistinctSites_	bpp::TwoTreeLikelihood	private
nbSites_	bpp::TwoTreeLikelihood	private
nbStates_	bpp::TwoTreeLikelihood	private
operator=(const TwoTreeLikelihood &lik)	bpp::TwoTreeLikelihood
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
pxy_	bpp::TwoTreeLikelihood	mutableprivate
rateDistribution_	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	protected
resetLikelihoodArray(VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
rootLikelihoods_	bpp::TwoTreeLikelihood	mutableprivate
rootLikelihoodsS_	bpp::TwoTreeLikelihood	mutableprivate
rootLikelihoodsSR_	bpp::TwoTreeLikelihood	mutableprivate
rootPatternLinks_	bpp::TwoTreeLikelihood	private
rootWeights_	bpp::TwoTreeLikelihood	private
seqnames_	bpp::TwoTreeLikelihood	private
setData(const SiteContainer &sites)	bpp::TwoTreeLikelihood	inlinevirtual
setMinimumBranchLength(double minimum)	bpp::TwoTreeLikelihood	inlinevirtual
setParameters(const ParameterList &parameters)	bpp::TwoTreeLikelihood
shrunkData_	bpp::TwoTreeLikelihood	private
tree_	bpp::AbstractTreeLikelihood	mutableprotected
TreeLikelihood()	bpp::TreeLikelihood	inline
TwoTreeLikelihood(const std::string &seq1, const std::string &seq2, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool verbose)	bpp::TwoTreeLikelihood
TwoTreeLikelihood(const TwoTreeLikelihood &lik)	bpp::TwoTreeLikelihood
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inlinevirtual
~DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~TreeLikelihood()	bpp::TreeLikelihood	inlinevirtual
~TwoTreeLikelihood()	bpp::TwoTreeLikelihood	virtual