bpp::DiscreteRatesAcrossSitesTreeLikelihood Class Reference

Interface for rate across sites (RAS) implementation. More...

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

Inheritance diagram for bpp::DiscreteRatesAcrossSitesTreeLikelihood:

Collaboration diagram for bpp::DiscreteRatesAcrossSitesTreeLikelihood:

List of all members.

Public Member Functions
	DiscreteRatesAcrossSitesTreeLikelihood ()
virtual	~DiscreteRatesAcrossSitesTreeLikelihood ()
virtual const DiscreteDistribution *	getRateDistribution () const =0
	Get the rate distribution used for the computation.
virtual DiscreteDistribution *	getRateDistribution ()=0
	Get the rate distribution used for the computation.
virtual double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the likelihood for a site knowing its rate class.
virtual double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the logarithm of the likelihood for a site knowing its rate class.
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.
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.
virtual VVdouble	getLikelihoodForEachSiteForEachRateClass () const =0
	Get the likelihood for each site and each rate class.
virtual VVdouble	getLogLikelihoodForEachSiteForEachRateClass () const =0
	Get the logarithm of the likelihood for each site and each rate class.
virtual VVVdouble	getLikelihoodForEachSiteForEachRateClassForEachState () const =0
	Get the likelihood for each site and each rate class and each state.
virtual VVVdouble	getLogLikelihoodForEachSiteForEachRateClassForEachState () const =0
	Get the logarithm of the likelihood for each site and each rate class and each state.
virtual VVdouble	getPosteriorProbabilitiesOfEachRate () const =0
	Get the posterior probability for each site of belonging to a particular rate class.
virtual std::vector< size_t >	getRateClassWithMaxPostProbOfEachSite () const =0
	Get the posterior rate class (the one with maximum posterior probability) for each site.
virtual Vdouble	getRateWithMaxPostProbOfEachSite () const =0
	Get the posterior rate (the one with maximum posterior probability) for each site.
virtual Vdouble	getPosteriorRateOfEachSite () const =0
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.
virtual ParameterList	getRateDistributionParameters () const =0
	Get the parameters associated to the rate distirbution.
virtual size_t	getNumberOfClasses () const =0
	Get the number of classes.
virtual VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node.
TreeLikelihood *	clone () 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 const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const =0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
virtual SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex)=0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
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

Interface for rate across sites (RAS) implementation.

This interface provides methods for dealing with RAS models.

Definition at line 56 of file DiscreteRatesAcrossSitesTreeLikelihood.h.

---

Constructor & Destructor Documentation

bpp::DiscreteRatesAcrossSitesTreeLikelihood::DiscreteRatesAcrossSitesTreeLikelihood

(

)

[inline]

Definition at line 60 of file DiscreteRatesAcrossSitesTreeLikelihood.h.

virtual bpp::DiscreteRatesAcrossSitesTreeLikelihood::~DiscreteRatesAcrossSitesTreeLikelihood

(

)

[inline, virtual]

Definition at line 61 of file DiscreteRatesAcrossSitesTreeLikelihood.h.

---

Member Function Documentation

TreeLikelihood* bpp::TreeLikelihood::clone

(

)

const [pure virtual, inherited]

Implements bpp::DerivableSecondOrder.

Implemented in bpp::NNIHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousClockTreeLikelihood, bpp::DRTreeLikelihood, bpp::DiscreteRatesAcrossSitesClockTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::ClockTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

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::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const [pure virtual]

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const [pure virtual]

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

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::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass

(

)

const [pure virtual]

Get the likelihood for each site and each rate class.

Returns:

A two-dimension vector with all likelihoods.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

virtual VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState

(

)

const [pure virtual]

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.

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::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const [pure virtual]

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const [pure virtual]

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

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::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass

(

)

const [pure virtual]

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.

virtual VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState

(

)

const [pure virtual]

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.

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::DiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses

(

)

const [pure virtual]

Get the number of classes.

Returns:

The Number of classes.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

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

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 VVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate

(

)

const [pure virtual]

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] = probablity for site i of belonging to rate class j.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

virtual Vdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite

(

)

const [pure virtual]

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.

virtual std::vector<size_t> bpp::DiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite

(

)

const [pure virtual]

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().

virtual const DiscreteDistribution* bpp::DiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution

(

)

const [pure virtual]

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::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::RASTools::getPosteriorRateDistribution().

virtual DiscreteDistribution* bpp::DiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution

(

)

[pure virtual]

Get the rate distribution used for the computation.

Returns:

A pointer toward the rate distribution of this instance.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

virtual ParameterList bpp::DiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters

(

)

const [pure virtual]

Get the parameters associated to the rate distirbution.

Returns:

A ParameterList object with all rate distribution parameters.

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

virtual Vdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite

(

)

const [pure virtual]

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.

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 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.

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

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

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

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

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 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 VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilitiesPerRateClass	(	int	nodeId,
		size_t	siteIndex
	)		const [pure virtual]

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, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

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.

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

• Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h