bpp::AbstractTreeLikelihood Class Reference

Partial implementation of the TreeLikelihood interface. More...

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

Inheritance diagram for bpp::AbstractTreeLikelihood:

Collaboration diagram for bpp::AbstractTreeLikelihood:

Classes
class	ConstNoPartitionBranchModelDescription
class	ConstNoPartitionBranchModelIterator
class	ConstNoPartitionSiteModelDescription
class	SimpleBranchIterator
	A very simple branch iterator. More...
class	SimpleSiteIterator
	A very simple site iterator. More...

Public Member Functions
	AbstractTreeLikelihood ()
	AbstractTreeLikelihood (const AbstractTreeLikelihood &lik)
AbstractTreeLikelihood &	operator= (const AbstractTreeLikelihood &lik)
virtual	~AbstractTreeLikelihood ()
	Abstract class destructor. More...
TreeLikelihoodInterface *	clone () const override=0
virtual void	setData (const AlignmentDataInterface &sites)=0
	Set the dataset for which the likelihood must be evaluated. More...
virtual TreeLikelihoodData &	likelihoodData ()=0
virtual const TreeLikelihoodData &	likelihoodData () 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 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 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 ParameterList	getDerivableParameters () const =0
	All derivable parameters. More...
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters. More...
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 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
bool	hasParameter (const std::string &name) const override
const ParameterList &	getParameters () const override
const Parameter &	parameter (const std::string &name) const override
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
double	getParameterValue (const std::string &name) const override
void	setAllParametersValues (const ParameterList &parameters) override
void	setParameterValue (const std::string &name, double value) override
void	setParametersValues (const ParameterList &parameters) override
bool	matchParametersValues (const ParameterList &parameters) override
void	removeConstraint (const std::string &name) override
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
size_t	getNumberOfParameters () const override
void	setNamespace (const std::string &prefix) override
std::string	getNamespace () const override
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
virtual void	fireParameterChanged (const ParameterList &parameters)
virtual Clonable *	clone () const=0
The TreeLikelihood interface.
bool	hasLikelihoodData () const
const AlignmentDataInterface &	data () const
	Get the dataset for which the likelihood must be evaluated. More...
std::shared_ptr< const Alphabet >	getAlphabet () const
	Get the alphabet associated to the dataset. More...
Vdouble	getLikelihoodPerSite () const
	Get the likelihood for each site. More...
Vdouble	getLogLikelihoodPerSite () const
	Get the logarithm of the likelihood for each site. More...
VVdouble	getLikelihoodPerSitePerState () const
	Get the likelihood for each site and for each state. More...
VVdouble	getLogLikelihoodPerSitePerState () const
	Get the logarithm of the likelihood for each site and for each state. More...
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
const Tree &	tree () const
	Get the tree (topology and branch lengths). More...
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed. More...
void	enableFirstOrderDerivatives (bool yn)
void	enableSecondOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
bool	enableSecondOrderDerivatives () const
bool	isInitialized () const
void	initialize ()
	Init the likelihood object. 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 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
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)
virtual void	addParameter_ (Parameter *parameter)
virtual void	addParameters_ (const ParameterList &parameters)
virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)
virtual void	shareParameters_ (const ParameterList &parameters)
virtual void	includeParameters_ (const ParameterList &parameters)
virtual void	deleteParameter_ (size_t index)
virtual void	deleteParameter_ (std::string &name)
virtual void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name)
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
Parameter &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
ParameterList &	getParameters_ () override

Protected Attributes
std::unique_ptr< const AlignmentDataInterface >	data_
std::shared_ptr< TreeTemplate< Node > >	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_

Private Attributes
ParameterList	parameters_
std::string	prefix_

Detailed Description

Partial implementation of the TreeLikelihood interface.

This class implements a few methods useful for most of likelihood computation methods.

It includes a tree_ and a data_ pointers. This objects are owned by the class, and hence hard copied when cloning, and destroyed by the destructor.

• The Parametrizable interface;
• The getTree() method;

It also adds an abstract method for recursive computations.

Definition at line 35 of file AbstractTreeLikelihood.h.

Constructor & Destructor Documentation

AbstractTreeLikelihood() [1/2]

bpp::AbstractTreeLikelihood::AbstractTreeLikelihood ( )

inline

Definition at line 215 of file AbstractTreeLikelihood.h.

AbstractTreeLikelihood() [2/2]

bpp::AbstractTreeLikelihood::AbstractTreeLikelihood ( const AbstractTreeLikelihood &  lik )

inline

Definition at line 223 of file AbstractTreeLikelihood.h.

References data_, and tree_.

~AbstractTreeLikelihood()

virtual bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood ( )

inlinevirtual

Abstract class destructor.

This destructor is empty.

Definition at line 253 of file AbstractTreeLikelihood.h.

Member Function Documentation

clone()

TreeLikelihoodInterface* bpp::TreeLikelihoodInterface::clone ( ) const

overridepure virtualinherited

Implements bpp::SecondOrderDerivable.

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

data()

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

inlinevirtual

Get the dataset for which the likelihood must be evaluated.

Returns

The site container where the sequences are stored.

Implements bpp::TreeLikelihoodInterface.

Definition at line 262 of file AbstractTreeLikelihood.h.

References data_.

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

enableDerivatives()

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

inlinevirtual

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implements bpp::TreeLikelihoodInterface.

Definition at line 270 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_, and computeSecondOrderDerivatives_.

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

enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 273 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_.

enableFirstOrderDerivatives() [2/2]

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

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 271 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_.

enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 274 of file AbstractTreeLikelihood.h.

References computeSecondOrderDerivatives_.

enableSecondOrderDerivatives() [2/2]

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

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 272 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_, and computeSecondOrderDerivatives_.

getAlphabet()

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

inlinevirtual

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 263 of file AbstractTreeLikelihood.h.

References data_.

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 getLikelihoodPerSite().

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 getLikelihoodPerSitePerState().

getLikelihoodPerSite()

Vdouble AbstractTreeLikelihood::getLikelihoodPerSite ( ) const

virtual

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 11 of file AbstractTreeLikelihood.cpp.

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

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

getLikelihoodPerSitePerState()

VVdouble AbstractTreeLikelihood::getLikelihoodPerSitePerState ( ) const

virtual

Get the likelihood for each site and for each state.

Returns

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

Implements bpp::TreeLikelihoodInterface.

Definition at line 35 of file AbstractTreeLikelihood.cpp.

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

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 getLogLikelihoodPerSite().

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 getLogLikelihoodPerSitePerState().

getLogLikelihoodPerSite()

Vdouble AbstractTreeLikelihood::getLogLikelihoodPerSite ( ) const

virtual

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 23 of file AbstractTreeLikelihood.cpp.

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

getLogLikelihoodPerSitePerState()

VVdouble AbstractTreeLikelihood::getLogLikelihoodPerSitePerState ( ) const

virtual

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 52 of file AbstractTreeLikelihood.cpp.

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

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.

getNumberOfSites()

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtual

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 268 of file AbstractTreeLikelihood.h.

References data_.

Referenced by getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), getLikelihoodPerSitePerState(), getLogLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), getLogLikelihoodPerSitePerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

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(), getLikelihoodPerSitePerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), getLogLikelihoodPerSitePerState(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate(), bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities().

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_().

hasLikelihoodData()

bool bpp::AbstractTreeLikelihood::hasLikelihoodData ( ) const

inlinevirtual

Returns

True if the TreeLikelihood object has a LikelihoodData.

Implements bpp::TreeLikelihoodInterface.

Definition at line 261 of file AbstractTreeLikelihood.h.

References data_.

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

initialize()

void bpp::AbstractTreeLikelihood::initialize ( )

inlinevirtual

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.

Implements bpp::TreeLikelihoodInterface.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 276 of file AbstractTreeLikelihood.h.

References initialized_.

isInitialized()

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtual

Returns

'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihoodInterface.

Definition at line 275 of file AbstractTreeLikelihood.h.

References initialized_.

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

likelihoodData() [1/2]

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

pure virtualinherited

Returns

The underlying likelihood data structure.

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

likelihoodData() [2/2]

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

pure virtualinherited

Returns

The underlying likelihood data structure.

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

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

operator=()

AbstractTreeLikelihood& bpp::AbstractTreeLikelihood::operator= ( const AbstractTreeLikelihood &  lik )

inline

Definition at line 235 of file AbstractTreeLikelihood.h.

References computeFirstOrderDerivatives_, computeSecondOrderDerivatives_, data_, initialized_, and tree_.

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

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()

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

inlinevirtual

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihoodInterface.

Definition at line 269 of file AbstractTreeLikelihood.h.

References tree_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), and bpp::NNIHomogeneousTreeLikelihood::topology().

Member Data Documentation

computeFirstOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_

protected

Definition at line 210 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), enableDerivatives(), enableFirstOrderDerivatives(), enableSecondOrderDerivatives(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and operator=().

computeSecondOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_

protected

Definition at line 211 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), enableDerivatives(), enableSecondOrderDerivatives(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and operator=().

data_

std::unique_ptr<const AlignmentDataInterface> bpp::AbstractTreeLikelihood::data_

protected

Definition at line 208 of file AbstractTreeLikelihood.h.

Referenced by AbstractTreeLikelihood(), data(), getAlphabet(), getNumberOfSites(), hasLikelihoodData(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protected

Definition at line 212 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), isInitialized(), operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

tree_

std::shared_ptr< TreeTemplate<Node> > bpp::AbstractTreeLikelihood::tree_

mutableprotected

Definition at line 209 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), AbstractTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), operator=(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and tree().

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

• Bpp/Phyl/Legacy/Likelihood/AbstractTreeLikelihood.h
• Bpp/Phyl/Legacy/Likelihood/AbstractTreeLikelihood.cpp