Likelihood framework based on a hmm of simple likelihoods. More...

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

Inheritance diagram for bpp::HmmProcessPhyloLikelihood:

Collaboration diagram for bpp::HmmProcessPhyloLikelihood:

Public Member Functions
	HmmProcessPhyloLikelihood (std::shared_ptr< const AlignmentDataInterface > data, std::shared_ptr< HmmSequenceEvolution > processSeqEvol, std::shared_ptr< CollectionNodes > collNodes, size_t nSeqEvol=0, size_t nData=0)

virtual	~HmmProcessPhyloLikelihood ()

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

void	fireParameterChanged (const ParameterList &parameters) override

std::shared_ptr< LikelihoodCalculationSingleProcess >	getLikelihoodCalculationForAProcess (size_t p)

DataLik	getLikelihoodForASiteForAProcess (size_t site, size_t p) const
	Get the likelihood for a site for a process. More...

VVdouble	getLikelihoodPerSitePerProcess () const

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

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

size_t	getNumberOfSubstitutionProcess () const
	Return the number of process used for computation. More...

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...

const Context &	context () const override

Context &	context () override

ValueRef< DataLik >	getLikelihoodNode () const override

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

bool	hasParameter (const std::string &name) const override

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

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

const Parameter &	parameter (const std::string &name) const override

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

double	getParameterValue (const std::string &name) const override

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParameterValue (const std::string &name, double value) override

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

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

void	removeConstraint (const std::string &name) override

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

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

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

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

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

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

The likelihood functions.
LikelihoodCalculation &	likelihoodCalculation () const override

std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const override

AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const override

std::shared_ptr< AlignedLikelihoodCalculation >	getAlignedLikelihoodCalculation () const override

VVdouble	getPosteriorProbabilitiesPerSitePerProcess () const override

const Eigen::MatrixXd &	getHmmTransitionMatrix () const

The Likelihood interface.
std::shared_ptr< const AlignmentDataInterface >	getData () const override
	Get the dataset for which the likelihood must be evaluated. More...

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

The data functions
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 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 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
	HmmProcessPhyloLikelihood (const HmmProcessPhyloLikelihood &mlc)

HmmProcessPhyloLikelihood *	clone () const override

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

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

Protected Attributes
std::vector< std::shared_ptr< LikelihoodCalculationSingleProcess > >	vLikCal_

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
std::shared_ptr< HmmPhyloEmissionProbabilities >	Hpep_

std::shared_ptr< HmmLikelihood_DF >	hmm_
	LikelihoodCalculation in context of HMM. More...

std::shared_ptr< MultiProcessSequenceEvolution >	mSeqEvol_
	to avoid the dynamic casts More...

ParameterList	parameters_

std::string	prefix_

Detailed Description

Likelihood framework based on a hmm of simple likelihoods.

The resulting likelihood is the likelihood of the given Hmm with the site emission probabilities proportional to the computed likelihoods of the process.

Definition at line 30 of file HmmProcessPhyloLikelihood.h.

Constructor & Destructor Documentation

◆ HmmProcessPhyloLikelihood() [1/2]

HmmProcessPhyloLikelihood::HmmProcessPhyloLikelihood	(	std::shared_ptr< const AlignmentDataInterface >	data,
		std::shared_ptr< HmmSequenceEvolution >	processSeqEvol,
		std::shared_ptr< CollectionNodes >	collNodes,
		size_t	nSeqEvol = `0`,
		size_t	nData = `0`
	)

Definition at line 15 of file HmmProcessPhyloLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractPhyloLikelihood::context(), hmm_, and Hpep_.

Referenced by clone().

◆ HmmProcessPhyloLikelihood() [2/2]

bpp::HmmProcessPhyloLikelihood::HmmProcessPhyloLikelihood ( const HmmProcessPhyloLikelihood & mlc )

inlineprotected

Definition at line 50 of file HmmProcessPhyloLikelihood.h.

◆ ~HmmProcessPhyloLikelihood()

virtual bpp::HmmProcessPhyloLikelihood::~HmmProcessPhyloLikelihood ( )

inlinevirtual

Definition at line 63 of file HmmProcessPhyloLikelihood.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()

AlignedLikelihoodCalculation& bpp::HmmProcessPhyloLikelihood::alignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 85 of file HmmProcessPhyloLikelihood.h.

References hmm_.

◆ clone()

HmmProcessPhyloLikelihood* bpp::HmmProcessPhyloLikelihood::clone ( ) const

inlineoverrideprotectedvirtual

Implements bpp::AbstractParametrizable.

Definition at line 60 of file HmmProcessPhyloLikelihood.h.

References HmmProcessPhyloLikelihood().

◆ 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_.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AutoCorrelationProcessPhyloLikelihood::AutoCorrelationProcessPhyloLikelihood(), HmmProcessPhyloLikelihood(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), bpp::MixtureProcessPhyloLikelihood::MixtureProcessPhyloLikelihood(), bpp::OneProcessSequencePhyloLikelihood::OneProcessSequencePhyloLikelihood(), and bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood().

◆ 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()

void HmmProcessPhyloLikelihood::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Reimplemented from bpp::AbstractParametrizableSequencePhyloLikelihood.

Definition at line 51 of file HmmProcessPhyloLikelihood.cpp.

References bpp::AbstractParametrizableSequencePhyloLikelihood::fireParameterChanged(), and hmm_.

◆ 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()

std::shared_ptr<AlignedLikelihoodCalculation> bpp::HmmProcessPhyloLikelihood::getAlignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 90 of file HmmProcessPhyloLikelihood.h.

References hmm_.

◆ getAlphabet()

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

inlineoverridevirtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 85 of file MultiProcessSequencePhyloLikelihood.h.

◆ getBranchLengthParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getBranchLengthParameters ( ) const

inlineoverridevirtualinherited

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()

std::shared_ptr<const AlignmentDataInterface> bpp::MultiProcessSequencePhyloLikelihood::getData ( ) const

inlineoverridevirtualinherited

Get the dataset for which the likelihood must be evaluated.

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

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 80 of file MultiProcessSequencePhyloLikelihood.h.

◆ getDerivableParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getDerivableParameters ( ) const

inlineoverridevirtualinherited

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().

◆ getHmmTransitionMatrix()

const Eigen::MatrixXd& bpp::HmmProcessPhyloLikelihood::getHmmTransitionMatrix ( ) const

inline

Definition at line 108 of file HmmProcessPhyloLikelihood.h.

References hmm_.

◆ getLikelihoodCalculation()

std::shared_ptr<LikelihoodCalculation> bpp::HmmProcessPhyloLikelihood::getLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 80 of file HmmProcessPhyloLikelihood.h.

References hmm_.

◆ getLikelihoodCalculationForAProcess()

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodCalculationForAProcess ( size_t p )

inlineinherited

Definition at line 95 of file MultiProcessSequencePhyloLikelihood.h.

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

◆ 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().

◆ getLikelihoodForASiteForAProcess()

DataLik bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodForASiteForAProcess	(	size_t	site,
		size_t	p
	)		const

inlineinherited

Get the likelihood for a site for a process.

Parameters

site	The site index to analyse.
p	the process index in the given order.

Returns: The likelihood for site site.

Definition at line 107 of file MultiProcessSequencePhyloLikelihood.h.

Referenced by bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess().

◆ 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.

◆ getLikelihoodPerSitePerProcess()

VVdouble MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess ( ) const

inherited

Definition at line 56 of file MultiProcessSequencePhyloLikelihood.cpp.

References bpp::convert(), bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodForASiteForAProcess(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), and bpp::MultiProcessSequencePhyloLikelihood::getNumberOfSubstitutionProcess().

Referenced by bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess().

◆ 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

inlineoverridevirtualinherited

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.

◆ getNumberOfSubstitutionProcess()

size_t bpp::MultiProcessSequencePhyloLikelihood::getNumberOfSubstitutionProcess ( ) const

inlineinherited

Return the number of process used for computation.

Definition at line 145 of file MultiProcessSequencePhyloLikelihood.h.

Referenced by bpp::MultiProcessSequencePhyloLikelihood::getLikelihoodPerSitePerProcess(), bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), and bpp::HmmPhyloAlphabet::HmmPhyloAlphabet().

◆ getPosteriorProbabilitiesPerSitePerProcess()

VVdouble bpp::HmmProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess ( ) const

inlineoverridevirtual

Implements bpp::MultiProcessSequencePhyloLikelihood.

Definition at line 100 of file HmmProcessPhyloLikelihood.h.

References bpp::copyEigenToBpp(), and hmm_.

◆ getRateDistributionParameters()

ParameterList bpp::AbstractParametrizableSequencePhyloLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtualinherited

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

inlineoverridevirtualinherited

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

inlineoverridevirtualinherited

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

inlinevirtualinherited

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()

bool bpp::MultiProcessSequencePhyloLikelihood::isInitialized ( ) const

inlineoverridevirtualinherited

Sets the computeLikelihoods_ to true.

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 122 of file MultiProcessSequencePhyloLikelihood.h.

◆ likelihoodCalculation()

LikelihoodCalculation& bpp::HmmProcessPhyloLikelihood::likelihoodCalculation ( ) const

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file HmmProcessPhyloLikelihood.h.

References hmm_.

◆ 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

inlineoverridevirtualinherited

The Sequence Evolution.

Implements bpp::SequencePhyloLikelihoodInterface.

Definition at line 97 of file SequencePhyloLikelihood.h.

References bpp::AbstractSequencePhyloLikelihood::seqEvol_.

◆ setData()

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

overridevirtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

sites	The data set to use.
nData	the number of the data (optional, default 0).

Reimplemented from bpp::AbstractSingleDataPhyloLikelihood.

Definition at line 44 of file MultiProcessSequencePhyloLikelihood.cpp.

References bpp::AbstractSingleDataPhyloLikelihood::setData(), and bpp::MultiProcessSequencePhyloLikelihood::vLikCal_.

◆ setNamespace()

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

overridevirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 45 of file HmmProcessPhyloLikelihood.cpp.

References hmm_, and bpp::AbstractParametrizableSequencePhyloLikelihood::setNamespace().

◆ 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().

◆ hmm_

std::shared_ptr<HmmLikelihood_DF> bpp::HmmProcessPhyloLikelihood::hmm_

mutableprivate

LikelihoodCalculation in context of HMM.

Definition at line 39 of file HmmProcessPhyloLikelihood.h.

Referenced by alignedLikelihoodCalculation(), fireParameterChanged(), getAlignedLikelihoodCalculation(), getHmmTransitionMatrix(), getLikelihoodCalculation(), getPosteriorProbabilitiesPerSitePerProcess(), HmmProcessPhyloLikelihood(), likelihoodCalculation(), and setNamespace().

◆ Hpep_

std::shared_ptr<HmmPhyloEmissionProbabilities> bpp::HmmProcessPhyloLikelihood::Hpep_

private

Definition at line 34 of file HmmProcessPhyloLikelihood.h.

Referenced by HmmProcessPhyloLikelihood().

◆ 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=().

◆ mSeqEvol_

std::shared_ptr<MultiProcessSequenceEvolution> bpp::MultiProcessSequencePhyloLikelihood::mSeqEvol_

privateinherited

to avoid the dynamic casts

Definition at line 39 of file MultiProcessSequencePhyloLikelihood.h.

Referenced by bpp::MultiProcessSequencePhyloLikelihood::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_

protectedinherited

the Sequence Evolution number

Definition at line 62 of file SequencePhyloLikelihood.h.

Referenced by bpp::AbstractSequencePhyloLikelihood::getSequenceEvolutionNumber(), and bpp::AbstractSequencePhyloLikelihood::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_

protectedinherited

the Sequence Evolution

Definition at line 57 of file SequencePhyloLikelihood.h.

◆ vLikCal_

std::vector<std::shared_ptr<LikelihoodCalculationSingleProcess> > bpp::MultiProcessSequencePhyloLikelihood::vLikCal_

mutableprotectedinherited

vector of pointers towards LikelihoodCalculationSingleProcess, used for the global likelihood.

Definition at line 46 of file MultiProcessSequencePhyloLikelihood.h.

Referenced by bpp::MixtureProcessPhyloLikelihood::MixtureProcessPhyloLikelihood(), bpp::MultiProcessSequencePhyloLikelihood::MultiProcessSequencePhyloLikelihood(), bpp::MultiProcessSequencePhyloLikelihood::operator=(), and bpp::MultiProcessSequencePhyloLikelihood::setData().

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/HmmProcessPhyloLikelihood.h
Bpp/Phyl/Likelihood/PhyloLikelihoods/HmmProcessPhyloLikelihood.cpp

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HmmProcessPhyloLikelihood() [1/2]

◆ HmmProcessPhyloLikelihood() [2/2]

◆ ~HmmProcessPhyloLikelihood()

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]

◆ fireParameterChanged()

◆ firstOrderDerivativeNode()

◆ getAlignedLikelihoodCalculation()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getData()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getHmmTransitionMatrix()

◆ getLikelihoodCalculation()

◆ getLikelihoodCalculationForAProcess()

◆ getLikelihoodForASite() [1/2]

◆ getLikelihoodForASite() [2/2]

◆ getLikelihoodForASiteForAProcess()

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLikelihoodPerSite() [1/2]

◆ getLikelihoodPerSite() [2/2]

◆ getLikelihoodPerSitePerProcess()

◆ 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]

◆ getNumberOfSubstitutionProcess()

◆ getPosteriorProbabilitiesPerSitePerProcess()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSequenceEvolution()

◆ getSequenceEvolutionNumber()

◆ getSubstitutionModelParameters()

◆ getSubstitutionProcessParameters()

◆ getValue()

◆ isInitialized()

◆ likelihoodCalculation()

◆ secondOrderDerivativeNode()

◆ sequenceEvolution()

◆ setData()

◆ setNamespace()

◆ setNData()

◆ setNumberOfSites()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_

◆ hmm_

◆ Hpep_

◆ minusLogLik_

◆ mSeqEvol_