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

Inheritance diagram for bpp::AbstractParametrizableSequencePhyloLikelihood:

Collaboration diagram for bpp::AbstractParametrizableSequencePhyloLikelihood:

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

	AbstractParametrizableSequencePhyloLikelihood (const AbstractParametrizableSequencePhyloLikelihood &apspl)

AbstractParametrizableSequencePhyloLikelihood &	operator= (const AbstractParametrizableSequencePhyloLikelihood &apspl)

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

void	setNamespace (const std::string &nameSpace) override

ParameterList	getNonDerivableParameters () const override

ParameterList	getDerivableParameters () const override

ParameterList	getBranchLengthParameters () const override
	Get the independent branch lengths parameters. More...

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

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

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

virtual ParameterList	getSubstitutionProcessParameters () const

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

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

const size_t	getSequenceEvolutionNumber () const override

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

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 LikelihoodCalculation &	likelihoodCalculation () const =0

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

virtual void	enableSecondOrderDerivatives (bool yn)=0

virtual bool	enableSecondOrderDerivatives () const=0

virtual void	enableSecondOrderDerivatives (bool yn) override

bool	enableSecondOrderDerivatives () const override

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

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

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

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

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

bool	enableFirstOrderDerivatives () const override

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

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

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

virtual void	setParameters (const ParameterList &parameters)=0

void	setParameters (const ParameterList &parameters) override

virtual double	getValue () const=0

double	getValue () const override

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 std::string	getNamespace () const=0

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

void	setNData (size_t nData)

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

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

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

virtual Clonable *	clone () const=0

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

The data functions
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...

Protected Member Functions
virtual void	fireParameterChanged (const ParameterList &parameters) override

SequencePhyloLikelihoodInterface *	clone () const override=0

virtual ParameterList &	getParameters_ ()=0

void	setNumberOfSites (size_t nbSites)

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

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

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_

Private Attributes
ParameterList	parameters_

std::string	prefix_

Detailed Description

Definition at line 126 of file SequencePhyloLikelihood.h.

Constructor & Destructor Documentation

◆ AbstractParametrizableSequencePhyloLikelihood() [1/2]

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

inline

Definition at line 131 of file SequencePhyloLikelihood.h.

References bpp::AbstractParametrizable::addParameters_().

◆ AbstractParametrizableSequencePhyloLikelihood() [2/2]

bpp::AbstractParametrizableSequencePhyloLikelihood::AbstractParametrizableSequencePhyloLikelihood ( const AbstractParametrizableSequencePhyloLikelihood & apspl )

inline

Definition at line 144 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.

◆ fireParameterChanged()

virtual void bpp::AbstractParametrizableSequencePhyloLikelihood::fireParameterChanged ( const ParameterList & parameters )

inlineoverrideprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Reimplemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, and bpp::AutoCorrelationProcessPhyloLikelihood.

Definition at line 157 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

Referenced by bpp::AutoCorrelationProcessPhyloLikelihood::fireParameterChanged(), and bpp::HmmProcessPhyloLikelihood::fireParameterChanged().

◆ 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

inlineoverridevirtualinherited

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 bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ getBranchLengthParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getBranchLengthParameters ( ) const

inlineoverridevirtual

Get the independent branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 184 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ 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()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 179 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ 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()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getNonDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 174 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ 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()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 194 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ getRootFrequenciesParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getRootFrequenciesParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 189 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ 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

inlineoverridevirtualinherited

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 102 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ getSequenceEvolutionNumber()

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

inlineoverridevirtualinherited

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 107 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::nSeqEvol_.

◆ getSubstitutionModelParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getSubstitutionModelParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 199 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ getSubstitutionProcessParameters()

virtual ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getSubstitutionProcessParameters ( ) const

inlinevirtual

Definition at line 204 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ 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=()

AbstractParametrizableSequencePhyloLikelihood& bpp::AbstractParametrizableSequencePhyloLikelihood::operator= ( const AbstractParametrizableSequencePhyloLikelihood & apspl )

inline

Definition at line 149 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::operator=().

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