bpp::DRNonHomogeneousTreeLikelihood Member List

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

AbstractDiscreteRatesAcrossSitesTreeLikelihood(DiscreteDistribution *rDist, bool verbose=true)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
AbstractDiscreteRatesAcrossSitesTreeLikelihood(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inline
AbstractNonHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=true)	bpp::AbstractNonHomogeneousTreeLikelihood
AbstractNonHomogeneousTreeLikelihood(const AbstractNonHomogeneousTreeLikelihood &lik)	bpp::AbstractNonHomogeneousTreeLikelihood
AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inline
AbstractTreeLikelihood(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
applyParameters()	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
brLenConstraint_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
brLenParameters_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
clone() const	bpp::DRNonHomogeneousTreeLikelihood	inlinevirtual
computeAllTransitionProbabilities()	bpp::AbstractNonHomogeneousTreeLikelihood	protectedvirtual
computeFirstOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
computeLikelihoodAtNode(int nodeId, VVVdouble &likelihoodArray) const	bpp::DRNonHomogeneousTreeLikelihood	inlinevirtual
computeLikelihoodAtNode_(const Node *node, VVVdouble &likelihoodArray) const	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeLikelihoodFromArrays(const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)	bpp::DRNonHomogeneousTreeLikelihood	protectedstatic
computeLikelihoodFromArrays(const std::vector< const VVVdouble *> &iLik, const std::vector< const VVVdouble *> &tProb, const VVVdouble *iLikR, const VVVdouble *tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)	bpp::DRNonHomogeneousTreeLikelihood	protectedstatic
computeRootLikelihood()	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeSecondOrderDerivatives_	bpp::AbstractTreeLikelihood	protected
computeSubtreeLikelihoodPostfix(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeSubtreeLikelihoodPrefix(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeTransitionProbabilitiesForNode(const Node *node)	bpp::AbstractNonHomogeneousTreeLikelihood	protectedvirtual
computeTreeD2LikelihoodAtNode(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeTreeD2Likelihoods()	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeTreeDLikelihoodAtNode(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeTreeDLikelihoods()	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
computeTreeLikelihood()	bpp::DRNonHomogeneousTreeLikelihood
d2pxy_	bpp::AbstractNonHomogeneousTreeLikelihood	mutableprotected
data_	bpp::AbstractTreeLikelihood	protected
DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inline
displayLikelihood(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protectedvirtual
displayLikelihoodArray(const VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
dpxy_	bpp::AbstractNonHomogeneousTreeLikelihood	mutableprotected
DRNonHomogeneousMixedTreeLikelihood class	bpp::DRNonHomogeneousTreeLikelihood	friend
DRNonHomogeneousTreeLikelihood(const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=false)	bpp::DRNonHomogeneousTreeLikelihood
DRNonHomogeneousTreeLikelihood(const Tree &tree, const SiteContainer &data, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool reparametrizeRoot=false)	bpp::DRNonHomogeneousTreeLikelihood
DRNonHomogeneousTreeLikelihood(const DRNonHomogeneousTreeLikelihood &lik)	bpp::DRNonHomogeneousTreeLikelihood
DRTreeLikelihood()	bpp::DRTreeLikelihood	inline
bpp::enableDerivatives(bool yn)=0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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::DRNonHomogeneousTreeLikelihood	protected
bpp::getAlphabet() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getAlphabet() const	bpp::AbstractTreeLikelihood	inlinevirtual
getAlphabetStateAsChar(size_t i) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getAlphabetStateAsInt(size_t i) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getAlphabetStates() const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getBranchLengthsParameters() const	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
bpp::getData() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getData() const	bpp::AbstractTreeLikelihood	inlinevirtual
bpp::getDerivableParameters() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getFirstOrderDerivative(const std::string &variable) const	bpp::DRNonHomogeneousTreeLikelihood
getLikelihood() const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLikelihoodData()	bpp::DRNonHomogeneousTreeLikelihood	inlinevirtual
getLikelihoodData() const	bpp::DRNonHomogeneousTreeLikelihood	inlinevirtual
getLikelihoodForASite(size_t site) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
bpp::getLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(size_t site, int state) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
bpp::getLikelihoodForEachSite() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	virtual
getLikelihoodForEachSiteForEachRateClass() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLikelihoodForEachSiteForEachRateClassForEachState() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
bpp::getLikelihoodForEachSiteForEachState() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachState() const	bpp::AbstractTreeLikelihood	virtual
getLogLikelihood() const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLogLikelihoodForASite(size_t site) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const	bpp::DRNonHomogeneousTreeLikelihood	virtual
bpp::getLogLikelihoodForASiteForAState(size_t site, int state) const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(size_t site, int state) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
bpp::getLogLikelihoodForEachSite() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSite() const	bpp::AbstractTreeLikelihood	virtual
getLogLikelihoodForEachSiteForEachRateClass() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getLogLikelihoodForEachSiteForEachRateClassForEachState() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
bpp::getLogLikelihoodForEachSiteForEachState() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachState() const	bpp::AbstractTreeLikelihood	virtual
getMaximumBranchLength() const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getMinimumBranchLength() const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getNewBranchModelIterator(int nodeId) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getNewSiteModelIterator(size_t siteIndex) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
bpp::getNonDerivableParameters() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getNumberOfClasses() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
bpp::getNumberOfSites() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfSites() const	bpp::AbstractTreeLikelihood	inlinevirtual
getNumberOfStates() const	bpp::AbstractNonHomogeneousTreeLikelihood	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::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getRateWithMaxPostProbOfEachSite() const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getRootFrequencies(size_t siteIndex) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getRootFrequenciesParameters() const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getSecondOrderDerivative(const std::string &variable) const	bpp::DRNonHomogeneousTreeLikelihood
getSecondOrderDerivative(const std::string &variable1, const std::string &variable2) const	bpp::DRNonHomogeneousTreeLikelihood	inline
getSiteIndex(size_t site) const	bpp::DRNonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex) const	bpp::NonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModel(int nodeId, size_t siteIndex)	bpp::NonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModelForNode(int nodeId) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModelForNode(int nodeId)	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModelParameters() const	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
getSubstitutionModelSet() const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
getSubstitutionModelSet()	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
bpp::getTransitionProbabilities(int nodeId, size_t siteIndex) const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(int nodeId, size_t siteIndex) const	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	virtual
getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
bpp::getTree() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTree() const	bpp::AbstractTreeLikelihood	inlinevirtual
getValue() const	bpp::DRNonHomogeneousTreeLikelihood
idToNode_	bpp::AbstractNonHomogeneousTreeLikelihood	mutableprotected
init_()	bpp::DRNonHomogeneousTreeLikelihood	private
initBranchLengthsParameters()	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
initialize()	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
initialized_	bpp::AbstractTreeLikelihood	protected
initParameters()	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
bpp::isInitialized() const =0	bpp::TreeLikelihood	pure virtual
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::isInitialized() const	bpp::AbstractTreeLikelihood	inlinevirtual
likelihoodData_	bpp::DRNonHomogeneousTreeLikelihood	mutableprotected
maximumBrLen_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
minimumBrLen_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
minusLogLik_	bpp::DRNonHomogeneousTreeLikelihood	protected
modelSet_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nbClasses_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nbDistinctSites_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nbNodes_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nbSites_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nbStates_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
nodes_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
operator=(const DRNonHomogeneousTreeLikelihood &lik)	bpp::DRNonHomogeneousTreeLikelihood
bpp::AbstractNonHomogeneousTreeLikelihood::operator=(const AbstractNonHomogeneousTreeLikelihood &lik)	bpp::AbstractNonHomogeneousTreeLikelihood
bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inline
bpp::AbstractTreeLikelihood::operator=(const AbstractTreeLikelihood &lik)	bpp::AbstractTreeLikelihood	inline
pxy_	bpp::AbstractNonHomogeneousTreeLikelihood	mutableprotected
rateDistribution_	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	protected
reparametrizeRoot_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
resetLikelihoodArray(VVVdouble &likelihoodArray)	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	static
resetLikelihoodArrays(const Node *node)	bpp::DRNonHomogeneousTreeLikelihood	protected
root1_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
root2_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
rootFreqs_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
setData(const SiteContainer &sites)	bpp::DRNonHomogeneousTreeLikelihood	virtual
setMaximumBranchLength(double maximum)	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
setMinimumBranchLength(double minimum)	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
setParameters(const ParameterList &parameters)	bpp::DRNonHomogeneousTreeLikelihood
setSubstitutionModelSet(SubstitutionModelSet *modelSet)	bpp::AbstractNonHomogeneousTreeLikelihood	virtual
tree_	bpp::AbstractTreeLikelihood	mutableprotected
TreeLikelihood()	bpp::TreeLikelihood	inline
verbose_	bpp::AbstractNonHomogeneousTreeLikelihood	protected
~AbstractDiscreteRatesAcrossSitesTreeLikelihood()	bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~AbstractNonHomogeneousTreeLikelihood()	bpp::AbstractNonHomogeneousTreeLikelihood	inlinevirtual
~AbstractTreeLikelihood()	bpp::AbstractTreeLikelihood	inlinevirtual
~DiscreteRatesAcrossSitesTreeLikelihood()	bpp::DiscreteRatesAcrossSitesTreeLikelihood	inlinevirtual
~DRNonHomogeneousTreeLikelihood()	bpp::DRNonHomogeneousTreeLikelihood	virtual
~DRTreeLikelihood()	bpp::DRTreeLikelihood	inlinevirtual
~TreeLikelihood()	bpp::TreeLikelihood	inlinevirtual