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

Inheritance diagram for bpp::AbstractPhyloLikelihood:

Collaboration diagram for bpp::AbstractPhyloLikelihood:

Classes
struct	StringPairHash

Public Member Functions
	AbstractPhyloLikelihood (Context &context)

	AbstractPhyloLikelihood (const AbstractPhyloLikelihood &apl)

AbstractPhyloLikelihood &	operator= (const AbstractPhyloLikelihood &apl)

virtual	~AbstractPhyloLikelihood ()

const Context &	context () const override

Context &	context () override

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

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

void	setParameters (const ParameterList &parameters) override

ValueRef< DataLik >	getLikelihoodNode () const override

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

virtual void	enableSecondOrderDerivatives (bool yn) override

bool	enableFirstOrderDerivatives () const override

bool	enableSecondOrderDerivatives () const override

double	getValue () const override

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

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

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

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

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

PhyloLikelihoodInterface *	clone () const =0

virtual LikelihoodCalculation &	likelihoodCalculation () const =0

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

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

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

The likelihood functions.
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...

Protected Member Functions
Node_DF &	accessVariableNode (const std::string &name) const

virtual ParameterList &	getParameters_ ()=0

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

Protected Attributes
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_

Detailed Description

Definition at line 18 of file AbstractPhyloLikelihood.h.

Constructor & Destructor Documentation

◆ AbstractPhyloLikelihood() [1/2]

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

inline

Definition at line 51 of file AbstractPhyloLikelihood.h.

◆ AbstractPhyloLikelihood() [2/2]

bpp::AbstractPhyloLikelihood::AbstractPhyloLikelihood ( const AbstractPhyloLikelihood & apl )

inline

Definition at line 56 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::getParameters(), and shareParameters().

◆ ~AbstractPhyloLikelihood()

virtual bpp::AbstractPhyloLikelihood::~AbstractPhyloLikelihood ( )

inlinevirtual

Definition at line 71 of file AbstractPhyloLikelihood.h.

Member Function Documentation

◆ accessVariableNode() [1/2]

static Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const Parameter & param )

inlinestaticprotected

Definition at line 188 of file AbstractPhyloLikelihood.h.

Referenced by accessVariableNode(), firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

◆ accessVariableNode() [2/2]

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

inlineprotected

Definition at line 193 of file AbstractPhyloLikelihood.h.

References accessVariableNode(), and bpp::SecondOrderDerivable::parameter().

◆ clone()

PhyloLikelihoodInterface* bpp::PhyloLikelihoodInterface::clone ( ) const

pure virtualinherited

Implements bpp::SecondOrderDerivable.

Implemented in bpp::SequencePhyloLikelihoodInterface, bpp::AlignedPhyloLikelihoodSetInterface, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::SingleDataPhyloLikelihoodInterface, bpp::PhyloLikelihoodSetInterface, bpp::AlignedPhyloLikelihoodInterface, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

◆ context() [1/2]

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References context_.

◆ context() [2/2]

Context& bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References context_.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

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

inlineoverridevirtual

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

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

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

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

◆ firstOrderDerivativeNode()

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

inline

Definition at line 139 of file AbstractPhyloLikelihood.h.

References accessVariableNode(), context_, firstOrderDerivativeNodes_, and getLikelihoodNode().

Referenced by getFirstOrderDerivative(), and secondOrderDerivativeNode().

◆ getBranchLengthParameters()

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().

◆ getDerivableParameters()

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

pure virtualinherited

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

◆ getFirstOrderDerivative()

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

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 131 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and firstOrderDerivativeNode().

◆ getLikelihoodCalculation()

virtual std::shared_ptr<LikelihoodCalculation> bpp::PhyloLikelihoodInterface::getLikelihoodCalculation ( ) const

pure virtualinherited

Returns: A shared pointer toward the LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

Referenced by getLikelihoodNode().

◆ getLikelihoodNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::getLikelihoodNode ( ) const

inlineoverridevirtual

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 firstOrderDerivativeNode(), and 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()

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

pure virtualinherited

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

◆ getRateDistributionParameters()

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.

◆ getRootFrequenciesParameters()

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.

◆ getSecondOrderDerivative() [1/2]

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

inlineoverridevirtual

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

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 160 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and secondOrderDerivativeNode().

◆ getSubstitutionModelParameters()

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.

◆ getValue()

double bpp::AbstractPhyloLikelihood::getValue ( ) const

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 124 of file AbstractPhyloLikelihood.h.

References bpp::convert(), getLikelihoodNode(), and minusLogLik_.

◆ isInitialized()

virtual bool bpp::AbstractPhyloLikelihood::isInitialized ( ) const

inlineoverridevirtual

Sets the computeLikelihoods_ to true.

Implements bpp::PhyloLikelihoodInterface.

Reimplemented in bpp::SingleProcessPhyloLikelihood, bpp::AbstractPhyloLikelihoodSet, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, and bpp::MultiProcessSequencePhyloLikelihood.

Definition at line 81 of file AbstractPhyloLikelihood.h.

◆ likelihoodCalculation()

virtual LikelihoodCalculation& bpp::PhyloLikelihoodInterface::likelihoodCalculation ( ) const

pure virtualinherited

Returns: The LikelihoodCalculation.

Implemented in bpp::AutoCorrelationProcessPhyloLikelihood, bpp::SingleProcessPhyloLikelihood, bpp::PartitionProcessPhyloLikelihood, bpp::OneProcessSequencePhyloLikelihood, bpp::OnABranchPhyloLikelihood, bpp::MixtureProcessPhyloLikelihood, bpp::HmmProcessPhyloLikelihood, bpp::AutoCorrelationProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

◆ operator=()

AbstractPhyloLikelihood& bpp::AbstractPhyloLikelihood::operator= ( const AbstractPhyloLikelihood & apl )

inline

Definition at line 63 of file AbstractPhyloLikelihood.h.

References context_, bpp::SecondOrderDerivable::getParameters(), minusLogLik_, and shareParameters().

Referenced by bpp::AbstractAlignedPhyloLikelihood::operator=(), and bpp::AbstractPhyloLikelihoodSet::operator=().

◆ secondOrderDerivativeNode()

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

inline

Definition at line 168 of file AbstractPhyloLikelihood.h.

References accessVariableNode(), context_, firstOrderDerivativeNode(), and secondOrderDerivativeNodes_.

Referenced by getSecondOrderDerivative().

◆ setParameters()

void bpp::AbstractPhyloLikelihood::setParameters ( const ParameterList & parameters )

inlineoverridevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 95 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::setParametersValues().

◆ shareParameters()

void bpp::AbstractPhyloLikelihood::shareParameters ( const ParameterList & variableNodes )

inline

Share Parameters, that are DF_parameters.

Definition at line 90 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::getParameters_(), and bpp::ParameterList::shareParameters().

Referenced by AbstractPhyloLikelihood(), and operator=().

Member Data Documentation

◆ context_

Context& bpp::AbstractPhyloLikelihood::context_

protected

Definition at line 34 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), context(), firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), operator=(), secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector().

◆ firstOrderDerivativeNodes_

std::unordered_map<std::string, ValueRef<DataLik> > bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_

mutableprotected

For Dataflow computing.

Definition at line 44 of file AbstractPhyloLikelihood.h.

Referenced by firstOrderDerivativeNode().

◆ minusLogLik_

DataLik bpp::AbstractPhyloLikelihood::minusLogLik_

mutableprotected

the value

Definition at line 39 of file AbstractPhyloLikelihood.h.

Referenced by getValue(), and operator=().

◆ secondOrderDerivativeNodes_

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

mutableprotected

Definition at line 48 of file AbstractPhyloLikelihood.h.

Referenced by secondOrderDerivativeNode().

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/AbstractPhyloLikelihood.h

Classes

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractPhyloLikelihood() [1/2]

◆ AbstractPhyloLikelihood() [2/2]

◆ ~AbstractPhyloLikelihood()

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ clone()

◆ context() [1/2]

◆ context() [2/2]

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ enableSecondOrderDerivatives() [1/2]

◆ enableSecondOrderDerivatives() [2/2]

◆ firstOrderDerivativeNode()

◆ getBranchLengthParameters()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getLikelihoodCalculation()

◆ getLikelihoodNode()

◆ getLogLikelihood()

◆ getNonDerivableParameters()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSubstitutionModelParameters()

◆ getValue()

◆ isInitialized()

◆ likelihoodCalculation()

◆ operator=()

◆ secondOrderDerivativeNode()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_

◆ minusLogLik_

◆ secondOrderDerivativeNodes_