Wraps a dataflow graph as a function: resultNode = f(variableNodes). More...

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

Inheritance diagram for bpp::OnABranchPhyloLikelihood:

Collaboration diagram for bpp::OnABranchPhyloLikelihood:

Public Member Functions
	OnABranchPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationSingleProcess > likCal, uint edgeId, const ParameterList &variableNodes)

	OnABranchPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationSingleProcess > likCal, uint edgeId)

	OnABranchPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationOnABranch > likCal, const ParameterList &variableNodes)

	OnABranchPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationOnABranch > likCal)
	: the parameters the independent parameters of the LikelihoodCalculation More...

OnABranchPhyloLikelihood *	clone () const override

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

size_t	getNumberOfDistinctSites () const

bool	isInitialized () const override
	Get the number of model classes. More...

void	setModel (std::shared_ptr< ConfiguredModel > model)

LikelihoodCalculation &	likelihoodCalculation () const override

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

AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const override

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

LikelihoodCalculationOnABranch &	likelihoodCalculationOnABranch () const

std::shared_ptr< LikelihoodCalculationOnABranch >	getLikelihoodCalculationOnABranch () const

ValueRef< RowLik >	getFirstOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	firstOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	getSecondOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	getSecondOrderDerivativeVector (const std::string &variable1, const std::string &variable2) const

ValueRef< RowLik >	secondOrderDerivativeVector (const std::string &variable1, const std::string &variable2) const

VVDataLik	getLikelihoodPerSitePerClass () const
	Get the posterior probabilities of each class, for each site. More...

std::vector< size_t >	getClassWithMaxPostProbPerSite () const

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

virtual const ParameterList &	getParameters () const=0

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

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

virtual void	setAllParametersValues (const ParameterList &parameters)=0

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

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

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

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

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

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

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

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

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

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

const ParameterList &	getParameters () const override

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

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

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

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

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

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

size_t	getNumberOfParameters () const override

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

std::string	getNamespace () const override

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

virtual void	fireParameterChanged (const ParameterList &parameters)

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

ParameterList	getDerivableParameters () const override

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

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

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

ParameterList	getRootFrequenciesParameters () const override
	Get the independent parameters associated to the root frequencies(s). 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
void	setNumberOfSites (size_t nbSites)

virtual ParameterList &	getParameters_ ()=0

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

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

virtual void	deleteParameters_ (const std::vector< std::string > &names)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override

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

Protected Attributes
std::shared_ptr< LikelihoodCalculationOnABranch >	likCal_

std::unordered_map< std::string, ValueRef< RowLik > >	firstOrderDerivativeVectors_
	For Dataflow computing. More...

std::unordered_map< std::pair< std::string, std::string >, ValueRef< RowLik >, StringPairHash >	secondOrderDerivativeVectors_

size_t	nbSites_

Context &	context_

DataLik	minusLogLik_
	the value More...

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

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

Private Attributes
ParameterList	parameters_

std::string	prefix_

Detailed Description

Wraps a dataflow graph as a function: resultNode = f(variableNodes).

Definition at line 29 of file OnABranchPhyloLikelihood.h.

Constructor & Destructor Documentation

◆ OnABranchPhyloLikelihood() [1/4]

bpp::OnABranchPhyloLikelihood::OnABranchPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationSingleProcess >	likCal,
		uint	edgeId,
		const ParameterList &	variableNodes
	)

inline

Definition at line 47 of file OnABranchPhyloLikelihood.h.

References bpp::AbstractParametrizable::shareParameters_().

Referenced by clone().

◆ OnABranchPhyloLikelihood() [2/4]

bpp::OnABranchPhyloLikelihood::OnABranchPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationSingleProcess >	likCal,
		uint	edgeId
	)

inline

Definition at line 59 of file OnABranchPhyloLikelihood.h.

◆ OnABranchPhyloLikelihood() [3/4]

bpp::OnABranchPhyloLikelihood::OnABranchPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationOnABranch >	likCal,
		const ParameterList &	variableNodes
	)

inline

Definition at line 69 of file OnABranchPhyloLikelihood.h.

References bpp::AbstractParametrizable::shareParameters_().

◆ OnABranchPhyloLikelihood() [4/4]

bpp::OnABranchPhyloLikelihood::OnABranchPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationOnABranch >	likCal
	)

inline

: the parameters the independent parameters of the LikelihoodCalculation

Definition at line 83 of file OnABranchPhyloLikelihood.h.

References likCal_, and bpp::AbstractParametrizable::shareParameters_().

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(), firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), 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::OnABranchPhyloLikelihood::alignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 212 of file OnABranchPhyloLikelihood.h.

References likCal_.

◆ clone()

OnABranchPhyloLikelihood * bpp::OnABranchPhyloLikelihood::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParametrizable.

Definition at line 100 of file OnABranchPhyloLikelihood.h.

References OnABranchPhyloLikelihood().

◆ context() [1/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/4]

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

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [3/4]

Context & bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [4/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

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

inlineoverridevirtualinherited

Tell if derivatives must be computed: for Function inheritance.

Implements bpp::SecondOrderDerivable.

Definition at line 113 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

◆ firstOrderDerivativeNode()

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

inlineinherited

Definition at line 139 of file AbstractPhyloLikelihood.h.

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

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

◆ firstOrderDerivativeVector()

ValueRef< RowLik > bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 239 of file OnABranchPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, firstOrderDerivativeVectors_, and getLikelihoodCalculationOnABranch().

Referenced by getFirstOrderDerivativeVector(), and secondOrderDerivativeVector().

◆ getAlignedLikelihoodCalculation()

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

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 217 of file OnABranchPhyloLikelihood.h.

References likCal_.

◆ getBranchLengthParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getBranchLengthParameters ( ) const

inlineoverridevirtual

Get the independent branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 162 of file OnABranchPhyloLikelihood.h.

◆ getClassWithMaxPostProbPerSite()

vector< size_t > OnABranchPhyloLikelihood::getClassWithMaxPostProbPerSite ( ) const

Definition at line 82 of file OnABranchPhyloLikelihood.cpp.

References getLikelihoodPerSitePerClass(), and getNumberOfSites().

◆ getDerivableParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 152 of file OnABranchPhyloLikelihood.h.

◆ 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().

◆ getFirstOrderDerivativeVector()

ValueRef< RowLik > bpp::OnABranchPhyloLikelihood::getFirstOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 234 of file OnABranchPhyloLikelihood.h.

References firstOrderDerivativeVector().

◆ getLikelihoodCalculation()

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

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 207 of file OnABranchPhyloLikelihood.h.

References likCal_.

◆ getLikelihoodCalculationOnABranch()

std::shared_ptr< LikelihoodCalculationOnABranch > bpp::OnABranchPhyloLikelihood::getLikelihoodCalculationOnABranch ( ) const

inline

Definition at line 227 of file OnABranchPhyloLikelihood.h.

References likCal_.

Referenced by firstOrderDerivativeVector(), and getLikelihoodPerSitePerClass().

◆ getLikelihoodForASite()

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().

◆ 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()

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(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite(), and bpp::SingleProcessPhyloLikelihood::getPosteriorRatePerSite().

◆ getLikelihoodPerSitePerClass()

VVDataLik OnABranchPhyloLikelihood::getLikelihoodPerSitePerClass ( ) const

Get the posterior probabilities of each class, for each site.

Returns: A 2D-vector (Sites X Class) of all posterior probabilities.

Definition at line 72 of file OnABranchPhyloLikelihood.cpp.

References bpp::copyEigenToBpp(), and getLikelihoodCalculationOnABranch().

Referenced by getClassWithMaxPostProbPerSite().

◆ 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()

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(), bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation(), and bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite().

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite().

◆ getNonDerivableParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getNonDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 147 of file OnABranchPhyloLikelihood.h.

◆ getNumberOfDistinctSites()

size_t bpp::OnABranchPhyloLikelihood::getNumberOfDistinctSites ( ) const

inline

Definition at line 112 of file OnABranchPhyloLikelihood.h.

References bpp::LikelihoodCalculationOnABranch::getNumberOfDistinctSites(), and likelihoodCalculationOnABranch().

◆ getNumberOfSites()

size_t bpp::OnABranchPhyloLikelihood::getNumberOfSites ( ) const

inlineoverridevirtual

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Reimplemented from bpp::AbstractAlignedPhyloLikelihood.

Definition at line 107 of file OnABranchPhyloLikelihood.h.

References bpp::LikelihoodCalculationOnABranch::getNumberOfSites(), and likelihoodCalculationOnABranch().

Referenced by getClassWithMaxPostProbPerSite().

◆ getRateDistributionParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 182 of file OnABranchPhyloLikelihood.h.

◆ getRootFrequenciesParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getRootFrequenciesParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 193 of file OnABranchPhyloLikelihood.h.

◆ getSecondOrderDerivative() [1/2]

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

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 155 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::getSecondOrderDerivative().

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

◆ 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().

◆ getSecondOrderDerivativeVector() [1/2]

ValueRef< RowLik > bpp::OnABranchPhyloLikelihood::getSecondOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 254 of file OnABranchPhyloLikelihood.h.

References getSecondOrderDerivativeVector().

Referenced by getSecondOrderDerivativeVector().

◆ getSecondOrderDerivativeVector() [2/2]

ValueRef< RowLik > bpp::OnABranchPhyloLikelihood::getSecondOrderDerivativeVector	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inline

Definition at line 259 of file OnABranchPhyloLikelihood.h.

References secondOrderDerivativeVector().

◆ getSubstitutionModelParameters()

ParameterList bpp::OnABranchPhyloLikelihood::getSubstitutionModelParameters ( ) const

inlineoverridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 172 of file OnABranchPhyloLikelihood.h.

◆ 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::OnABranchPhyloLikelihood::isInitialized ( ) const

inlineoverridevirtual

Get the number of model classes.

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

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 132 of file OnABranchPhyloLikelihood.h.

References bpp::LikelihoodCalculation::isInitialized(), and likelihoodCalculationOnABranch().

◆ likelihoodCalculation()

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

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 202 of file OnABranchPhyloLikelihood.h.

References likCal_.

◆ likelihoodCalculationOnABranch()

LikelihoodCalculationOnABranch & bpp::OnABranchPhyloLikelihood::likelihoodCalculationOnABranch ( ) const

inline

Definition at line 222 of file OnABranchPhyloLikelihood.h.

References likCal_.

Referenced by getNumberOfDistinctSites(), getNumberOfSites(), and isInitialized().

◆ 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().

◆ secondOrderDerivativeVector()

ValueRef< RowLik > bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inline

Definition at line 265 of file OnABranchPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, firstOrderDerivativeVector(), and secondOrderDerivativeVectors_.

Referenced by getSecondOrderDerivativeVector().

◆ setModel()

void bpp::OnABranchPhyloLikelihood::setModel ( std::shared_ptr< ConfiguredModel > model )

inline

Definition at line 137 of file OnABranchPhyloLikelihood.h.

References likCal_.

◆ 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(), firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), bpp::AbstractPhyloLikelihood::operator=(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), 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().

◆ firstOrderDerivativeVectors_

std::unordered_map<std::string, ValueRef<RowLik> > bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVectors_

mutableprotected

For Dataflow computing.

Definition at line 40 of file OnABranchPhyloLikelihood.h.

Referenced by firstOrderDerivativeVector().

◆ likCal_

std::shared_ptr<LikelihoodCalculationOnABranch> bpp::OnABranchPhyloLikelihood::likCal_

mutableprotected

Definition at line 35 of file OnABranchPhyloLikelihood.h.

Referenced by alignedLikelihoodCalculation(), getAlignedLikelihoodCalculation(), getLikelihoodCalculation(), getLikelihoodCalculationOnABranch(), likelihoodCalculation(), likelihoodCalculationOnABranch(), OnABranchPhyloLikelihood(), and setModel().

◆ 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().

◆ 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().

◆ secondOrderDerivativeVectors_

std::unordered_map<std::pair<std::string, std::string>, ValueRef<RowLik>, StringPairHash> bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVectors_

mutableprotected

Definition at line 44 of file OnABranchPhyloLikelihood.h.

Referenced by secondOrderDerivativeVector().

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

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

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ OnABranchPhyloLikelihood() [1/4]

◆ OnABranchPhyloLikelihood() [2/4]

◆ OnABranchPhyloLikelihood() [3/4]

◆ OnABranchPhyloLikelihood() [4/4]

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ alignedLikelihoodCalculation()

◆ clone()

◆ context() [1/4]

◆ context() [2/4]

◆ context() [3/4]

◆ context() [4/4]

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ enableSecondOrderDerivatives() [1/2]

◆ enableSecondOrderDerivatives() [2/2]

◆ firstOrderDerivativeNode()

◆ firstOrderDerivativeVector()

◆ getAlignedLikelihoodCalculation()

◆ getBranchLengthParameters()

◆ getClassWithMaxPostProbPerSite()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getFirstOrderDerivativeVector()

◆ getLikelihoodCalculation()

◆ getLikelihoodCalculationOnABranch()

◆ getLikelihoodForASite()

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLikelihoodPerSite()

◆ getLikelihoodPerSitePerClass()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite()

◆ getNonDerivableParameters()

◆ getNumberOfDistinctSites()

◆ getNumberOfSites()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSecondOrderDerivativeVector() [1/2]

◆ getSecondOrderDerivativeVector() [2/2]

◆ getSubstitutionModelParameters()

◆ getValue()

◆ isInitialized()

◆ likelihoodCalculation()

◆ likelihoodCalculationOnABranch()

◆ secondOrderDerivativeNode()

◆ secondOrderDerivativeVector()

◆ setModel()

◆ setNumberOfSites()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_

◆ firstOrderDerivativeVectors_

◆ likCal_

◆ minusLogLik_

◆ nbSites_

◆ secondOrderDerivativeNodes_

◆ secondOrderDerivativeVectors_