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

Inheritance diagram for bpp::AbstractSequencePhyloLikelihood:

Collaboration diagram for bpp::AbstractSequencePhyloLikelihood:

Public Member Functions
	AbstractSequencePhyloLikelihood (Context &context, std::shared_ptr< SequenceEvolution > se, size_t nSE=0, size_t nData=0)

	AbstractSequencePhyloLikelihood (const AbstractSequencePhyloLikelihood &aspl)

AbstractSequencePhyloLikelihood &	operator= (const AbstractSequencePhyloLikelihood &aspl)

const SequenceEvolution &	sequenceEvolution () const override
	The Sequence Evolution. More...

std::shared_ptr< const SequenceEvolution >	getSequenceEvolution () const override

const size_t	getSequenceEvolutionNumber () const override

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

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

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

void	setNData (size_t nData)

size_t	getNumberOfStates () const
	Get the number the states. More...

size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...

DataLik	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site (on uncompressed data) More...

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

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

virtual bool	isInitialized () const override
	Sets the computeLikelihoods_ to true. More...

const Context &	context () const override

Context &	context () override

ValueRef< DataLik >	getLikelihoodNode () const override

virtual void	enableSecondOrderDerivatives (bool yn) override

bool	enableSecondOrderDerivatives () const override

double	getSecondOrderDerivative (const std::string &variable) const override

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const override

virtual void	enableFirstOrderDerivatives (bool yn) override
	Tell if derivatives must be computed: for Function inheritance. More...

bool	enableFirstOrderDerivatives () const override

double	getFirstOrderDerivative (const std::string &variable) const override

void	setParameters (const ParameterList &parameters) override

double	getValue () const override

void	shareParameters (const ParameterList &variableNodes)
	Share Parameters, that are DF_parameters. More...

ValueRef< DataLik >	firstOrderDerivativeNode (const std::string &variable) const

ValueRef< DataLik >	secondOrderDerivativeNode (const std::string &variable1, const std::string &variable2) const

the Likelihood interface
std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the dataset. More...

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...

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
SequencePhyloLikelihoodInterface *	clone () const override=0

virtual ParameterList &	getParameters_ ()=0

void	setNumberOfSites (size_t nbSites)

Node_DF &	accessVariableNode (const std::string &name) const

Static Protected Member Functions
static Node_DF &	accessVariableNode (const Parameter &param)

Protected Attributes
std::shared_ptr< SequenceEvolution >	seqEvol_
	the Sequence Evolution More...

size_t	nSeqEvol_
	the Sequence Evolution number More...

size_t	nbStates_

size_t	nData_
	Number of the concerned data. More...

size_t	nbSites_

Context &	context_

DataLik	minusLogLik_
	the value More...

std::unordered_map< std::string, ValueRef< DataLik > >	firstOrderDerivativeNodes_
	For Dataflow computing. More...

std::unordered_map< std::pair< std::string, std::string >, ValueRef< DataLik >, StringPairHash >	secondOrderDerivativeNodes_

Detailed Description

Definition at line 49 of file SequencePhyloLikelihood.h.

Constructor & Destructor Documentation

◆ AbstractSequencePhyloLikelihood() [1/2]

bpp::AbstractSequencePhyloLikelihood::AbstractSequencePhyloLikelihood	(	Context &	context,
		std::shared_ptr< SequenceEvolution >	se,
		size_t	nSE = `0`,
		size_t	nData = `0`
	)

inline

Definition at line 65 of file SequencePhyloLikelihood.h.

◆ AbstractSequencePhyloLikelihood() [2/2]

bpp::AbstractSequencePhyloLikelihood::AbstractSequencePhyloLikelihood ( const AbstractSequencePhyloLikelihood & aspl )

inline

Definition at line 78 of file SequencePhyloLikelihood.h.

Member Function Documentation

◆ accessVariableNode() [1/2]

static Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const Parameter & param )

inlinestaticprotectedinherited

Definition at line 188 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

◆ accessVariableNode() [2/2]

Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const std::string & name ) const

inlineprotectedinherited

Definition at line 193 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), and bpp::SecondOrderDerivable::parameter().

◆ 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 virtualinherited

Implements bpp::SingleDataPhyloLikelihoodInterface.

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

◆ context() [1/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/4]

const Context& bpp::AbstractPhyloLikelihood::context ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [3/4]

Context& bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [4/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( bool yn )

inlineoverridevirtualinherited

Tell if derivatives must be computed: for Function inheritance.

Implements bpp::SecondOrderDerivable.

Definition at line 113 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( bool yn )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

◆ firstOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode ( const std::string & variable ) const

inlineinherited

Definition at line 139 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_, and bpp::AbstractPhyloLikelihood::getLikelihoodNode().

Referenced by bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

◆ 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()

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

inlineoverridevirtual

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 116 of file SequencePhyloLikelihood.h.

References seqEvol_.

◆ 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.

◆ getFirstOrderDerivative()

double bpp::AbstractPhyloLikelihood::getFirstOrderDerivative ( const std::string & variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 131 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode().

◆ 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() [1/2]

DataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite ( size_t site ) const

inlinevirtualinherited

Get the likelihood for a site (on uncompressed data)

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 143 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation(), and bpp::AlignedLikelihoodCalculation::getLikelihoodForASite().

◆ getLikelihoodForASite() [2/2]

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() [1/2]

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

pure virtualinherited

Returns: the LikDF node where the Likelihood is computed.

Implemented in bpp::AbstractPhyloLikelihood.

◆ getLikelihoodNode() [2/2]

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::getLikelihoodNode ( ) const

inlineoverridevirtualinherited

Returns: the LikDF node where the Likelihood is computed.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 100 of file AbstractPhyloLikelihood.h.

References bpp::PhyloLikelihoodInterface::getLikelihoodCalculation().

Referenced by bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::getValue().

◆ getLikelihoodPerSite() [1/2]

VDataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite ( ) const

inlinevirtualinherited

Get the likelihood for each site.

Returns: A vector with all site likelihoods.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 167 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

Referenced by bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), and bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite().

◆ getLikelihoodPerSite() [2/2]

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() [1/2]

double bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite ( size_t site ) const

inlinevirtualinherited

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.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 154 of file AlignedPhyloLikelihood.h.

References bpp::convert(), and bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

◆ getLogLikelihoodForASite() [2/2]

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() [1/2]

size_t bpp::AbstractSingleDataPhyloLikelihood::getNData ( ) const

inlinevirtualinherited

Get the number of dataset concerned.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 126 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

◆ getNData() [2/2]

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() [1/2]

size_t bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Implements bpp::AlignedPhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, and bpp::OnABranchPhyloLikelihood.

Definition at line 135 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet(), bpp::AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood(), bpp::OneProcessSequencePhyloLikelihood::getClassWithMaxPostProbPerSite(), bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite(), and bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies().

◆ getNumberOfSites() [2/2]

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() [1/2]

size_t bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Get the number the states.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 136 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nbStates_.

◆ getNumberOfStates() [2/2]

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.

◆ getSecondOrderDerivative() [1/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative ( const std::string & variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 155 of file AbstractPhyloLikelihood.h.

◆ getSecondOrderDerivative() [2/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 160 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

◆ getSequenceEvolution()

std::shared_ptr<const SequenceEvolution> bpp::AbstractSequencePhyloLikelihood::getSequenceEvolution ( ) const

inlineoverridevirtual

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 102 of file SequencePhyloLikelihood.h.

References seqEvol_.

◆ getSequenceEvolutionNumber()

const size_t bpp::AbstractSequencePhyloLikelihood::getSequenceEvolutionNumber ( ) const

inlineoverridevirtual

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 107 of file SequencePhyloLikelihood.h.

References nSeqEvol_.

◆ 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.

◆ getValue()

double bpp::AbstractPhyloLikelihood::getValue ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 124 of file AbstractPhyloLikelihood.h.

References bpp::convert(), bpp::AbstractPhyloLikelihood::getLikelihoodNode(), and bpp::AbstractPhyloLikelihood::minusLogLik_.

◆ isInitialized() [1/2]

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.

◆ isInitialized() [2/2]

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

inlineoverridevirtualinherited

Sets the computeLikelihoods_ to true.

Implements bpp::PhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, and bpp::MultiProcessSequencePhyloLikelihood.

Definition at line 81 of file AbstractPhyloLikelihood.h.

◆ 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.

◆ operator=()

AbstractSequencePhyloLikelihood& bpp::AbstractSequencePhyloLikelihood::operator= ( const AbstractSequencePhyloLikelihood & aspl )

inline

Definition at line 84 of file SequencePhyloLikelihood.h.

References nSeqEvol_, bpp::AbstractSingleDataPhyloLikelihood::operator=(), and seqEvol_.

Referenced by bpp::AbstractParametrizableSequencePhyloLikelihood::operator=(), and bpp::PartitionProcessPhyloLikelihood::operator=().

◆ secondOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlineinherited

Definition at line 168 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_.

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

◆ sequenceEvolution()

const SequenceEvolution& bpp::AbstractSequencePhyloLikelihood::sequenceEvolution ( ) const

inlineoverridevirtual

The Sequence Evolution.

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 97 of file SequencePhyloLikelihood.h.

References seqEvol_.

◆ setData() [1/2]

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

inlinevirtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

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

Implements bpp::SingleDataPhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::MultiProcessSequencePhyloLikelihood, and bpp::PartitionProcessPhyloLikelihood.

Definition at line 119 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nbStates_, bpp::AbstractSingleDataPhyloLikelihood::nData_, and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

Referenced by bpp::PartitionProcessPhyloLikelihood::setData(), bpp::MultiProcessSequencePhyloLikelihood::setData(), bpp::OneProcessSequencePhyloLikelihood::setData(), bpp::AbstractParametrizableSequencePhyloLikelihood::setData(), and bpp::SingleProcessPhyloLikelihood::setData().

◆ setData() [2/2]

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.

◆ setNData()

void bpp::AbstractSingleDataPhyloLikelihood::setNData ( size_t nData )

inlineinherited

Definition at line 131 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

◆ setNumberOfSites()

void bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites ( size_t nbSites )

inlineprotectedinherited

Definition at line 173 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet(), bpp::AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

◆ setParameters()

void bpp::AbstractPhyloLikelihood::setParameters ( const ParameterList & parameters )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 95 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::setParametersValues().

◆ shareParameters()

void bpp::AbstractPhyloLikelihood::shareParameters ( const ParameterList & variableNodes )

inlineinherited

Share Parameters, that are DF_parameters.

Definition at line 90 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::getParameters_(), and bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractPhyloLikelihood::AbstractPhyloLikelihood(), and bpp::AbstractPhyloLikelihood::operator=().

Member Data Documentation

◆ context_

Context& bpp::AbstractPhyloLikelihood::context_

protectedinherited

Definition at line 34 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), bpp::AbstractPhyloLikelihood::operator=(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

◆ firstOrderDerivativeNodes_

std::unordered_map<std::string, ValueRef<DataLik> > bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_

mutableprotectedinherited

For Dataflow computing.

Definition at line 44 of file AbstractPhyloLikelihood.h.

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

◆ minusLogLik_

DataLik bpp::AbstractPhyloLikelihood::minusLogLik_

mutableprotectedinherited

the value

Definition at line 39 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::getValue(), and bpp::AbstractPhyloLikelihood::operator=().

◆ nbSites_

size_t bpp::AbstractAlignedPhyloLikelihood::nbSites_

protectedinherited

Definition at line 111 of file AlignedPhyloLikelihood.h.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::AbstractAlignedPhyloLikelihood::operator=(), and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

◆ nbStates_

size_t bpp::AbstractSingleDataPhyloLikelihood::nbStates_

protectedinherited

Definition at line 87 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

◆ nData_

size_t bpp::AbstractSingleDataPhyloLikelihood::nData_

protectedinherited

Number of the concerned data.

Definition at line 92 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNData(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), bpp::AbstractSingleDataPhyloLikelihood::setData(), and bpp::AbstractSingleDataPhyloLikelihood::setNData().

◆ nSeqEvol_

size_t bpp::AbstractSequencePhyloLikelihood::nSeqEvol_

protected

the Sequence Evolution number

Definition at line 62 of file SequencePhyloLikelihood.h.

Referenced by getSequenceEvolutionNumber(), and operator=().

◆ secondOrderDerivativeNodes_

std::unordered_map<std::pair<std::string, std::string>, ValueRef<DataLik>, StringPairHash> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_

mutableprotectedinherited

Definition at line 48 of file AbstractPhyloLikelihood.h.

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

◆ seqEvol_

std::shared_ptr<SequenceEvolution> bpp::AbstractSequencePhyloLikelihood::seqEvol_

protected

the Sequence Evolution

Definition at line 57 of file SequencePhyloLikelihood.h.

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/SequencePhyloLikelihood.h

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractSequencePhyloLikelihood() [1/2]

◆ AbstractSequencePhyloLikelihood() [2/2]

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ alignedLikelihoodCalculation()

◆ clone()

◆ context() [1/4]

◆ context() [2/4]

◆ context() [3/4]

◆ context() [4/4]

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ enableSecondOrderDerivatives() [1/2]

◆ enableSecondOrderDerivatives() [2/2]

◆ firstOrderDerivativeNode()

◆ getAlignedLikelihoodCalculation()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getData()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getLikelihoodCalculation()

◆ getLikelihoodForASite() [1/2]

◆ getLikelihoodForASite() [2/2]

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLikelihoodPerSite() [1/2]

◆ getLikelihoodPerSite() [2/2]

◆ getLogLikelihood()

◆ getLogLikelihoodForASite() [1/2]

◆ getLogLikelihoodForASite() [2/2]

◆ getNData() [1/2]

◆ getNData() [2/2]

◆ getNonDerivableParameters()

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumberOfStates() [1/2]

◆ getNumberOfStates() [2/2]

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSequenceEvolution()

◆ getSequenceEvolutionNumber()

◆ getSubstitutionModelParameters()

◆ getValue()

◆ isInitialized() [1/2]

◆ isInitialized() [2/2]

◆ likelihoodCalculation()

◆ operator=()

◆ secondOrderDerivativeNode()

◆ sequenceEvolution()

◆ setData() [1/2]

◆ setData() [2/2]

◆ setNData()

◆ setNumberOfSites()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_

◆ minusLogLik_

◆ nbSites_

◆ nbStates_

◆ nData_

◆ nSeqEvol_

◆ secondOrderDerivativeNodes_

◆ seqEvol_