Joint interface SetOf+Aligned PhylLikelihood. More...

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

Inheritance diagram for bpp::AlignedPhyloLikelihoodSetInterface:

Collaboration diagram for bpp::AlignedPhyloLikelihoodSetInterface:

Public Member Functions
AlignedPhyloLikelihoodSetInterface *	clone () const override=0

virtual std::shared_ptr< const AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl) const =0

virtual std::shared_ptr< AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl)=0

virtual const AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl) const =0

virtual AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl)=0

virtual DataLik	getLikelihoodForASiteForAPhyloLikelihood (size_t site, size_t nPhyl) const =0
	Get the likelihood for a site for an aligned phyloLikelihood. More...

virtual double	getLogLikelihoodForASiteForAPhyloLikelihood (size_t site, size_t nPhyl) const =0
	Get the log likelihood for a site for an aligned phyloLikelihood. More...

virtual std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer ()=0

virtual std::shared_ptr< const PhyloLikelihoodContainer >	getPhyloContainer () const =0

virtual const std::vector< size_t > &	getNumbersOfPhyloLikelihoods () const =0

virtual bool	addPhyloLikelihood (size_t nPhyl, const std::string &suff="")=0
	adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood. More...

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 PhyloLikelihood storage.
virtual bool	hasPhyloLikelihood (size_t nPhyl)=0

virtual std::shared_ptr< const PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) const =0

virtual std::shared_ptr< PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl)=0

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...

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...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

Detailed Description

Joint interface SetOf+Aligned PhylLikelihood.

Definition at line 20 of file AlignedPhyloLikelihoodSet.h.

Member Function Documentation

◆ addPhyloLikelihood()

virtual bool bpp::PhyloLikelihoodSetInterface::addPhyloLikelihood	(	size_t	nPhyl,
		const std::string &	suff = `""`
	)

pure virtualinherited

adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood.

Parameters

nPhyl	number of the phylolikelihood
suff	for parameters names if use specific parameters names

Returns: if the PhyloLikelihood has been added.

Implemented in bpp::AbstractPhyloLikelihoodSet, and bpp::AbstractAlignedPhyloLikelihoodSet.

◆ 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().

◆ alignedPhyloLikelihood() [1/2]

virtual const AlignedPhyloLikelihoodInterface& bpp::AlignedPhyloLikelihoodSetInterface::alignedPhyloLikelihood ( size_t nPhyl ) const

pure virtual

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

◆ alignedPhyloLikelihood() [2/2]

virtual AlignedPhyloLikelihoodInterface& bpp::AlignedPhyloLikelihoodSetInterface::alignedPhyloLikelihood ( size_t nPhyl )

pure virtual

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

◆ clone()

AlignedPhyloLikelihoodSetInterface* bpp::AlignedPhyloLikelihoodSetInterface::clone ( ) const

overridepure virtual

Implements bpp::AlignedPhyloLikelihoodInterface.

Implemented in bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, 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 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().

◆ getAlignedPhyloLikelihood() [1/2]

virtual std::shared_ptr<const AlignedPhyloLikelihoodInterface> bpp::AlignedPhyloLikelihoodSetInterface::getAlignedPhyloLikelihood ( size_t nPhyl ) const

pure virtual

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

Referenced by bpp::HmmPhyloAlphabet::HmmPhyloAlphabet().

◆ getAlignedPhyloLikelihood() [2/2]

virtual std::shared_ptr<AlignedPhyloLikelihoodInterface> bpp::AlignedPhyloLikelihoodSetInterface::getAlignedPhyloLikelihood ( size_t nPhyl )

pure virtual

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

◆ 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 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().

◆ getLikelihoodForASiteForAPhyloLikelihood()

virtual DataLik bpp::AlignedPhyloLikelihoodSetInterface::getLikelihoodForASiteForAPhyloLikelihood	(	size_t	site,
		size_t	nPhyl
	)		const

pure virtual

Get the likelihood for a site for an aligned phyloLikelihood.

Parameters

site	The site index to analyse.
nPhyl	the phyloLikelihood index.

Returns: The likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

◆ 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().

◆ getLogLikelihoodForASiteForAPhyloLikelihood()

virtual double bpp::AlignedPhyloLikelihoodSetInterface::getLogLikelihoodForASiteForAPhyloLikelihood	(	size_t	site,
		size_t	nPhyl
	)		const

pure virtual

Get the log likelihood for a site for an aligned phyloLikelihood.

Parameters

site	The site index to analyse.
nPhyl	the phyloLikelihood index.

Returns: The log likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihoodSet.

Referenced by 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 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().

◆ getNumbersOfPhyloLikelihoods()

virtual const std::vector<size_t>& bpp::PhyloLikelihoodSetInterface::getNumbersOfPhyloLikelihoods ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

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

◆ getPhyloContainer() [1/2]

virtual std::shared_ptr<const PhyloLikelihoodContainer> bpp::PhyloLikelihoodSetInterface::getPhyloContainer ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloContainer() [2/2]

virtual std::shared_ptr<PhyloLikelihoodContainer> bpp::PhyloLikelihoodSetInterface::getPhyloContainer ( )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloLikelihood() [1/2]

virtual std::shared_ptr<const PhyloLikelihoodInterface> bpp::PhyloLikelihoodSetInterface::getPhyloLikelihood ( size_t nPhyl ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloLikelihood() [2/2]

virtual std::shared_ptr<PhyloLikelihoodInterface> bpp::PhyloLikelihoodSetInterface::getPhyloLikelihood ( size_t nPhyl )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ 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.

◆ hasPhyloLikelihood()

virtual bool bpp::PhyloLikelihoodSetInterface::hasPhyloLikelihood ( size_t nPhyl )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ 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.

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/AlignedPhyloLikelihoodSet.h

Public Member Functions

Protected Member Functions

Detailed Description

Member Function Documentation

◆ addPhyloLikelihood()

◆ alignedLikelihoodCalculation()

◆ alignedPhyloLikelihood() [1/2]

◆ alignedPhyloLikelihood() [2/2]

◆ clone()

◆ context() [1/2]

◆ context() [2/2]

◆ getAlignedLikelihoodCalculation()

◆ getAlignedPhyloLikelihood() [1/2]

◆ getAlignedPhyloLikelihood() [2/2]

◆ getBranchLengthParameters()

◆ getDerivableParameters()

◆ getLikelihoodCalculation()

◆ getLikelihoodForASite()

◆ getLikelihoodForASiteForAPhyloLikelihood()

◆ getLikelihoodNode()

◆ getLikelihoodPerSite()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getLogLikelihoodForASiteForAPhyloLikelihood()

◆ getNonDerivableParameters()

◆ getNumberOfSites()

◆ getNumbersOfPhyloLikelihoods()

◆ getPhyloContainer() [1/2]

◆ getPhyloContainer() [2/2]

◆ getPhyloLikelihood() [1/2]

◆ getPhyloLikelihood() [2/2]

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSubstitutionModelParameters()

◆ hasPhyloLikelihood()

◆ isInitialized()

◆ likelihoodCalculation()