Interface for likelihood computation with a global clock. More...

#include <Bpp/Phyl/Likelihood/ClockTreeLikelihood.h>

Inheritance diagram for bpp::ClockTreeLikelihood:

Collaboration diagram for bpp::ClockTreeLikelihood:

Public Member Functions
ClockTreeLikelihood *	clone () const =0

virtual	~ClockTreeLikelihood ()

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

virtual const SiteContainer *	getData () const =0
	Get the dataset for which the likelihood must be evaluated. More...

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

virtual bool	isInitialized () const =0

virtual TreeLikelihoodData *	getLikelihoodData ()=0

virtual const TreeLikelihoodData *	getLikelihoodData () 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	getLikelihoodForEachSite () const =0
	Get the likelihood for each site. More...

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

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

virtual VVdouble	getLogLikelihoodForEachSiteForEachState () 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 &	getTree () 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 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...

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 const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const =0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...

virtual SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex)=0 throw (NodeNotFoundException)
	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 throw (IndexOutOfBoundsException)
	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...

Detailed Description

Interface for likelihood computation with a global clock.

Deprecated:: See GlobalClockTreeLikelihoodFunctionWrapper as a more general replacement.

Definition at line 58 of file ClockTreeLikelihood.h.

Constructor & Destructor Documentation

◆ ~ClockTreeLikelihood()

virtual bpp::ClockTreeLikelihood::~ClockTreeLikelihood ( )

inlinevirtual

Definition at line 66 of file ClockTreeLikelihood.h.

Member Function Documentation

◆ clone()

ClockTreeLikelihood* bpp::ClockTreeLikelihood::clone ( ) const

pure virtual

Implements bpp::TreeLikelihood.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::DiscreteRatesAcrossSitesClockTreeLikelihood.

◆ enableDerivatives()

virtual void bpp::TreeLikelihood::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 const Alphabet* bpp::TreeLikelihood::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::TreeLikelihood::getAlphabetStateAsChar ( size_t i ) const

pure virtualinherited

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

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

◆ getAlphabetStateAsInt()

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

pure virtualinherited

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

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

◆ getAlphabetStates()

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

pure virtualinherited

Returns: the alphabet states corresponding to all model states.

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

◆ getBranchLengthsParameters()

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

pure virtualinherited

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

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

Referenced by bpp::OptimizationTools::ScaleFunction::ScaleFunction().

◆ getData()

virtual const SiteContainer* bpp::TreeLikelihood::getData ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns: A pointer toward the site container where the sequences are stored.

Implemented in bpp::AbstractTreeLikelihood.

◆ getDerivableParameters()

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

pure virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns: A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getLikelihood()

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

pure virtualinherited

Get the likelihood for the whole dataset.

Returns: The likelihood of the dataset.

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

◆ getLikelihoodData() [1/2]

virtual TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( )

pure virtualinherited

Returns: The underlying likelihood data structure.

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

◆ getLikelihoodData() [2/2]

virtual const TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) const

pure virtualinherited

Returns: The underlying likelihood data structure.

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

◆ getLikelihoodForASite()

virtual double bpp::TreeLikelihood::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::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

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

◆ getLikelihoodForASiteForAState()

virtual double bpp::TreeLikelihood::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::getLikelihoodForEachSiteForEachState().

◆ getLikelihoodForEachSite()

virtual Vdouble bpp::TreeLikelihood::getLikelihoodForEachSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

◆ getLikelihoodForEachSiteForEachState()

virtual VVdouble bpp::TreeLikelihood::getLikelihoodForEachSiteForEachState ( ) 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::TreeLikelihood::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::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

◆ getLogLikelihoodForASite()

virtual double bpp::TreeLikelihood::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::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

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

◆ getLogLikelihoodForASiteForAState()

virtual double bpp::TreeLikelihood::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::getLogLikelihoodForEachSiteForEachState().

◆ getLogLikelihoodForEachSite()

virtual Vdouble bpp::TreeLikelihood::getLogLikelihoodForEachSite ( ) 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.

◆ getLogLikelihoodForEachSiteForEachState()

virtual VVdouble bpp::TreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) 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.

◆ getNewBranchModelIterator()

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

pure virtualinherited

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

◆ getNewSiteModelIterator()

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

pure virtualinherited

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

◆ getNonDerivableParameters()

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

pure virtualinherited

All non derivable parameters.

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

Returns: A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getNumberOfSites()

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

pure virtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch().

◆ getNumberOfStates()

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

pure virtualinherited

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

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

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

◆ getRootFrequencies()

virtual const std::vector<double>& bpp::TreeLikelihood::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, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

◆ getSiteIndex()

virtual size_t bpp::TreeLikelihood::getSiteIndex	(	size_t	site	)	const
throw	(	IndexOutOfBoundsException
	)

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::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.

◆ getSubstitutionModel() [1/2]

virtual const SubstitutionModel* bpp::TreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		const
throw	(	NodeNotFoundException
	)

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::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

◆ getSubstitutionModel() [2/2]

virtual SubstitutionModel* bpp::TreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)
throw	(	NodeNotFoundException
	)

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::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

◆ getSubstitutionModelParameters()

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

pure virtualinherited

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

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

◆ getTransitionProbabilities()

virtual VVdouble bpp::TreeLikelihood::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.

◆ getTree()

virtual const Tree& bpp::TreeLikelihood::getTree ( ) const

pure virtualinherited

Get the tree (topology and branch lengths).

Returns: The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::SubstitutionMappingTools::getNormalizedCountsPerBranch(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_().

◆ initialize()

virtual void bpp::TreeLikelihood::initialize	(		)
throw	(	Exception
	)

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::AbstractTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

◆ isInitialized()

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

pure virtualinherited

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

Implemented in bpp::AbstractTreeLikelihood.

◆ setData()

virtual void bpp::TreeLikelihood::setData ( const SiteContainer & sites )

pure virtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

sites The data set to use.

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

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

Bpp/Phyl/Likelihood/ClockTreeLikelihood.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~ClockTreeLikelihood()

Member Function Documentation

◆ clone()

◆ enableDerivatives()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getBranchLengthsParameters()

◆ getData()

◆ getDerivableParameters()

◆ getLikelihood()

◆ getLikelihoodData() [1/2]

◆ getLikelihoodData() [2/2]

◆ getLikelihoodForASite()

◆ getLikelihoodForASiteForAState()

◆ getLikelihoodForEachSite()

◆ getLikelihoodForEachSiteForEachState()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getLogLikelihoodForASiteForAState()

◆ getLogLikelihoodForEachSite()

◆ getLogLikelihoodForEachSiteForEachState()

◆ getNewBranchModelIterator()

◆ getNewSiteModelIterator()

◆ getNonDerivableParameters()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getRootFrequencies()

◆ getSiteIndex()

◆ getSubstitutionModel() [1/2]

◆ getSubstitutionModel() [2/2]

◆ getSubstitutionModelParameters()

◆ getTransitionProbabilities()

◆ getTree()

◆ initialize()

◆ isInitialized()

◆ setData()