The PhyloLikelihoodFormula class, for phylogenetic likelihood on several independent data. More...

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

Inheritance diagram for bpp::PhyloLikelihoodFormula:

Collaboration diagram for bpp::PhyloLikelihoodFormula:

Public Member Functions
	PhyloLikelihoodFormula (Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::string &formula, bool inCollection=true)

virtual	~PhyloLikelihoodFormula ()

void	readFormula (const std::string &formula, bool inCollection=true)

std::string	output () const

std::shared_ptr< PhyloLikelihoodContainer >	getPhyloContainer () override

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

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

virtual bool	addPhyloLikelihood (size_t nPhyl, const std::string &suff="") override
	adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood. 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 void	setNamespace (const std::string &prefix)=0

void	setNamespace (const std::string &prefix) 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	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 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

Inherited from PhyloLikelihood
bool	isInitialized () const override

virtual void	fireParameterChanged (const ParameterList &params) override

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 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
	PhyloLikelihoodFormula (const PhyloLikelihoodFormula &sd)

PhyloLikelihoodFormula &	operator= (const PhyloLikelihoodFormula &sd)

PhyloLikelihoodFormula *	clone () const

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

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_

Private Attributes
std::unique_ptr< ComputationTree >	compTree_

std::shared_ptr< LikelihoodCalculation >	likCal_

ParameterList	parameters_

std::string	prefix_

The likelihood functions.
LikelihoodCalculation &	likelihoodCalculation () const

std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const

ValueRef< DataLik >	makeLikelihoods ()
	Build the LikelihoodNode from the computation Tree. More...

ValueRef< DataLik >	makeLikelihoodsFromOperator (std::shared_ptr< Operator > op)
	Build the LikelihoodNode from a node of the computation Tree. More...

Detailed Description

The PhyloLikelihoodFormula class, for phylogenetic likelihood on several independent data.

WARNING: This formula applies on the log-likelihoods (ie getValues())

Definition at line 21 of file PhyloLikelihoodFormula.h.

Constructor & Destructor Documentation

◆ PhyloLikelihoodFormula() [1/2]

PhyloLikelihoodFormula::PhyloLikelihoodFormula	(	Context &	context,
		std::shared_ptr< PhyloLikelihoodContainer >	pC,
		const std::string &	formula,
		bool	inCollection = `true`
	)

Definition at line 16 of file PhyloLikelihoodFormula.cpp.

Referenced by clone().

◆ ~PhyloLikelihoodFormula()

virtual bpp::PhyloLikelihoodFormula::~PhyloLikelihoodFormula ( )

inlinevirtual

Definition at line 32 of file PhyloLikelihoodFormula.h.

◆ PhyloLikelihoodFormula() [2/2]

bpp::PhyloLikelihoodFormula::PhyloLikelihoodFormula ( const PhyloLikelihoodFormula & sd )

inlineprotected

Definition at line 35 of file PhyloLikelihoodFormula.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 AbstractPhyloLikelihoodSet::addPhyloLikelihood	(	size_t	nPhyl,
		const std::string &	suff = `""`
	)

overridevirtualinherited

adds a PhyloLikelihood already stored in the PhyloLikelihoodContainer, iff it is an AbstractPhyloLikelihood.

Parameters

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

Returns: if the PhyloLikelihood has been added.

Implements bpp::PhyloLikelihoodSetInterface.

Reimplemented in bpp::AbstractAlignedPhyloLikelihoodSet.

Definition at line 45 of file PhyloLikelihoodSet.cpp.

References bpp::AbstractPhyloLikelihood::context_, bpp::ConfiguredParameter::create(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractPhyloLikelihoodSet::nPhylo_, bpp::Parameter::setName(), bpp::AbstractParametrizable::shareParameter_(), bpp::AbstractParametrizable::shareParameters_(), bpp::TextTools::toString(), and bpp::AbstractPhyloLikelihoodSet::vLikCal_.

Referenced by bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet(), bpp::AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood(), bpp::PartitionProcessPhyloLikelihood::PartitionProcessPhyloLikelihood(), and readFormula().

◆ clone()

PhyloLikelihoodFormula* bpp::PhyloLikelihoodFormula::clone ( ) const

inlineprotectedvirtual

Implements bpp::AbstractParametrizable.

Definition at line 52 of file PhyloLikelihoodFormula.h.

References PhyloLikelihoodFormula().

◆ context() [1/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/4]

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

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [3/4]

Context& bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [4/4]

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

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

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

inlineoverridevirtualinherited

Tell if derivatives must be computed: for Function inheritance.

Implements bpp::SecondOrderDerivable.

Definition at line 113 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

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

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

◆ fireParameterChanged()

virtual void bpp::AbstractPhyloLikelihoodSet::fireParameterChanged ( const ParameterList & params )

inlineoverridevirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Reimplemented in bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Definition at line 208 of file PhyloLikelihoodSet.h.

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

Referenced by bpp::AlignedPhyloLikelihoodAutoCorrelation::fireParameterChanged(), and bpp::AlignedPhyloLikelihoodHmm::fireParameterChanged().

◆ firstOrderDerivativeNode()

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

inlineinherited

Definition at line 139 of file AbstractPhyloLikelihood.h.

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

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

◆ getBranchLengthParameters()

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()

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().

◆ getLikelihoodCalculation()

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

inlinevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 80 of file PhyloLikelihoodFormula.h.

References likCal_.

◆ 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().

◆ 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().

◆ getNonDerivableParameters()

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_.

◆ getNumbersOfPhyloLikelihoods()

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() [1/2]

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() [2/2]

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(), readFormula(), and bpp::PartitionProcessPhyloLikelihood::setData().

◆ getPhyloLikelihood() [1/2]

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() [2/2]

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_.

◆ getRateDistributionParameters()

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()

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()

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()

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 readFormula().

◆ isInitialized()

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::PhyloLikelihoodFormula::likelihoodCalculation ( ) const

inlinevirtual

Returns: The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file PhyloLikelihoodFormula.h.

References likCal_.

◆ makeLikelihoods()

ValueRef<DataLik> bpp::PhyloLikelihoodFormula::makeLikelihoods ( )

inlineprivate

Build the LikelihoodNode from the computation Tree.

Definition at line 90 of file PhyloLikelihoodFormula.h.

References compTree_, and makeLikelihoodsFromOperator().

◆ makeLikelihoodsFromOperator()

ValueRef< DataLik > PhyloLikelihoodFormula::makeLikelihoodsFromOperator ( std::shared_ptr< Operator > op )

private

Build the LikelihoodNode from a node of the computation Tree.

Definition at line 72 of file PhyloLikelihoodFormula.cpp.

References bpp::AbstractPhyloLikelihood::context_, bpp::NumericConstant< T >::create(), bpp::CWiseNegate< T >::create(), bpp::CWiseInverse< T >::create(), bpp::CWiseLog< T >::create(), bpp::CWiseExp< T >::create(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), and bpp::AbstractParametrizable::shareParameters_().

Referenced by makeLikelihoods().

◆ operator=()

PhyloLikelihoodFormula& bpp::PhyloLikelihoodFormula::operator= ( const PhyloLikelihoodFormula & sd )

inlineprotected

Definition at line 43 of file PhyloLikelihoodFormula.h.

References compTree_, likCal_, and bpp::AbstractPhyloLikelihoodSet::operator=().

◆ output()

std::string PhyloLikelihoodFormula::output ( ) const

@ output

Definition at line 67 of file PhyloLikelihoodFormula.cpp.

References compTree_.

Referenced by bpp::PhylogeneticsApplicationTools::getPhyloLikelihoodContainer(), and readFormula().

◆ readFormula()

void PhyloLikelihoodFormula::readFormula	(	const std::string &	formula,
		bool	inCollection = `true`
	)

@ input

Definition at line 36 of file PhyloLikelihoodFormula.cpp.

References bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), compTree_, bpp::AbstractPhyloLikelihoodSet::getPhyloContainer(), bpp::AbstractPhyloLikelihoodSet::getPhyloLikelihood(), bpp::StringTokenizer::hasMoreToken(), bpp::AbstractPhyloLikelihoodSet::hasPhyloLikelihood(), bpp::StringTokenizer::nextToken(), output(), and bpp::TextTools::toString().

◆ 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().

◆ 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

◆ compTree_

std::unique_ptr<ComputationTree> bpp::PhyloLikelihoodFormula::compTree_

private

Definition at line 25 of file PhyloLikelihoodFormula.h.

Referenced by makeLikelihoods(), operator=(), output(), and readFormula().

◆ 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(), 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().

◆ likCal_

std::shared_ptr<LikelihoodCalculation> bpp::PhyloLikelihoodFormula::likCal_

private

Definition at line 27 of file PhyloLikelihoodFormula.h.

Referenced by getLikelihoodCalculation(), likelihoodCalculation(), and 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=().

◆ 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/PhyloLikelihoodFormula.h
Bpp/Phyl/Likelihood/PhyloLikelihoods/PhyloLikelihoodFormula.cpp

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

The likelihood functions.

Detailed Description

Constructor & Destructor Documentation

◆ PhyloLikelihoodFormula() [1/2]

◆ ~PhyloLikelihoodFormula()

◆ PhyloLikelihoodFormula() [2/2]

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ addPhyloLikelihood()

◆ 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()

◆ getBranchLengthParameters()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getLikelihoodCalculation()

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLogLikelihood()

◆ getNonDerivableParameters()

◆ getNumbersOfPhyloLikelihoods()

◆ getPhyloContainer() [1/2]

◆ getPhyloContainer() [2/2]

◆ getPhyloLikelihood() [1/2]

◆ getPhyloLikelihood() [2/2]

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSubstitutionModelParameters()

◆ getValue()

◆ hasPhyloLikelihood()

◆ isInitialized()

◆ likelihoodCalculation()

◆ makeLikelihoods()

◆ makeLikelihoodsFromOperator()

◆ operator=()

◆ output()

◆ readFormula()

◆ secondOrderDerivativeNode()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ compTree_

◆ context_

◆ firstOrderDerivativeNodes_

◆ likCal_

◆ minusLogLik_

◆ nPhylo_

◆ pPhyloCont_

◆ secondOrderDerivativeNodes_

◆ vLikCal_