bpp-phyl3: bpp::AbstractNonHomogeneousTreeLikelihood Class Reference

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, and bpp::DRNonHomogeneousTreeLikelihood.

◆ computeAllTransitionProbabilities()

void AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( )

protectedvirtual

Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.

Definition at line 370 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References computeTransitionProbabilitiesForNode(), modelSet_, nbNodes_, nodes_, and rootFreqs_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), initialize(), and setSubstitutionModelSet().

◆ computeTransitionProbabilitiesForNode()

void AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node * node )

protectedvirtual

Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 383 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, d2pxy_, dpxy_, bpp::Node::getDistanceToFather(), bpp::Node::getId(), modelSet_, nbClasses_, nbStates_, pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged().

◆ data() [1/2]

const AlignmentDataInterface& bpp::AbstractTreeLikelihood::data ( ) const

inlinevirtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns: The site container where the sequences are stored.

Definition at line 262 of file AbstractTreeLikelihood.h.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood().

◆ data() [2/2]

virtual const AlignmentDataInterface& bpp::TreeLikelihoodInterface::data ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns: The site container where the sequences are stored.

Implemented in bpp::AbstractTreeLikelihood.

◆ displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble & likelihoodArray )

staticinherited

Print the likelihood array to terminal (debugging tool).

Parameters

likelihoodArray the likelihood array.

Definition at line 251 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().

◆ enableDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool yn )

inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Definition at line 270 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood().

◆ enableDerivatives() [2/2]

virtual void bpp::TreeLikelihoodInterface::enableDerivatives ( bool yn )

pure virtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 273 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

◆ enableFirstOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 271 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 274 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

◆ enableSecondOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 272 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

◆ getAlphabet() [1/2]

std::shared_ptr<const Alphabet> bpp::AbstractTreeLikelihood::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Definition at line 263 of file AbstractTreeLikelihood.h.

◆ getAlphabet() [2/2]

virtual std::shared_ptr<const Alphabet> bpp::TreeLikelihoodInterface::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

◆ getAlphabetStateAsChar()

std::string bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar ( size_t i ) const

inlineoverridevirtual

Returns: the alphabet state corresponding to the given model state.

Definition at line 145 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getAlphabetStateAsInt()

int bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsInt ( size_t i ) const

inlineoverridevirtual

Returns: the alphabet state corresponding to the given model state.

Definition at line 143 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStates ( ) const

inlineoverridevirtual

Returns: the alphabet states corresponding to all model states.

Definition at line 141 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getBranchLengthsParameters()

ParameterList AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const

overridevirtual

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Definition at line 249 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References brLenParameters_, bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParametrizable::getParameters(), and bpp::AbstractTreeLikelihood::initialized_.

◆ getDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns: A ParameterList.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState().

Definition at line 37 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getBranchLengthsParameters(), and bpp::AbstractTreeLikelihood::initialized_.

◆ getDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getDerivableParameters ( ) const

pure virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns: A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLikelihood()

virtual double bpp::TreeLikelihoodInterface::getLikelihood ( ) const

pure virtualinherited

Get the likelihood for the whole dataset.

Returns: The likelihood of the dataset.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

◆ getLikelihoodForASite()

virtual double bpp::TreeLikelihoodInterface::getLikelihoodForASite ( size_t site ) const

pure virtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodPerSite().

◆ getLikelihoodForASiteForARateClass()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

pure virtualinherited

Get the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns: The likelihood for the specified site and rate class.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass().

◆ getLikelihoodForASiteForARateClassForAState()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const

pure virtualinherited

Get the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns: The likelihood for the specified site and rate class and ancestral state.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

◆ getLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The likelihood for site site and state state.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

pure virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodPerSitePerState().

◆ getLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLikelihoodPerSite ( ) const

virtualinherited

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Definition at line 11 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite().

◆ getLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

◆ getLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the likelihood for each site and each rate class.

Returns: A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 57 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

◆ getLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the likelihood for each site and each rate class and each state.

Returns: A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 120 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLikelihoodPerSitePerState ( ) const

virtualinherited

Get the likelihood for each site and for each state.

Returns: A 2d vector with all likelihoods for each site and for each state.

Definition at line 35 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the likelihood for each site and for each state.

Returns: A 2d vector with all likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

◆ getLogLikelihood()

virtual double bpp::TreeLikelihoodInterface::getLogLikelihood ( ) const

pure virtualinherited

Get the logarithm of the likelihood for the whole dataset.

Returns: The logarithm of the likelihood of the dataset.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

◆ getLogLikelihoodForASite()

virtual double bpp::TreeLikelihoodInterface::getLogLikelihoodForASite ( size_t site ) const

pure virtualinherited

Get the logarithm of the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The logarithm of the likelihood for site site.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodPerSite().

◆ getLogLikelihoodForASiteForARateClass()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

pure virtualinherited

Get the logarithm of the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns: The logarithm of the likelihood for the specified site and rate class.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass().

◆ getLogLikelihoodForASiteForARateClassForAState()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const

pure virtualinherited

Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns: The logarithm of the likelihood for the specified site and rate class and ancestral state..

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState().

◆ getLogLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The logarithm of the likelihood for site site and state state.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::log(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 88 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLogLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

pure virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The logarithm of the likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodPerSitePerState().

◆ getLogLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLogLikelihoodPerSite ( ) const

virtualinherited

Get the logarithm of the likelihood for each site.

Returns: A vector with all log likelihoods for each site.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Definition at line 23 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

◆ getLogLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSite ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site.

Returns: A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel().

◆ getLogLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class.

Returns: A two-dimension vector with all log likelihoods: V[i][j] = likelihood of site i and rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 102 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLogLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class and each state.

Returns: A three-dimension vector with all log likelihoods: V[i][j][k} = likelihood of site i and rate class j and state k.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 143 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLogLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLogLikelihoodPerSitePerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns: A 2d vector with all log likelihoods for each site and for each state.

Definition at line 52 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLogLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns: A 2d vector with all log likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

◆ getMaximumBranchLength()

virtual double bpp::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const

inlinevirtual

Definition at line 244 of file AbstractNonHomogeneousTreeLikelihood.h.

References maximumBrLen_.

◆ getMinimumBranchLength()

virtual double bpp::AbstractNonHomogeneousTreeLikelihood::getMinimumBranchLength ( ) const

inlinevirtual

Definition at line 243 of file AbstractNonHomogeneousTreeLikelihood.h.

References minimumBrLen_.

◆ getModelForNode() [1/2]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractNonHomogeneousTreeLikelihood::getModelForNode ( int nodeId ) const

inlineoverridevirtual

Get the model associated to a given node.

Parameters

nodeId The id of the request node.

Returns: A pointer toward the corresponding model.

Exceptions

NodeNotFoundException This exception may be thrown if the node is not found (depending on the implementation).

Definition at line 158 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getModelForNode() [2/2]

std::shared_ptr<TransitionModelInterface> bpp::AbstractNonHomogeneousTreeLikelihood::getModelForNode ( int nodeId )

inlineoverridevirtual

Get the substitution model associated to a given node.

Parameters

nodeId The id of the request node.

Returns: A pointer toward the corresponding model.

Exceptions

NodeNotFoundException This exception may be thrown if the node is not found (depending on the implementation).

Definition at line 163 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getModelForSite() [1/2]

std::shared_ptr<const TransitionModelInterface> bpp::NonHomogeneousTreeLikelihood::getModelForSite	(	int	nodeId,
		size_t	siteIndex
	)		const

inlineoverridevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: A pointer toward the corresponding model.

Definition at line 32 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getModelForNode().

◆ getModelForSite() [2/2]

std::shared_ptr<TransitionModelInterface> bpp::NonHomogeneousTreeLikelihood::getModelForSite	(	int	nodeId,
		size_t	siteIndex
	)

inlineoverridevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: A pointer toward the corresponding model.

Exceptions

NodeNotFoundException This exception may be thrown if the node is not found (depending on the implementation).

Definition at line 37 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getModelForNode().

◆ getNewBranchModelIterator()

ConstBranchModelIterator* bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator ( int nodeId ) const

inlineoverridevirtual

Definition at line 172 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_, and nbDistinctSites_.

◆ getNewSiteModelIterator()

ConstSiteModelIterator* bpp::AbstractNonHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t siteIndex ) const

inlineoverridevirtual

Definition at line 177 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getNonDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns: A ParameterList.

References bpp::ParameterList::addParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::TreeLikelihoodInterface::getSubstitutionModelParameters(), and bpp::AbstractTreeLikelihood::initialized_.

Definition at line 46 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getNonDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getNonDerivableParameters ( ) const

pure virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns: A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getNumberOfClasses()

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const

inlinevirtualinherited

Get the number of classes.

Returns: The number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 90 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getNumberOfSites() [1/2]

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Definition at line 268 of file AbstractTreeLikelihood.h.

◆ getNumberOfSites() [2/2]

virtual size_t bpp::TreeLikelihoodInterface::getNumberOfSites ( ) const

pure virtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

◆ getNumberOfStates()

size_t bpp::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates ( ) const

inlineoverridevirtual

Returns: the number of model states of the underlying Markov chain.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 139 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getPosteriorProbabilitiesPerRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate ( ) const

virtualinherited

Get the posterior probability for each site of belonging to a particular rate class.

Returns: A two-dimension vector with all posterior probabilities: V[i][j] = probability for site i of belonging to rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 166 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getPosteriorRatePerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite ( ) const

virtualinherited

Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.

Returns: A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 184 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateClassWithMaxPostProbPerSite()

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate class (the one with maximum posterior probability) for each site.

Returns: A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 203 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

◆ getRateDistribution() [1/2]

std::shared_ptr<DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateDistribution() [2/2]

std::shared_ptr<const DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A const pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 70 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateDistributionParameters()

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtual

Get the parameters associated to the rate distribution.

Returns: A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 153 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::RNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::RNonHomogeneousTreeLikelihood::getSecondOrderDerivative().

◆ getRateWithMaxPostProbPerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate (the one with maximum posterior probability) for each site.

Returns: A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 217 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRootFrequencies()

const std::vector<double>& bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequencies ( size_t siteIndex ) const

inlineoverridevirtual

Get the values of the frequencies for each state in the alphabet at the root node.

For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.

For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.

Parameters

siteIndex The index of the alignment position.

See also: getSiteIndex

Returns: A vector with ancestral frequencies for each state in the alphabet;

Definition at line 168 of file AbstractNonHomogeneousTreeLikelihood.h.

References rootFreqs_.

◆ getRootFrequenciesParameters()

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters ( ) const

inlineoverridevirtual

Returns: The parameters on which the root frequencies depend.

Definition at line 201 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getSiteIndex()

virtual size_t bpp::TreeLikelihoodInterface::getSiteIndex ( size_t site ) const

pure virtualinherited

Get the index (used for inner computations) of a given site (original alignment column).

Parameters

site	An alignment position.

Returns: The site index corresponding to the given input alignment position.

Implemented in bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, and bpp::DRNonHomogeneousTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies().

◆ getSubstitutionModelParameters()

ParameterList AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const

overridevirtual

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::RNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::RNonHomogeneousTreeLikelihood::getSecondOrderDerivative().

Definition at line 258 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and modelSet_.

◆ getSubstitutionModelSet() [1/2]

std::shared_ptr<const SubstitutionModelSet> bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) const

inlineoverridevirtual

Returns: The set of substitution models associated to this instance.

Definition at line 191 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getSubstitutionModelSet() [2/2]

std::shared_ptr<SubstitutionModelSet> bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( )

inlineoverridevirtual

Returns: The set of substitution models associated to this instance.

Definition at line 195 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ getTransitionProbabilities() [1/2]

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const

virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::TreeLikelihoodInterface::getNumberOfStates(), bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 275 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getTransitionProbabilities() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const

pure virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies_().

◆ getTransitionProbabilitiesPerRateClass()

VVVdouble bpp::AbstractNonHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass	(	int	nodeId,
		size_t	siteIndex
	)		const

inlineoverridevirtual

Retrieves all Pij(t) for a particular branch, defined by the upper node.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The position in the alignment.

Returns: An array of dimension 3, where a[c][x][y] is the probability of substituting from x to y while being in rate class c.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 170 of file AbstractNonHomogeneousTreeLikelihood.h.

References pxy_.

◆ hasLikelihoodData() [1/2]

bool bpp::AbstractTreeLikelihood::hasLikelihoodData ( ) const

inlinevirtualinherited

Returns: True if the TreeLikelihood object has a LikelihoodData.

Definition at line 261 of file AbstractTreeLikelihood.h.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

◆ hasLikelihoodData() [2/2]

virtual bool bpp::TreeLikelihoodInterface::hasLikelihoodData ( ) const

pure virtualinherited

Returns: True if the TreeLikelihood object has a LikelihoodData.

Implemented in bpp::AbstractTreeLikelihood.

◆ init_()

void AbstractNonHomogeneousTreeLikelihood::init_	(	const Tree &	tree,
		std::shared_ptr< SubstitutionModelSet >	modelSet,
		std::shared_ptr< DiscreteDistributionInterface >	rDist,
		bool	verbose
	)

private

Method called by constructor.

Definition at line 128 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References brLenConstraint_, bpp::TreeTools::checkIds(), bpp::Node::getId(), idToNode_, maximumBrLen_, minimumBrLen_, nbClasses_, nbNodes_, nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, root1_, root2_, setSubstitutionModelSet(), bpp::AbstractTreeLikelihood::tree(), bpp::AbstractTreeLikelihood::tree_, and verbose_.

Referenced by AbstractNonHomogeneousTreeLikelihood().

◆ initBranchLengthsParameters()

void AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters ( bool verbose = true )

virtual

◆ initialize()

void AbstractNonHomogeneousTreeLikelihood::initialize ( )

overridevirtual

Init the likelihood object.

This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.

Exceptions

Exception if something bad happened, for instance if no data are associated to the likelihood function.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 234 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::data_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and initParameters().

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize().

◆ initParameters()

void AbstractNonHomogeneousTreeLikelihood::initParameters ( )

virtual

This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.

Definition at line 267 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), brLenParameters_, initBranchLengthsParameters(), modelSet_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), initialize(), and setSubstitutionModelSet().

◆ isInitialized() [1/2]

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

Returns: 'true' is the likelihood function has been initialized.

Definition at line 275 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), bpp::RNonHomogeneousTreeLikelihood::getValue(), and bpp::DRHomogeneousTreeLikelihood::getValue().

◆ isInitialized() [2/2]

virtual bool bpp::TreeLikelihoodInterface::isInitialized ( ) const

pure virtualinherited

Returns: 'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractTreeLikelihood.

◆ likelihoodData() [1/2]

virtual const TreeLikelihoodData& bpp::TreeLikelihoodInterface::likelihoodData ( ) const

pure virtualinherited

Returns: The underlying likelihood data structure.

Implemented in bpp::DRTreeLikelihoodInterface, bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, and bpp::DRNonHomogeneousTreeLikelihood.

◆ likelihoodData() [2/2]

virtual TreeLikelihoodData& bpp::TreeLikelihoodInterface::likelihoodData ( )

pure virtualinherited

Returns: The underlying likelihood data structure.

Implemented in bpp::DRTreeLikelihoodInterface, bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, and bpp::DRNonHomogeneousTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies().

◆ operator=()

AbstractNonHomogeneousTreeLikelihood & AbstractNonHomogeneousTreeLikelihood::operator= ( const AbstractNonHomogeneousTreeLikelihood & lik )

Assignation operator.

This operator is to be called by the derived class operator.

Definition at line 93 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References brLenConstraint_, brLenParameters_, d2pxy_, dpxy_, bpp::Node::getId(), idToNode_, maximumBrLen_, minimumBrLen_, modelSet_, nbClasses_, nbDistinctSites_, nbNodes_, nbSites_, nbStates_, nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), pxy_, reparametrizeRoot_, root1_, root2_, rootFreqs_, bpp::AbstractTreeLikelihood::tree_, and verbose_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::operator=(), and bpp::RNonHomogeneousTreeLikelihood::operator=().

◆ rateDistribution() [1/2]

DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 85 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ rateDistribution() [2/2]

const DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A const reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 80 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble & likelihoodArray )

staticinherited

Set all conditional likelihoods to 1.

Parameters

likelihoodArray the likelihood array.

Definition at line 231 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ setData()

virtual void bpp::TreeLikelihoodInterface::setData ( const AlignmentDataInterface & sites )

pure virtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

sites The data set to use.

Implemented in bpp::NNIHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::setModel(), and setSubstitutionModelSet().

◆ setMaximumBranchLength()

virtual void bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength ( double maximum )

inlinevirtual

Definition at line 234 of file AbstractNonHomogeneousTreeLikelihood.h.

References brLenConstraint_, initBranchLengthsParameters(), maximumBrLen_, minimumBrLen_, and bpp::TextTools::toString().

◆ setMinimumBranchLength()

virtual void bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength ( double minimum )

inlinevirtual

Definition at line 225 of file AbstractNonHomogeneousTreeLikelihood.h.

References brLenConstraint_, initBranchLengthsParameters(), maximumBrLen_, minimumBrLen_, and bpp::TextTools::toString().

◆ setSubstitutionModelSet()

void AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet ( std::shared_ptr< SubstitutionModelSet > model )

overridevirtual

Returns: Set the substitution models for this instance.

Exceptions

Exception If the model could not be set (for instance, because of a wrong alphabet type).

Definition at line 159 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References computeAllTransitionProbabilities(), d2pxy_, bpp::AbstractTreeLikelihood::data_, dpxy_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::Node::getId(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, initParameters(), modelSet_, nbClasses_, nbNodes_, nbStates_, nodes_, pxy_, and bpp::TreeLikelihoodInterface::setData().

Referenced by init_().

◆ substitutionModelSet() [1/2]

const SubstitutionModelSet& bpp::AbstractNonHomogeneousTreeLikelihood::substitutionModelSet ( ) const

inlineoverridevirtual

Returns: The set of substitution models associated to this instance.

Definition at line 193 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ substitutionModelSet() [2/2]

SubstitutionModelSet& bpp::AbstractNonHomogeneousTreeLikelihood::substitutionModelSet ( )

inlineoverridevirtual

Returns: The set of substitution models associated to this instance.

Definition at line 197 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

◆ tree() [1/2]

const Tree& bpp::AbstractTreeLikelihood::tree ( ) const

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns: The tree of this TreeLikelihood object.