PhyloLikelihoods based on Sequence Evolution class, ie for which there is a (set of) processes able to build a sequence. More...

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

Inheritance diagram for bpp::SequencePhyloLikelihoodInterface:

Collaboration diagram for bpp::SequencePhyloLikelihoodInterface:

Public Member Functions
virtual const SequenceEvolution &	sequenceEvolution () const =0
	The Sequence Evolution. More...

virtual std::shared_ptr< const SequenceEvolution >	getSequenceEvolution () const =0

virtual const size_t	getSequenceEvolutionNumber () 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 void	setData (std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0)=0
	Set the dataset for which the likelihood must be evaluated. More...

virtual std::shared_ptr< const AlignmentDataInterface >	getData () const =0
	Get the dataset for which the likelihood must be evaluated. More...

virtual size_t	getNData () const =0
	Get the number of dataset concerned. More...

virtual size_t	getNumberOfStates () const =0
	Get the number the states. More...

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the dataset. More...

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	~SequencePhyloLikelihoodInterface ()

SequencePhyloLikelihoodInterface *	clone () const override=0

virtual ParameterList &	getParameters_ ()=0

Detailed Description

PhyloLikelihoods based on Sequence Evolution class, ie for which there is a (set of) processes able to build a sequence.

Interface

Definition at line 29 of file SequencePhyloLikelihood.h.

Constructor & Destructor Documentation

◆ ~SequencePhyloLikelihoodInterface()

virtual bpp::SequencePhyloLikelihoodInterface::~SequencePhyloLikelihoodInterface ( )

inlineprotectedvirtual

Definition at line 33 of file SequencePhyloLikelihood.h.

Member Function Documentation

◆ alignedLikelihoodCalculation()

virtual AlignedLikelihoodCalculation& bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation ( ) 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::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

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

◆ clone()

SequencePhyloLikelihoodInterface* bpp::SequencePhyloLikelihoodInterface::clone ( ) const

overrideprotectedpure virtual

Implements bpp::SingleDataPhyloLikelihoodInterface.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, and bpp::AutoCorrelationProcessPhyloLikelihood.

◆ 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 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::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

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

◆ getAlphabet()

virtual std::shared_ptr<const Alphabet> bpp::SingleDataPhyloLikelihoodInterface::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractSequencePhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, and bpp::MultiProcessSequencePhyloLikelihood.

◆ 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().

◆ getData()

virtual std::shared_ptr<const AlignmentDataInterface> bpp::SingleDataPhyloLikelihoodInterface::getData ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

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

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, and bpp::MultiProcessSequencePhyloLikelihood.

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

◆ 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 virtualinherited

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 virtualinherited

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 virtualinherited

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().

◆ getNData()

virtual size_t bpp::SingleDataPhyloLikelihoodInterface::getNData ( ) const

pure virtualinherited

Get the number of dataset concerned.

Implemented in bpp::AbstractSingleDataPhyloLikelihood.

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

◆ 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 virtualinherited

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().

◆ getNumberOfStates()

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

pure virtualinherited

Get the number the states.

Implemented in bpp::AbstractSingleDataPhyloLikelihood.

◆ 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.

◆ getSequenceEvolution()

virtual std::shared_ptr<const SequenceEvolution> bpp::SequencePhyloLikelihoodInterface::getSequenceEvolution ( ) const

pure virtual

Implemented in bpp::AbstractSequencePhyloLikelihood.

◆ getSequenceEvolutionNumber()

virtual const size_t bpp::SequencePhyloLikelihoodInterface::getSequenceEvolutionNumber ( ) const

pure virtual

Implemented in bpp::AbstractSequencePhyloLikelihood.

◆ 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.

◆ sequenceEvolution()

virtual const SequenceEvolution& bpp::SequencePhyloLikelihoodInterface::sequenceEvolution ( ) const

pure virtual

The Sequence Evolution.

Implemented in bpp::AbstractSequencePhyloLikelihood.

◆ setData()

virtual void bpp::SingleDataPhyloLikelihoodInterface::setData	(	std::shared_ptr< const AlignmentDataInterface >	sites,
		size_t	nData = `0`
	)

pure virtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

sites	The data set to use.
nData	the number of the data

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood, bpp::AbstractSingleDataPhyloLikelihood, and bpp::PartitionProcessPhyloLikelihood.

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/SequencePhyloLikelihood.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ~SequencePhyloLikelihoodInterface()

Member Function Documentation

◆ alignedLikelihoodCalculation()

◆ clone()

◆ context() [1/2]

◆ context() [2/2]

◆ getAlignedLikelihoodCalculation()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getData()

◆ getDerivableParameters()

◆ getLikelihoodCalculation()

◆ getLikelihoodForASite()

◆ getLikelihoodNode()

◆ getLikelihoodPerSite()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getNData()

◆ getNonDerivableParameters()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSequenceEvolution()

◆ getSequenceEvolutionNumber()

◆ getSubstitutionModelParameters()

◆ isInitialized()

◆ likelihoodCalculation()

◆ sequenceEvolution()

◆ setData()