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

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

Inheritance diagram for bpp::AlignedPhyloLikelihoodHmm:

Collaboration diagram for bpp::AlignedPhyloLikelihoodHmm:

Public Member Functions
	AlignedPhyloLikelihoodHmm (Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true)

virtual	~AlignedPhyloLikelihoodHmm ()

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

void	fireParameterChanged (const ParameterList &parameters) override

const HmmPhyloAlphabet	hmmStateAlphabet () const

std::shared_ptr< const HmmPhyloAlphabet >	getHmmStateAlphabet () const

bool	addPhyloLikelihood (size_t nPhyl, const std::string &suff) override
	adds a PhyloLikelihood already stored in the m ap, iff it is an AlignedPhyloLikelihood of the same size More...

std::shared_ptr< const AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl) const override

std::shared_ptr< AlignedPhyloLikelihoodInterface >	getAlignedPhyloLikelihood (size_t nPhyl) override

const AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl) const override

AlignedPhyloLikelihoodInterface &	alignedPhyloLikelihood (size_t nPhyl) override

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

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

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

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

std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer () override

std::shared_ptr< const PhyloLikelihoodContainer >	getPhyloContainer () const override

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

const std::vector< size_t > &	getNumbersOfPhyloLikelihoods () const override

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

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...

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	getPosteriorProbabilitiesPerSitePerAligned () const

Vdouble	getPosteriorProbabilitiesForASitePerAligned (size_t site) const

const Eigen::MatrixXd &	getHmmTransitionMatrix () const

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

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

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

The PhyloLikelihood storage.
bool	hasPhyloLikelihood (size_t nPhyl) override

std::shared_ptr< const PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) const override

std::shared_ptr< PhyloLikelihoodInterface >	getPhyloLikelihood (size_t nPhyl) override

The data functions
virtual bool	isInitialized () const =0

virtual const Context &	context () const =0

virtual Context &	context ()=0

Inherited from PhyloLikelihood
bool	isInitialized () const override

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...

Retrieve some particular parameters subsets.
ParameterList	getNonDerivableParameters () const override

ParameterList	getDerivableParameters () const override

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

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

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

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

The data functions
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...

The likelihood functions.
virtual DataLik	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site. More...

virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the log likelihood for a site, and its derivatives. More...

virtual VDataLik	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...

Protected Member Functions
	AlignedPhyloLikelihoodHmm (const AlignedPhyloLikelihoodHmm &mlc)

AlignedPhyloLikelihoodHmm &	operator= (const AlignedPhyloLikelihoodHmm &mlc)

AlignedPhyloLikelihoodHmm *	clone () const override

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

void	setNumberOfSites (size_t nbSites)

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

Protected Attributes
std::shared_ptr< PhyloLikelihoodContainer >	pPhyloCont_
	pointer to a PhyloLikelihoodContainer More...

std::vector< size_t >	nPhylo_
	vector of AbstractPhyloLikelihood numbers More...

std::vector< std::shared_ptr< LikelihoodCalculation > >	vLikCal_

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_

size_t	nbSites_

Private Attributes
std::shared_ptr< HmmPhyloAlphabet >	hma_

std::shared_ptr< FullHmmTransitionMatrix >	htm_

std::shared_ptr< HmmPhyloEmissionProbabilities >	hpep_

std::shared_ptr< HmmLikelihood_DF >	hmm_

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 AlignedPhyloLikelihoodHmm.h.

Constructor & Destructor Documentation

◆ AlignedPhyloLikelihoodHmm() [1/2]

AlignedPhyloLikelihoodHmm::AlignedPhyloLikelihoodHmm	(	Context &	context,
		std::shared_ptr< PhyloLikelihoodContainer >	pC,
		const std::vector< size_t > &	nPhylo,
		bool	inCollection = `true`
	)

Definition at line 15 of file AlignedPhyloLikelihoodHmm.cpp.

Referenced by clone().

◆ ~AlignedPhyloLikelihoodHmm()

virtual bpp::AlignedPhyloLikelihoodHmm::~AlignedPhyloLikelihoodHmm ( )

inlinevirtual

Definition at line 49 of file AlignedPhyloLikelihoodHmm.h.

◆ AlignedPhyloLikelihoodHmm() [2/2]

bpp::AlignedPhyloLikelihoodHmm::AlignedPhyloLikelihoodHmm ( const AlignedPhyloLikelihoodHmm & mlc )

inlineprotected

Definition at line 52 of file AlignedPhyloLikelihoodHmm.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().

◆ addPhyloLikelihood()

bool AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood	(	size_t	nPhyl,
		const std::string &	suff
	)

overridevirtualinherited

adds a PhyloLikelihood already stored in the m ap, iff it is an AlignedPhyloLikelihood of the same size

Parameters

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

Returns: if the PhyloLikelihood has been added.

Reimplemented from bpp::AbstractPhyloLikelihoodSet.

Definition at line 60 of file AlignedPhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractAlignedPhyloLikelihoodSet::getAlignedPhyloLikelihood(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

◆ alignedLikelihoodCalculation()

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

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 109 of file AlignedPhyloLikelihoodHmm.h.

References hmm_.

◆ alignedPhyloLikelihood() [1/2]

const AlignedPhyloLikelihoodInterface& bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood ( size_t nPhyl ) const

inlineoverridevirtualinherited

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 120 of file AlignedPhyloLikelihoodSet.h.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood(), and bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood().

◆ alignedPhyloLikelihood() [2/2]

AlignedPhyloLikelihoodInterface& bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood ( size_t nPhyl )

inlineoverridevirtualinherited

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 125 of file AlignedPhyloLikelihoodSet.h.

◆ clone()

AlignedPhyloLikelihoodHmm* bpp::AlignedPhyloLikelihoodHmm::clone ( ) const

inlineoverrideprotectedvirtual

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 74 of file AlignedPhyloLikelihoodHmm.h.

References AlignedPhyloLikelihoodHmm().

◆ 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()

void AlignedPhyloLikelihoodHmm::fireParameterChanged ( const ParameterList & parameters )

overridevirtual

Reimplemented from bpp::AbstractPhyloLikelihoodSet.

Definition at line 47 of file AlignedPhyloLikelihoodHmm.cpp.

References bpp::AbstractPhyloLikelihoodSet::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::AlignedPhyloLikelihoodHmm::getAlignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 114 of file AlignedPhyloLikelihoodHmm.h.

References hmm_.

◆ getAlignedPhyloLikelihood() [1/2]

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

inlineoverridevirtualinherited

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 110 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

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

◆ getAlignedPhyloLikelihood() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 115 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

◆ getBranchLengthParameters() [1/2]

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().

◆ getBranchLengthParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getBranchLengthParameters ( ) const

overridevirtualinherited

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 107 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ getDerivableParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getDerivableParameters ( ) const

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getDerivableParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getDerivableParameters ( ) const

overridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 95 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ 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().

◆ getHmmStateAlphabet()

std::shared_ptr<const HmmPhyloAlphabet> bpp::AlignedPhyloLikelihoodHmm::getHmmStateAlphabet ( ) const

inline

Definition at line 89 of file AlignedPhyloLikelihoodHmm.h.

References hma_.

◆ getHmmTransitionMatrix()

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

inline

Definition at line 140 of file AlignedPhyloLikelihoodHmm.h.

References hmm_.

◆ getLikelihoodCalculation()

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

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 104 of file AlignedPhyloLikelihoodHmm.h.

References hmm_.

◆ 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().

◆ getLikelihoodForASiteForAPhyloLikelihood()

DataLik bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood	(	size_t	site,
		size_t	nPhyl
	)		const

inlineoverridevirtualinherited

Get the likelihood for a site for an aligned phyloLikelihood.

Parameters

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

Returns: The likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 130 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood(), and bpp::AlignedPhyloLikelihoodInterface::getLikelihoodForASite().

◆ 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().

◆ getLogLikelihoodForASiteForAPhyloLikelihood()

double bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood	(	size_t	site,
		size_t	nPhyl
	)		const

inlineoverridevirtualinherited

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

Parameters

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

Returns: The log likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodSetInterface.

Definition at line 135 of file AlignedPhyloLikelihoodSet.h.

References bpp::AbstractAlignedPhyloLikelihoodSet::alignedPhyloLikelihood(), and bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite().

◆ getNonDerivableParameters() [1/2]

virtual ParameterList bpp::PhyloLikelihoodInterface::getNonDerivableParameters ( ) const

pure virtualinherited

Implemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractParametrizableSequencePhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, and bpp::OnABranchPhyloLikelihood.

◆ getNonDerivableParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getNonDerivableParameters ( ) const

overridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 84 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ 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().

◆ getNumbersOfPhyloLikelihoods() [1/2]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

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

◆ getNumbersOfPhyloLikelihoods() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 139 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::nPhylo_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and bpp::PartitionProcessPhyloLikelihood::getData().

◆ getPhyloContainer() [1/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloContainer() [2/4]

std::shared_ptr<const PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::getPhyloContainer ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 134 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

◆ getPhyloContainer() [3/4]

std::shared_ptr<PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::getPhyloContainer ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 129 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::PartitionProcessPhyloLikelihood::getData(), bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood(), bpp::PhyloLikelihoodFormula::readFormula(), and bpp::PartitionProcessPhyloLikelihood::setData().

◆ getPhyloContainer() [4/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloLikelihood() [1/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPhyloLikelihood() [2/4]

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

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 169 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

◆ getPhyloLikelihood() [3/4]

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

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 175 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::pPhyloCont_.

◆ getPhyloLikelihood() [4/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ getPosteriorProbabilitiesForASitePerAligned()

Vdouble bpp::AlignedPhyloLikelihoodHmm::getPosteriorProbabilitiesForASitePerAligned ( size_t site ) const

inline

Definition at line 132 of file AlignedPhyloLikelihoodHmm.h.

References bpp::copyEigenToBpp(), and hmm_.

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

◆ getPosteriorProbabilitiesPerSitePerAligned()

VVdouble bpp::AlignedPhyloLikelihoodHmm::getPosteriorProbabilitiesPerSitePerAligned ( ) const

inline

Definition at line 124 of file AlignedPhyloLikelihoodHmm.h.

References bpp::copyEigenToBpp(), and hmm_.

◆ getRateDistributionParameters() [1/2]

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.

◆ getRateDistributionParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getRateDistributionParameters ( ) const

overridevirtualinherited

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 129 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ getRootFrequenciesParameters() [1/2]

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.

◆ getRootFrequenciesParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getRootFrequenciesParameters ( ) const

overridevirtualinherited

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 140 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ 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().

◆ getSubstitutionModelParameters() [1/2]

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.

◆ getSubstitutionModelParameters() [2/2]

ParameterList AbstractPhyloLikelihoodSet::getSubstitutionModelParameters ( ) const

overridevirtualinherited

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 118 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ 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_.

◆ hasPhyloLikelihood() [1/2]

bool bpp::AbstractPhyloLikelihoodSet::hasPhyloLikelihood ( size_t nPhyl )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 164 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::nPhylo_.

Referenced by bpp::PhyloLikelihoodFormula::readFormula().

◆ hasPhyloLikelihood() [2/2]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihoodSet.

◆ hmmStateAlphabet()

const HmmPhyloAlphabet bpp::AlignedPhyloLikelihoodHmm::hmmStateAlphabet ( ) const

inline

Definition at line 84 of file AlignedPhyloLikelihoodHmm.h.

References hma_.

◆ 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]

bool bpp::AbstractPhyloLikelihoodSet::isInitialized ( ) const

inlineoverridevirtualinherited

Returns: 'true' is the likelihood function has been initialized.

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 197 of file PhyloLikelihoodSet.h.

References bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), and bpp::AbstractPhyloLikelihoodSet::nPhylo_.

◆ likelihoodCalculation()

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

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 99 of file AlignedPhyloLikelihoodHmm.h.

References hmm_.

◆ operator=()

AlignedPhyloLikelihoodHmm& bpp::AlignedPhyloLikelihoodHmm::operator= ( const AlignedPhyloLikelihoodHmm & mlc )

inlineprotected

Definition at line 64 of file AlignedPhyloLikelihoodHmm.h.

References hma_, hmm_, hpep_, htm_, and bpp::AbstractAlignedPhyloLikelihoodSet::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().

◆ setNamespace()

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

overridevirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 41 of file AlignedPhyloLikelihoodHmm.cpp.

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

◆ 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().

◆ hma_

std::shared_ptr<HmmPhyloAlphabet> bpp::AlignedPhyloLikelihoodHmm::hma_

private

Definition at line 34 of file AlignedPhyloLikelihoodHmm.h.

Referenced by getHmmStateAlphabet(), hmmStateAlphabet(), and operator=().

◆ hmm_

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

mutableprivate

Definition at line 40 of file AlignedPhyloLikelihoodHmm.h.

Referenced by alignedLikelihoodCalculation(), fireParameterChanged(), getAlignedLikelihoodCalculation(), getHmmTransitionMatrix(), getLikelihoodCalculation(), getPosteriorProbabilitiesForASitePerAligned(), getPosteriorProbabilitiesPerSitePerAligned(), likelihoodCalculation(), operator=(), and setNamespace().

◆ hpep_

std::shared_ptr<HmmPhyloEmissionProbabilities> bpp::AlignedPhyloLikelihoodHmm::hpep_

private

Definition at line 38 of file AlignedPhyloLikelihoodHmm.h.

Referenced by operator=().

◆ htm_

std::shared_ptr<FullHmmTransitionMatrix> bpp::AlignedPhyloLikelihoodHmm::htm_

private

Definition at line 36 of file AlignedPhyloLikelihoodHmm.h.

Referenced by operator=().

◆ 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().

◆ nPhylo_

std::vector<size_t> bpp::AbstractPhyloLikelihoodSet::nPhylo_

protectedinherited

vector of AbstractPhyloLikelihood numbers

Definition at line 79 of file PhyloLikelihoodSet.h.

◆ pPhyloCont_

std::shared_ptr<PhyloLikelihoodContainer> bpp::AbstractPhyloLikelihoodSet::pPhyloCont_

protectedinherited

pointer to a PhyloLikelihoodContainer

Definition at line 74 of file PhyloLikelihoodSet.h.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getAlignedPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::AbstractPhyloLikelihoodSet::operator=(), and bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood().

◆ 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().

◆ vLikCal_

std::vector<std::shared_ptr<LikelihoodCalculation> > bpp::AbstractPhyloLikelihoodSet::vLikCal_

mutableprotectedinherited

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

Definition at line 85 of file PhyloLikelihoodSet.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), and bpp::AbstractPhyloLikelihoodSet::operator=().

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

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

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AlignedPhyloLikelihoodHmm() [1/2]

◆ ~AlignedPhyloLikelihoodHmm()

◆ AlignedPhyloLikelihoodHmm() [2/2]

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ addPhyloLikelihood()

◆ alignedLikelihoodCalculation()

◆ alignedPhyloLikelihood() [1/2]

◆ alignedPhyloLikelihood() [2/2]

◆ 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()

◆ getAlignedPhyloLikelihood() [1/2]

◆ getAlignedPhyloLikelihood() [2/2]

◆ getBranchLengthParameters() [1/2]

◆ getBranchLengthParameters() [2/2]

◆ getDerivableParameters() [1/2]

◆ getDerivableParameters() [2/2]

◆ getFirstOrderDerivative()

◆ getHmmStateAlphabet()

◆ getHmmTransitionMatrix()

◆ getLikelihoodCalculation()

◆ getLikelihoodForASite() [1/2]

◆ getLikelihoodForASite() [2/2]

◆ getLikelihoodForASiteForAPhyloLikelihood()

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLikelihoodPerSite() [1/2]

◆ getLikelihoodPerSite() [2/2]

◆ getLogLikelihood()

◆ getLogLikelihoodForASite() [1/2]

◆ getLogLikelihoodForASite() [2/2]

◆ getLogLikelihoodForASiteForAPhyloLikelihood()

◆ getNonDerivableParameters() [1/2]

◆ getNonDerivableParameters() [2/2]

◆ getNumberOfSites() [1/2]

◆ getNumberOfSites() [2/2]

◆ getNumbersOfPhyloLikelihoods() [1/2]

◆ getNumbersOfPhyloLikelihoods() [2/2]

◆ getPhyloContainer() [1/4]

◆ getPhyloContainer() [2/4]

◆ getPhyloContainer() [3/4]

◆ getPhyloContainer() [4/4]

◆ getPhyloLikelihood() [1/4]

◆ getPhyloLikelihood() [2/4]

◆ getPhyloLikelihood() [3/4]

◆ getPhyloLikelihood() [4/4]

◆ getPosteriorProbabilitiesForASitePerAligned()

◆ getPosteriorProbabilitiesPerSitePerAligned()

◆ getRateDistributionParameters() [1/2]

◆ getRateDistributionParameters() [2/2]

◆ getRootFrequenciesParameters() [1/2]

◆ getRootFrequenciesParameters() [2/2]

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSubstitutionModelParameters() [1/2]

◆ getSubstitutionModelParameters() [2/2]

◆ getValue()

◆ hasPhyloLikelihood() [1/2]

◆ hasPhyloLikelihood() [2/2]

◆ hmmStateAlphabet()

◆ isInitialized() [1/2]

◆ isInitialized() [2/2]