The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer. More...

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

Inheritance diagram for bpp::AbstractPhyloLikelihoodSet:

Collaboration diagram for bpp::AbstractPhyloLikelihoodSet:

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

	AbstractPhyloLikelihoodSet (Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true, const std::string &prefix="")

virtual	~AbstractPhyloLikelihoodSet ()

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...

virtual PhyloLikelihoodSetInterface *	clone () const =0

virtual LikelihoodCalculation &	likelihoodCalculation () const =0

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

virtual void	enableSecondOrderDerivatives (bool yn)=0

virtual bool	enableSecondOrderDerivatives () const=0

virtual double	getSecondOrderDerivative (const std::string &variable) const=0

virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) 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 void	enableFirstOrderDerivatives (bool yn)=0

virtual bool	enableFirstOrderDerivatives () const=0

virtual double	getFirstOrderDerivative (const std::string &variable) const=0

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

virtual void	setParameters (const ParameterList &parameters)=0

virtual double	getValue () const=0

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

const Context &	context () const override

Context &	context () override

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...

bool	enableFirstOrderDerivatives () const override

virtual void	enableSecondOrderDerivatives (bool yn) 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

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 Clonable *	clone () const=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

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
	AbstractPhyloLikelihoodSet (const AbstractPhyloLikelihoodSet &sd)

AbstractPhyloLikelihoodSet &	operator= (const AbstractPhyloLikelihoodSet &sd)

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< 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
ParameterList	parameters_

std::string	prefix_

Detailed Description

The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodContainer.

Definition at line 65 of file PhyloLikelihoodSet.h.

Constructor & Destructor Documentation

◆ AbstractPhyloLikelihoodSet() [1/3]

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

Parameters

context	the Context
pC	PhyloLikelihoodContainer from which the Set is buit
inCollection	: avoid suffix addition to parameter names
prefix	optional string

Definition at line 10 of file PhyloLikelihoodSet.cpp.

References addPhyloLikelihood(), getNumbersOfPhyloLikelihoods(), getPhyloContainer(), and bpp::TextTools::toString().

◆ AbstractPhyloLikelihoodSet() [2/3]

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

Definition at line 27 of file PhyloLikelihoodSet.cpp.

References addPhyloLikelihood(), and bpp::TextTools::toString().

◆ ~AbstractPhyloLikelihoodSet()

virtual bpp::AbstractPhyloLikelihoodSet::~AbstractPhyloLikelihoodSet ( )

inlinevirtual

Definition at line 107 of file PhyloLikelihoodSet.h.

◆ AbstractPhyloLikelihoodSet() [3/3]

bpp::AbstractPhyloLikelihoodSet::AbstractPhyloLikelihoodSet ( const AbstractPhyloLikelihoodSet & sd )

inlineprotected

Definition at line 110 of file PhyloLikelihoodSet.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 = `""`
	)

overridevirtual

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(), getPhyloLikelihood(), bpp::AbstractParametrizable::hasParameter(), nPhylo_, bpp::Parameter::setName(), bpp::AbstractParametrizable::shareParameter_(), bpp::AbstractParametrizable::shareParameters_(), bpp::TextTools::toString(), and vLikCal_.

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

◆ clone()

virtual PhyloLikelihoodSetInterface* bpp::PhyloLikelihoodSetInterface::clone ( ) const

pure virtualinherited

Implements bpp::PhyloLikelihoodInterface.

Implemented in bpp::AlignedPhyloLikelihoodSetInterface, bpp::PartitionProcessPhyloLikelihood, bpp::AlignedPhyloLikelihoodMixture, bpp::AlignedPhyloLikelihoodHmm, bpp::PhyloLikelihoodFormula, bpp::AlignedPhyloLikelihoodProduct, and bpp::AlignedPhyloLikelihoodAutoCorrelation.

◆ 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 )

inlineoverridevirtual

Reimplemented from bpp::AbstractParametrizable.

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

Definition at line 208 of file PhyloLikelihoodSet.h.

References getPhyloLikelihood(), and 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

overridevirtual

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 107 of file PhyloLikelihoodSet.cpp.

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

◆ getDerivableParameters()

ParameterList AbstractPhyloLikelihoodSet::getDerivableParameters ( ) const

overridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 95 of file PhyloLikelihoodSet.cpp.

References getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and 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()

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 bpp::AbstractPhyloLikelihood::getLikelihoodNode().

◆ 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

overridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 84 of file PhyloLikelihoodSet.cpp.

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

◆ getNumbersOfPhyloLikelihoods()

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 139 of file PhyloLikelihoodSet.h.

References nPhylo_.

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

◆ getPhyloContainer() [1/2]

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 134 of file PhyloLikelihoodSet.h.

References pPhyloCont_.

◆ getPhyloContainer() [2/2]

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 129 of file PhyloLikelihoodSet.h.

References pPhyloCont_.

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

◆ getPhyloLikelihood() [1/2]

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 169 of file PhyloLikelihoodSet.h.

References pPhyloCont_.

Referenced by addPhyloLikelihood(), fireParameterChanged(), getBranchLengthParameters(), getDerivableParameters(), bpp::PartitionProcessPhyloLikelihood::getLikelihoodCalculationForASite(), getNonDerivableParameters(), bpp::PartitionProcessPhyloLikelihood::getPhyloLikelihoodForASite(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), isInitialized(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), and bpp::PhyloLikelihoodFormula::readFormula().

◆ getPhyloLikelihood() [2/2]

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

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 175 of file PhyloLikelihoodSet.h.

References pPhyloCont_.

◆ getRateDistributionParameters()

ParameterList AbstractPhyloLikelihoodSet::getRateDistributionParameters ( ) const

overridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 129 of file PhyloLikelihoodSet.cpp.

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

◆ getRootFrequenciesParameters()

ParameterList AbstractPhyloLikelihoodSet::getRootFrequenciesParameters ( ) const

overridevirtual

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

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 140 of file PhyloLikelihoodSet.cpp.

References getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and 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

overridevirtual

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 118 of file PhyloLikelihoodSet.cpp.

References getPhyloLikelihood(), bpp::ParameterList::includeParameters(), and 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 )

inlineoverridevirtual

Implements bpp::PhyloLikelihoodSetInterface.

Definition at line 164 of file PhyloLikelihoodSet.h.

References nPhylo_.

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

◆ isInitialized()

bool bpp::AbstractPhyloLikelihoodSet::isInitialized ( ) const

inlineoverridevirtual

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

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 197 of file PhyloLikelihoodSet.h.

References getPhyloLikelihood(), and nPhylo_.

◆ 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=()

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

inlineprotected

Definition at line 118 of file PhyloLikelihoodSet.h.

References nPhylo_, bpp::AbstractPhyloLikelihood::operator=(), pPhyloCont_, and vLikCal_.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::operator=(), bpp::PartitionProcessPhyloLikelihood::operator=(), and bpp::PhyloLikelihoodFormula::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().

◆ 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 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().

◆ 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_

protected

vector of AbstractPhyloLikelihood numbers

Definition at line 79 of file PhyloLikelihoodSet.h.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet(), addPhyloLikelihood(), fireParameterChanged(), getBranchLengthParameters(), getDerivableParameters(), getNonDerivableParameters(), getNumbersOfPhyloLikelihoods(), getRateDistributionParameters(), getRootFrequenciesParameters(), getSubstitutionModelParameters(), hasPhyloLikelihood(), isInitialized(), bpp::PartitionProcessPhyloLikelihood::makeLikCal_(), and operator=().

◆ pPhyloCont_

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

protected

pointer to a PhyloLikelihoodContainer

Definition at line 74 of file PhyloLikelihoodSet.h.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getAlignedPhyloLikelihood(), getPhyloContainer(), getPhyloLikelihood(), 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_

mutableprotected

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

Definition at line 85 of file PhyloLikelihoodSet.h.

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

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

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

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractPhyloLikelihoodSet() [1/3]

◆ AbstractPhyloLikelihoodSet() [2/3]

◆ ~AbstractPhyloLikelihoodSet()

◆ AbstractPhyloLikelihoodSet() [3/3]

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()

◆ operator=()

◆ secondOrderDerivativeNode()

◆ setParameters()

◆ shareParameters()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_

◆ minusLogLik_

◆ nPhylo_

◆ pPhyloCont_

◆ secondOrderDerivativeNodes_

◆ vLikCal_