Interface for double-recursive (DR) implementation of the likelihood computation. More...

#include <Bpp/Phyl/Legacy/Likelihood/DRTreeLikelihood.h>

Inheritance diagram for bpp::DRTreeLikelihoodInterface:

Collaboration diagram for bpp::DRTreeLikelihoodInterface:

Public Member Functions
	DRTreeLikelihoodInterface ()

virtual	~DRTreeLikelihoodInterface ()

DRTreeLikelihoodInterface *	clone () const override=0

virtual void	computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const =0
	Compute the likelihood array at a given node. More...

virtual std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const =0
	Get the rate distribution used for the computation. More...

virtual std::shared_ptr< DiscreteDistributionInterface >	getRateDistribution ()=0
	Get the rate distribution used for the computation. More...

virtual const DiscreteDistributionInterface &	rateDistribution () const =0
	Get the rate distribution used for the computation. More...

virtual DiscreteDistributionInterface &	rateDistribution ()=0
	Get the rate distribution used for the computation. More...

virtual double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the likelihood for a site knowing its rate class. More...

virtual double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the logarithm of the likelihood for a site knowing its rate class. More...

virtual double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the likelihood for a site knowing its rate class and its ancestral state. More...

virtual double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...

virtual VVdouble	getLikelihoodPerSitePerRateClass () const =0
	Get the likelihood for each site and each rate class. More...

virtual VVdouble	getLogLikelihoodPerSitePerRateClass () const =0
	Get the logarithm of the likelihood for each site and each rate class. More...

virtual VVVdouble	getLikelihoodPerSitePerRateClassPerState () const =0
	Get the likelihood for each site and each rate class and each state. More...

virtual VVVdouble	getLogLikelihoodPerSitePerRateClassPerState () const =0
	Get the logarithm of the likelihood for each site and each rate class and each state. More...

virtual VVdouble	getPosteriorProbabilitiesPerRate () const =0
	Get the posterior probability for each site of belonging to a particular rate class. More...

virtual std::vector< size_t >	getRateClassWithMaxPostProbPerSite () const =0
	Get the posterior rate class (the one with maximum posterior probability) for each site. More...

virtual Vdouble	getRateWithMaxPostProbPerSite () const =0
	Get the posterior rate (the one with maximum posterior probability) for each site. More...

virtual Vdouble	getPosteriorRatePerSite () const =0
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More...

virtual ParameterList	getRateDistributionParameters () const =0
	Get the parameters associated to the rate distribution. More...

virtual size_t	getNumberOfClasses () const =0
	Get the number of classes. More...

virtual VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node. More...

virtual void	setData (const AlignmentDataInterface &sites)=0
	Set the dataset for which the likelihood must be evaluated. More...

virtual const AlignmentDataInterface &	data () const =0
	Get the dataset for which the likelihood must be evaluated. More...

virtual void	initialize ()=0
	Init the likelihood object. More...

virtual bool	isInitialized () const =0

virtual bool	hasLikelihoodData () const =0

virtual double	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site. More...

virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the logarithm of the likelihood for a site. More...

virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state. More...

virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state. More...

virtual Vdouble	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...

virtual Vdouble	getLogLikelihoodPerSite () const =0
	Get the logarithm of the likelihood for each site. More...

virtual VVdouble	getLikelihoodPerSitePerState () const =0
	Get the likelihood for each site and for each state. More...

virtual VVdouble	getLogLikelihoodPerSitePerState () const =0
	Get the logarithm of the likelihood for each site and for each state. More...

virtual double	getLikelihood () const =0
	Get the likelihood for the whole dataset. More...

virtual double	getLogLikelihood () const =0
	Get the logarithm of the likelihood for the whole dataset. More...

virtual const Tree &	tree () const =0
	Get the tree (topology and branch lengths). More...

virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...

virtual size_t	getNumberOfStates () const =0

virtual int	getAlphabetStateAsInt (size_t i) const =0

virtual std::string	getAlphabetStateAsChar (size_t i) const =0

virtual const std::vector< int > &	getAlphabetStates () const =0

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the dataset. More...

virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed. More...

virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters. More...

virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters. More...

virtual void	enableSecondOrderDerivatives (bool yn)=0

virtual bool	enableSecondOrderDerivatives () const=0

virtual double	getSecondOrderDerivative (const std::string &variable) const=0

virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const=0

virtual double	d2f (const std::string &variable, const ParameterList &parameters)

virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)

virtual void	enableFirstOrderDerivatives (bool yn)=0

virtual bool	enableFirstOrderDerivatives () const=0

virtual double	getFirstOrderDerivative (const std::string &variable) const=0

virtual double	df (const std::string &variable, const ParameterList &parameters)

virtual void	setParameters (const ParameterList &parameters)=0

virtual double	getValue () const=0

virtual double	f (const ParameterList &parameters)

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

Get the likelihood data structure associated to this class.
virtual DRASDRTreeLikelihoodData &	likelihoodData () override=0

virtual const DRASDRTreeLikelihoodData &	likelihoodData () const override=0

Retrieve some particular parameters subsets.
virtual ParameterList	getBranchLengthsParameters () const =0
	Get the branch lengths parameters. More...

virtual ParameterList	getSubstitutionModelParameters () const =0
	Get the parameters associated to substitution model(s). More...

virtual std::shared_ptr< const TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex) const =0
	Get the substitution model associated to a given node and alignment column. More...

virtual std::shared_ptr< TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex)=0
	Get the substitution model associated to a given node and alignment column. More...

virtual VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...

virtual ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const =0

virtual ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const =0

virtual size_t	getSiteIndex (size_t site) const =0
	Get the index (used for inner computations) of a given site (original alignment column). More...

virtual const std::vector< double > &	getRootFrequencies (size_t siteIndex) const =0
	Get the values of the frequencies for each state in the alphabet at the root node. More...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Detailed Description

Interface for double-recursive (DR) implementation of the likelihood computation.

In the DR implementation, three conditional likelihoods are stored at each node, corresponding to the three connected substrees (in case of multifurcations, there may have even more). The DR implementation hence uses 3x more memory than the simple recursive (R) implementation. However, the likelihood of the tree can be computed independently at each node of the tree, which is very convenient for topology estimation (the likelihood change of each NNI movement can be computed directly), ancestral state reconstruction (all marginal ancestral states can be computed in one pass over the tree), or for substitution mapping.

This interface provides

a method to access the DR likelihood data structure,
a method to compute the likelihood array at each node.

For now, this interface inherits from DiscreteRatesAcrossSitesTreeLikelihood and not TreeLikelihood, since the data structure available accounts for rate across site variation. This may change in the future.

See also: DRTreeLikelihoodTools

Definition at line 37 of file DRTreeLikelihood.h.

Constructor & Destructor Documentation

◆ DRTreeLikelihoodInterface()

bpp::DRTreeLikelihoodInterface::DRTreeLikelihoodInterface ( )

inline

Definition at line 41 of file DRTreeLikelihood.h.

◆ ~DRTreeLikelihoodInterface()

virtual bpp::DRTreeLikelihoodInterface::~DRTreeLikelihoodInterface ( )

inlinevirtual

Definition at line 42 of file DRTreeLikelihood.h.

Member Function Documentation

◆ clone()

DRTreeLikelihoodInterface* bpp::DRTreeLikelihoodInterface::clone ( ) const

overridepure virtual

Implements bpp::TreeLikelihoodInterface.

Implemented in bpp::NNIHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

◆ computeLikelihoodAtNode()

virtual void bpp::DRTreeLikelihoodInterface::computeLikelihoodAtNode	(	int	nodeId,
		VVVdouble &	likelihoodArray
	)		const

pure virtual

Compute the likelihood array at a given node.

Parameters

nodeId	The id of the node to consider.
likelihoodArray	The array where to store the results.

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

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate().

◆ data()

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.

◆ enableDerivatives()

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.

◆ getAlphabet()

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()

virtual std::string bpp::TreeLikelihoodInterface::getAlphabetStateAsChar ( size_t i ) const

pure virtualinherited

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

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ getAlphabetStateAsInt()

virtual int bpp::TreeLikelihoodInterface::getAlphabetStateAsInt ( size_t i ) const

pure virtualinherited

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

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ getAlphabetStates()

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

pure virtualinherited

Returns: the alphabet states corresponding to all model states.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ getBranchLengthsParameters()

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

pure virtualinherited

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

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

◆ getDerivableParameters()

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.

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

◆ getLikelihoodForASiteForAState()

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()

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()

virtual VVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodPerSitePerRateClass ( ) const

pure virtualinherited

Get the likelihood for each site and each rate class.

Returns: A two-dimension vector with all likelihoods.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLikelihoodPerSitePerRateClassPerState()

virtual VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodPerSitePerRateClassPerState ( ) const

pure virtualinherited

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

Returns: A three-dimension vector with all likelihoods.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLikelihoodPerSitePerState()

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()

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()

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()

virtual VVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodPerSitePerRateClass ( ) const

pure 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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLogLikelihoodPerSitePerRateClassPerState()

virtual VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodPerSitePerRateClassPerState ( ) const

pure 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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLogLikelihoodPerSitePerState()

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.

◆ getModelForSite() [1/2]

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

pure virtualinherited

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.

Implemented in bpp::NonHomogeneousTreeLikelihood, and bpp::HomogeneousTreeLikelihood.

◆ getModelForSite() [2/2]

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

pure virtualinherited

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).

Implemented in bpp::NonHomogeneousTreeLikelihood, and bpp::HomogeneousTreeLikelihood.

◆ getNewBranchModelIterator()

virtual ConstBranchModelIterator* bpp::TreeLikelihoodInterface::getNewBranchModelIterator ( int nodeId ) const

pure virtualinherited

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ getNewSiteModelIterator()

virtual ConstSiteModelIterator* bpp::TreeLikelihoodInterface::getNewSiteModelIterator ( size_t siteIndex ) const

pure virtualinherited

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ getNonDerivableParameters()

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()

virtual size_t bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getNumberOfClasses ( ) const

pure virtualinherited

Get the number of classes.

Returns: The number of classes.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ getNumberOfSites()

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()

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

pure virtualinherited

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

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies(), bpp::TreeLikelihoodTools::getAncestralFrequencies_(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLikelihoodPerSitePerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLogLikelihoodPerSitePerState(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate(), bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities().

◆ getPosteriorProbabilitiesPerRate()

virtual VVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getPosteriorProbabilitiesPerRate ( ) const

pure 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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getPosteriorRatePerSite()

virtual Vdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getPosteriorRatePerSite ( ) const

pure 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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getRateClassWithMaxPostProbPerSite()

virtual std::vector<size_t> bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getRateClassWithMaxPostProbPerSite ( ) const

pure virtualinherited

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

Returns: A vector with all rate classes indexes.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::RASTools::getPosteriorRateDistribution().

◆ getRateDistribution() [1/2]

virtual std::shared_ptr<const DiscreteDistributionInterface> bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getRateDistribution ( ) const

pure virtualinherited

Get the rate distribution used for the computation.

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

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate(), and bpp::RASTools::getPosteriorRateDistribution().

◆ getRateDistribution() [2/2]

virtual std::shared_ptr<DiscreteDistributionInterface> bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getRateDistribution ( )

pure virtualinherited

Get the rate distribution used for the computation.

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

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getRateDistributionParameters()

virtual ParameterList bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getRateDistributionParameters ( ) const

pure virtualinherited

Get the parameters associated to the rate distribution.

Returns: A ParameterList object with all rate distribution parameters.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getRateWithMaxPostProbPerSite()

virtual Vdouble bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getRateWithMaxPostProbPerSite ( ) const

pure virtualinherited

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

Returns: A vector with all rate classes indexes.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getRootFrequencies()

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

pure virtualinherited

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;

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

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

◆ 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()

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

pure virtualinherited

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

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

◆ getTransitionProbabilities()

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()

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

pure virtualinherited

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.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

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

◆ hasLikelihoodData()

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

pure virtualinherited

Returns: True if the TreeLikelihood object has a LikelihoodData.

Implemented in bpp::AbstractTreeLikelihood.

◆ initialize()

virtual void bpp::TreeLikelihoodInterface::initialize ( )

pure virtualinherited

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.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::AbstractTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

◆ isInitialized()

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 DRASDRTreeLikelihoodData& bpp::DRTreeLikelihoodInterface::likelihoodData ( ) const

overridepure virtual

Returns: The underlying likelihood data structure.

Implements bpp::TreeLikelihoodInterface.

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

◆ likelihoodData() [2/2]

virtual DRASDRTreeLikelihoodData& bpp::DRTreeLikelihoodInterface::likelihoodData ( )

overridepure virtual

Returns: The underlying likelihood data structure.

Implements bpp::TreeLikelihoodInterface.

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

Referenced by bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ rateDistribution() [1/2]

virtual const DiscreteDistributionInterface& bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::rateDistribution ( ) const

pure virtualinherited

Get the rate distribution used for the computation.

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

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ rateDistribution() [2/2]

virtual DiscreteDistributionInterface& bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::rateDistribution ( )

pure virtualinherited

Get the rate distribution used for the computation.

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

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ 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 bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

◆ tree()

virtual const Tree& bpp::TreeLikelihoodInterface::tree ( ) const

pure virtualinherited

Get the tree (topology and branch lengths).

Returns: The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel(), bpp::TreeLikelihoodTools::getAncestralFrequencies(), bpp::TreeLikelihoodTools::getAncestralFrequencies_(), and bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate().

The documentation for this class was generated from the following file:

Bpp/Phyl/Legacy/Likelihood/DRTreeLikelihood.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DRTreeLikelihoodInterface()

◆ ~DRTreeLikelihoodInterface()

Member Function Documentation

◆ clone()

◆ computeLikelihoodAtNode()

◆ data()

◆ enableDerivatives()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getBranchLengthsParameters()

◆ getDerivableParameters()

◆ getLikelihood()

◆ getLikelihoodForASite()

◆ getLikelihoodForASiteForARateClass()

◆ getLikelihoodForASiteForARateClassForAState()

◆ getLikelihoodForASiteForAState()

◆ getLikelihoodPerSite()

◆ getLikelihoodPerSitePerRateClass()

◆ getLikelihoodPerSitePerRateClassPerState()

◆ getLikelihoodPerSitePerState()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getLogLikelihoodForASiteForARateClass()

◆ getLogLikelihoodForASiteForARateClassForAState()

◆ getLogLikelihoodForASiteForAState()

◆ getLogLikelihoodPerSite()

◆ getLogLikelihoodPerSitePerRateClass()

◆ getLogLikelihoodPerSitePerRateClassPerState()

◆ getLogLikelihoodPerSitePerState()

◆ getModelForSite() [1/2]

◆ getModelForSite() [2/2]

◆ getNewBranchModelIterator()

◆ getNewSiteModelIterator()

◆ getNonDerivableParameters()

◆ getNumberOfClasses()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getPosteriorProbabilitiesPerRate()

◆ getPosteriorRatePerSite()

◆ getRateClassWithMaxPostProbPerSite()

◆ getRateDistribution() [1/2]

◆ getRateDistribution() [2/2]

◆ getRateDistributionParameters()

◆ getRateWithMaxPostProbPerSite()

◆ getRootFrequencies()

◆ getSiteIndex()

◆ getSubstitutionModelParameters()

◆ getTransitionProbabilities()

◆ getTransitionProbabilitiesPerRateClass()

◆ hasLikelihoodData()

◆ initialize()

◆ isInitialized()

◆ likelihoodData() [1/2]

◆ likelihoodData() [2/2]

◆ rateDistribution() [1/2]

◆ rateDistribution() [2/2]

◆ setData()

◆ tree()