The AlignedPhyloLikelihood interface, for phylogenetic likelihood. More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihood.h>

Inheritance diagram for bpp::AlignedPhyloLikelihoodInterface:

Collaboration diagram for bpp::AlignedPhyloLikelihoodInterface:

Public Member Functions
	AlignedPhyloLikelihoodInterface ()

virtual	~AlignedPhyloLikelihoodInterface ()

virtual AlignedPhyloLikelihoodInterface *	clone () const =0

virtual LikelihoodCalculation &	likelihoodCalculation () const =0

virtual std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const =0

virtual void	enableSecondOrderDerivatives (bool yn)=0

virtual bool	enableSecondOrderDerivatives () const=0

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

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

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

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

virtual void	enableFirstOrderDerivatives (bool yn)=0

virtual bool	enableFirstOrderDerivatives () const=0

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

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

virtual void	setParameters (const ParameterList &parameters)=0

virtual double	getValue () const=0

virtual double	f (const ParameterList &parameters)

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

virtual const ParameterList &	getParameters () const=0

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

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

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

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

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

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

virtual size_t	getNumberOfParameters () const=0

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

virtual std::string	getNamespace () const=0

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

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

The likelihood functions.
virtual AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const =0

virtual std::shared_ptr< AlignedLikelihoodCalculation >	getAlignedLikelihoodCalculation () const =0

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

virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the log likelihood for a site, and its derivatives. More...

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

The data functions
virtual bool	isInitialized () const =0

virtual const Context &	context () const =0

virtual Context &	context ()=0

The likelihood functions.
virtual ValueRef< DataLik >	getLikelihoodNode () const =0

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

Retrieve some particular independent parameters subsets.
Get the derivates of the LogLikelihood.
virtual ParameterList	getNonDerivableParameters () const =0

virtual ParameterList	getDerivableParameters () const =0

virtual ParameterList	getBranchLengthParameters () const =0
	Get the independent branch lengths parameters. More...

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

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

virtual ParameterList	getRootFrequenciesParameters () const =0
	Get the independent parameters associated to the root frequencies(s). More...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Friends
class	AlignedPhyloLikelihoodSet

Detailed Description

The AlignedPhyloLikelihood interface, for phylogenetic likelihood.

This interface defines the common methods needed to compute a likelihood from an alignment of data (involving several process & alphabets, if needed), where all sites are independent (eq it does not match for HMM phylolikelihoods).

Definition at line 30 of file AlignedPhyloLikelihood.h.

Constructor & Destructor Documentation

◆ AlignedPhyloLikelihoodInterface()

bpp::AlignedPhyloLikelihoodInterface::AlignedPhyloLikelihoodInterface ( )

inline

Definition at line 34 of file AlignedPhyloLikelihood.h.

◆ ~AlignedPhyloLikelihoodInterface()

virtual bpp::AlignedPhyloLikelihoodInterface::~AlignedPhyloLikelihoodInterface ( )

inlinevirtual

Definition at line 35 of file AlignedPhyloLikelihood.h.

Member Function Documentation

◆ alignedLikelihoodCalculation()

virtual AlignedLikelihoodCalculation& bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation ( ) const

pure virtual

Returns: The LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite().

◆ clone()

virtual AlignedPhyloLikelihoodInterface* bpp::AlignedPhyloLikelihoodInterface::clone ( ) const

pure virtual

Implements bpp::PhyloLikelihoodInterface.

Implemented in bpp::SequencePhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodSetInterface, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::SingleDataPhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

◆ context() [1/2]

virtual const Context& bpp::PhyloLikelihoodInterface::context ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/2]

virtual Context& bpp::PhyloLikelihoodInterface::context ( )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ getAlignedLikelihoodCalculation()

virtual std::shared_ptr<AlignedLikelihoodCalculation> bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation ( ) const

pure virtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite(), and bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite().

◆ getBranchLengthParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getBranchLengthParameters ( ) const

pure virtualinherited

Get the independent branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

Referenced by bpp::BppPhylogeneticsApplication::displayParameters().

◆ getDerivableParameters()

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

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getLikelihoodCalculation()

virtual std::shared_ptr<LikelihoodCalculation> bpp::PhyloLikelihoodInterface::getLikelihoodCalculation ( ) const

pure virtualinherited

Returns: A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by bpp::AbstractPhyloLikelihood::getLikelihoodNode().

◆ getLikelihoodForASite()

virtual DataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodForASite ( size_t site ) const

pure virtual

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood().

◆ getLikelihoodNode()

virtual ValueRef<DataLik> bpp::PhyloLikelihoodInterface::getLikelihoodNode ( ) const

pure virtualinherited

Returns: the LikDF node where the Likelihood is computed.

Implemented in bpp::AbstractPhyloLikelihood.

◆ getLikelihoodPerSite()

virtual VDataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtual

Get the likelihood for each site.

Returns: A vector with all site likelihoods.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

◆ getLogLikelihood()

double bpp::PhyloLikelihoodInterface::getLogLikelihood ( ) const

inlineinherited

Get the logarithm of the likelihood for the whole dataset.

Returns: The logarithm of the likelihood of the dataset.

Definition at line 66 of file PhyloLikelihood.h.

References bpp::SecondOrderDerivable::getValue().

◆ getLogLikelihoodForASite()

virtual double bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite ( size_t site ) const

pure virtual

Get the log likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns: The (D)log likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

◆ getNonDerivableParameters()

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

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getNumberOfSites()

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

pure virtual

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OnABranchPhyloLikelihood, and bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::HmmPhyloAlphabet::HmmPhyloAlphabet(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

◆ getRateDistributionParameters()

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

pure virtualinherited

Get the independent parameters associated to the rate distribution(s).

Returns: A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getRootFrequenciesParameters()

virtual ParameterList bpp::PhyloLikelihoodInterface::getRootFrequenciesParameters ( ) const

pure virtualinherited

Get the independent parameters associated to the root frequencies(s).

Returns: A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getSubstitutionModelParameters()

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

pure virtualinherited

Get the independent parameters associated to substitution model(s).

Returns: A ParameterList.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ isInitialized()

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

pure virtualinherited

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

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood, and bpp::AbstractPhyloLikelihood.

◆ likelihoodCalculation()

virtual LikelihoodCalculation& bpp::PhyloLikelihoodInterface::likelihoodCalculation ( ) const

pure virtualinherited

Returns: The LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Friends And Related Function Documentation

◆ AlignedPhyloLikelihoodSet

friend class AlignedPhyloLikelihoodSet

friend

Definition at line 102 of file AlignedPhyloLikelihood.h.

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihood.h

Public Member Functions

Protected Member Functions

Friends

Detailed Description

Constructor & Destructor Documentation

◆ AlignedPhyloLikelihoodInterface()

◆ ~AlignedPhyloLikelihoodInterface()

Member Function Documentation

◆ alignedLikelihoodCalculation()

◆ clone()

◆ context() [1/2]

◆ context() [2/2]

◆ getAlignedLikelihoodCalculation()

◆ getBranchLengthParameters()

◆ getDerivableParameters()

◆ getLikelihoodCalculation()

◆ getLikelihoodForASite()

◆ getLikelihoodNode()

◆ getLikelihoodPerSite()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getNonDerivableParameters()

◆ getNumberOfSites()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSubstitutionModelParameters()

◆ isInitialized()

◆ likelihoodCalculation()

Friends And Related Function Documentation

◆ AlignedPhyloLikelihoodSet