Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models. More...

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

Inheritance diagram for bpp::NonHomogeneousTreeLikelihood:

Collaboration diagram for bpp::NonHomogeneousTreeLikelihood:

Public Member Functions
NonHomogeneousTreeLikelihood *	clone () const =0
const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
virtual const SubstitutionModel *	getSubstitutionModelForNode (int nodeId) const =0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node.
virtual SubstitutionModel *	getSubstitutionModelForNode (int nodeId)=0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node.
virtual const SubstitutionModelSet *	getSubstitutionModelSet () const =0
virtual SubstitutionModelSet *	getSubstitutionModelSet ()=0
virtual void	setSubstitutionModelSet (SubstitutionModelSet *model)=0 throw (Exception)
virtual ParameterList	getRootFrequenciesParameters () const =0
virtual void	setData (const SiteContainer &sites)=0
	Set the dataset for which the likelihood must be evaluated.
virtual const SiteContainer *	getData () const =0
	Get the dataset for which the likelihood must be evaluated.
virtual void	initialize ()=0 throw (Exception)
	Init the likelihood object.
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.
virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the logarithm of the likelihood for a site.
virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state.
virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state.
virtual Vdouble	getLikelihoodForEachSite () const =0
	Get the likelihood for each site.
virtual Vdouble	getLogLikelihoodForEachSite () const =0
	Get the logarithm of the likelihood for each site.
virtual VVdouble	getLikelihoodForEachSiteForEachState () const =0
	Get the likelihood for each site and for each state.
virtual VVdouble	getLogLikelihoodForEachSiteForEachState () const =0
	Get the logarithm of the likelihood for each site and for each state.
virtual double	getLikelihood () const =0
	Get the likelihood for the whole dataset.
virtual double	getLogLikelihood () const =0
	Get the logarithm of the likelihood for the whole dataset.
virtual const Tree &	getTree () const =0
	Get the tree (topology and branch lengths).
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset.
virtual size_t	getNumberOfStates () const =0
	Get the number of states in the alphabet associated to the dataset.
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the dataset.
virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed.
virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters.
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters.
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 &	getParameter (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 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
Retrieve some particular parameters subsets.
virtual ParameterList	getBranchLengthsParameters () const =0
	Get the branch lengths parameters.
virtual ParameterList	getSubstitutionModelParameters () const =0
	Get the parameters associated to substitution model(s).
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.
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).
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.

Detailed Description

Specialization of the TreeLikelihood interface for the branch non-homogeneous and non-stationary models.

The main difference is that the likelihood depends on the position of the root. The frequencies at the root of the tree are new parameters, which are not necessarily equal to the equilibrium frequencies of the substitution model.

This interface further assumes that the substitution model is the same for all sites, for a given branch.

See also:: SubstitutionModelSet.

Definition at line 60 of file NonHomogeneousTreeLikelihood.h.

Member Function Documentation

NonHomogeneousTreeLikelihood* bpp::NonHomogeneousTreeLikelihood::clone ( ) const [pure virtual]

Implements bpp::TreeLikelihood.

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

virtual void bpp::TreeLikelihood::enableDerivatives ( bool yn ) [pure virtual, inherited]

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters:

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

virtual const Alphabet* bpp::TreeLikelihood::getAlphabet ( ) const [pure virtual, inherited]

Get the alphabet associated to the dataset.

Returns:: the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

virtual ParameterList bpp::TreeLikelihood::getBranchLengthsParameters ( ) const [pure virtual, inherited]

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().

virtual const SiteContainer* bpp::TreeLikelihood::getData ( ) const [pure virtual, inherited]

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.

virtual ParameterList bpp::TreeLikelihood::getDerivableParameters ( ) const [pure virtual, inherited]

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns:: A ParameterList.

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

virtual double bpp::TreeLikelihood::getLikelihood ( ) const [pure virtual, inherited]

Get the likelihood for the whole dataset.

Returns:: The likelihood of the dataset.

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

virtual TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) [pure virtual, inherited]

Returns:: The underlying likelihood data structure.

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

virtual const TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) const [pure virtual, inherited]

Returns:: The underlying likelihood data structure.

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

virtual double bpp::TreeLikelihood::getLikelihoodForASite ( size_t site ) const [pure virtual, inherited]

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

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

virtual double bpp::TreeLikelihood::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[pure virtual, inherited]`

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().

virtual Vdouble bpp::TreeLikelihood::getLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the likelihood for each site.

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

Implemented in bpp::AbstractTreeLikelihood.

virtual VVdouble bpp::TreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

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.

virtual double bpp::TreeLikelihood::getLogLikelihood ( ) const [pure virtual, inherited]

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::DRNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

virtual double bpp::TreeLikelihood::getLogLikelihoodForASite ( size_t site ) const [pure virtual, inherited]

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

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

virtual double bpp::TreeLikelihood::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[pure virtual, inherited]`

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().

virtual Vdouble bpp::TreeLikelihood::getLogLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the logarithm of the likelihood for each site.

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

Implemented in bpp::AbstractTreeLikelihood.

virtual VVdouble bpp::TreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

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.

virtual ConstBranchModelIterator* bpp::TreeLikelihood::getNewBranchModelIterator ( int nodeId ) const [pure virtual, inherited]

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

virtual ConstSiteModelIterator* bpp::TreeLikelihood::getNewSiteModelIterator ( size_t siteIndex ) const [pure virtual, inherited]

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

virtual ParameterList bpp::TreeLikelihood::getNonDerivableParameters ( ) const [pure virtual, inherited]

All non derivable parameters.

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

Returns:: A ParameterList.

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

virtual size_t bpp::TreeLikelihood::getNumberOfSites ( ) const [pure virtual, inherited]

Get the number of sites in the dataset.

Returns:: the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

virtual size_t bpp::TreeLikelihood::getNumberOfStates ( ) const [pure virtual, inherited]

Get the number of states in the alphabet associated to the dataset.

Returns:: the number of states in the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

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

virtual const std::vector<double>& bpp::TreeLikelihood::getRootFrequencies ( size_t siteIndex ) const [pure virtual, inherited]

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.

virtual ParameterList bpp::NonHomogeneousTreeLikelihood::getRootFrequenciesParameters ( ) const [pure virtual]

Returns:: The parameters on which the root frequencies depend.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

Referenced by bpp::PhylogeneticsApplicationTools::optimizeParameters().

virtual size_t bpp::TreeLikelihood::getSiteIndex ( size_t site ) const throw (IndexOutOfBoundsException) [pure virtual, inherited]

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.

const SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		const throw (NodeNotFoundException) `[inline, virtual]`

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).

Implements bpp::TreeLikelihood.

Definition at line 69 of file NonHomogeneousTreeLikelihood.h.

References getSubstitutionModelForNode().

SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		throw (NodeNotFoundException) `[inline, virtual]`

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).

Implements bpp::TreeLikelihood.

Definition at line 74 of file NonHomogeneousTreeLikelihood.h.

References getSubstitutionModelForNode().

virtual const SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode ( int nodeId ) const throw (NodeNotFoundException) [pure virtual]

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).

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

Referenced by getSubstitutionModel().

virtual SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode ( int nodeId ) throw (NodeNotFoundException) [pure virtual]

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).

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

virtual ParameterList bpp::TreeLikelihood::getSubstitutionModelParameters ( ) const [pure virtual, inherited]

Get the parameters associated to substitution model(s).

Returns:: A ParameterList.

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

virtual const SubstitutionModelSet* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) const [pure virtual]

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

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

virtual SubstitutionModelSet* bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) [pure virtual]

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

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

virtual VVdouble bpp::TreeLikelihood::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const `[pure virtual, inherited]`

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.

virtual const Tree& bpp::TreeLikelihood::getTree ( ) const [pure virtual, inherited]

Get the tree (topology and branch lengths).

Returns:: The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

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

virtual void bpp::TreeLikelihood::initialize ( ) throw (Exception) [pure virtual, inherited]

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

virtual bool bpp::TreeLikelihood::isInitialized ( ) const [pure virtual, inherited]

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

Implemented in bpp::AbstractTreeLikelihood.

virtual void bpp::TreeLikelihood::setData ( const SiteContainer & sites ) [pure virtual, inherited]

Set the dataset for which the likelihood must be evaluated.

Parameters:

sites The data set to use.

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

virtual void bpp::NonHomogeneousTreeLikelihood::setSubstitutionModelSet ( SubstitutionModelSet * model ) throw (Exception) [pure virtual]

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).

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood.

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

Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h

Public Member Functions

Detailed Description

Member Function Documentation