bpp::AbstractParameterAliasable Class Reference

A partial implementation of the Parametrizable interface. More...

#include <Bpp/Numeric/AbstractParameterAliasable.h>

Inheritance diagram for bpp::AbstractParameterAliasable:

Collaboration diagram for bpp::AbstractParameterAliasable:

Public Member Functions
	AbstractParameterAliasable (const std::string &prefix)
	AbstractParameterAliasable (const AbstractParameterAliasable &ap)
AbstractParameterAliasable &	operator= (const AbstractParameterAliasable &ap)
virtual	~AbstractParameterAliasable ()
void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names. More...
bool	hasIndependentParameter (const std::string &name) const
const ParameterList &	getIndependentParameters () const
	Get the minimal list of parameters to set the model. More...
size_t	getNumberOfIndependentParameters () const
	Get the number of independent parameters. More...
void	aliasParameters (const std::string &p1, const std::string &p2)
	alias the parameters. More...
void	unaliasParameters (const std::string &p1, const std::string &p2)
	Detach two parameters previously set as 'aliased'. More...
void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
	alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
ParameterList	getAliasedParameters (const ParameterList &pl) const
	Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More...
ParameterList	getFromParameters (const ParameterList &pl) const
	Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not). More...
virtual std::vector< std::string >	getAlias (const std::string &name) const
virtual std::map< std::string, std::string >	getAliases () const
std::string	getFrom (const std::string &name) const
bool	hasParameter (const std::string &name) const override
	Tell if there is a parameter with specified name. More...
const ParameterList &	getParameters () const override
	Get all parameters available. More...
const Parameter &	parameter (const std::string &name) const override
	Get the parameter with specified name. More...
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
double	getParameterValue (const std::string &name) const override
	Get the value for parameter of name 'name'. More...
void	setAllParametersValues (const ParameterList &parameters) override
	Set the parameters values to be equals to those of parameters. More...
void	setParameterValue (const std::string &name, double value) override
	Set the value of parameter with name name to be equal to value. More...
void	setParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...
bool	matchParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...
void	removeConstraint (const std::string &name) override
	Remove the constraint associated with one parameter, if any. More...
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
	Set/Change the constraint associated with one parameter. More...
size_t	getNumberOfParameters () const override
	Get the number of parameters. More...
std::string	getNamespace () const override
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
	Resolves a parameter name according to the current namespace. More...
virtual void	fireParameterChanged (const ParameterList &parameters)
	Notify the class when one or several parameters have changed. More...
virtual Clonable *	clone () const =0
	Create a copy of this object and send a pointer to it. More...

Protected Member Functions
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)
void	shareParameters_ (const ParameterList &parameters)
void	includeParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index)
void	deleteParameter_ (std::string &name)
void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)
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
	Get all parameters available. More...

Private Attributes
ParameterList	independentParameters_
std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

Detailed Description

A partial implementation of the Parametrizable interface.

Parameters are stored in a protected ParameterList object.

The abstract fireParameterChanged() method is provided so that the derived class know when a parameter has changed, and can be updated. All methods call the corresponding method in ParameterList and then call the fireParameterChanged() method.

Definition at line 104 of file AbstractParameterAliasable.h.

Constructor & Destructor Documentation

AbstractParameterAliasable() [1/2]

bpp::AbstractParameterAliasable::AbstractParameterAliasable ( const std::string &  prefix )

inline

Definition at line 118 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::operator=().

AbstractParameterAliasable() [2/2]

AbstractParameterAliasable::AbstractParameterAliasable

(

const AbstractParameterAliasable &

ap

)

Definition at line 11 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getParameters_(), independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

~AbstractParameterAliasable()

virtual bpp::AbstractParameterAliasable::~AbstractParameterAliasable ( )

inlinevirtual

Definition at line 128 of file AbstractParameterAliasable.h.

Member Function Documentation

addParameter_()

void bpp::AbstractParameterAliasable::addParameter_ ( Parameter *  parameter )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 196 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::getName(), and bpp::ParameterList::shareParameter().

Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ConstantDistribution::ConstantDistribution(), bpp::DirichletDiscreteDistribution::DirichletDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::Simplex::Simplex(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().

addParameters_()

void bpp::AbstractParameterAliasable::addParameters_ ( const ParameterList &  parameters )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 202 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameters_(), bpp::AliasParameterListener::getName(), bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), and bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions().

aliasParameters() [1/2]

void AbstractParameterAliasable::aliasParameters ( const std::string &  p1, const std::string &  p2  )

virtual

alias the parameters.

Parameters

p1	name of the parameter to which the other parameter is aliased
p2	name of the aliased parameter, which will be deleted from independent parameters list

Implements bpp::ParameterAliasable.

Definition at line 67 of file AbstractParameterAliasable.cpp.

References bpp::Parameter::addParameterListener(), aliasListenersRegister_, bpp::ParameterList::deleteParameter(), bpp::ApplicationTools::displayWarning(), bpp::Parameter::getConstraint(), bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::Parameter::hasConstraint(), bpp::AbstractParametrizable::hasParameter(), bpp::ParameterList::hasParameter(), independentParameters_, bpp::Parameter::setConstraint(), bpp::ParameterList::shareParameters(), bpp::ParameterList::size(), and bpp::ParameterList::whichParameterHasName().

Referenced by bpp::ParametrizableCollection< N >::addObject(), and aliasParameters().

aliasParameters() [2/2]

void AbstractParameterAliasable::aliasParameters ( std::map< std::string, std::string > &  unparsedParams, bool  verbose  )

virtual

alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden.

Parameters

unparsedParams	the map of the links : <A,B> matches for A->B aliasing.
verbose	verbosity

Implements bpp::ParameterAliasable.

Definition at line 120 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), aliasParameters(), bpp::ParameterList::clone(), bpp::Parameter::clone(), bpp::ApplicationTools::displayResult(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::matchParametersValues(), bpp::ParameterList::parameter(), bpp::ParameterList::size(), and bpp::TextTools::toString().

clone()

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

pure virtualinherited

Create a copy of this object and send a pointer to it.

Returns

A pointer toward the copy object.

Implemented in bpp::TestFunction, bpp::InfinityDerivableSecondOrderWrapper, bpp::InfinityDerivableFirstOrderWrapper, bpp::InfinityFunctionWrapper, bpp::LinearMatrix< Scalar >, bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >, bpp::StdErr, bpp::FunctionStopCondition, bpp::ColMatrix< Scalar >, bpp::PlaceboTransformedParameter, bpp::StdOut, bpp::GlobalGraph, bpp::ParametersStopCondition, bpp::StlOutputStreamWrapper, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::IntervalTransformedParameter, bpp::MetaOptimizer, bpp::IntervalConstraint, bpp::BppUnsignedInteger, bpp::StlOutputStream, bpp::SecondOrderDerivable, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::BppInteger, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::Parameter, bpp::Simplex, bpp::LowMemoryRescaledHmmLikelihood, bpp::Table< T >, bpp::AbstractNumericalDerivative, bpp::BppDouble, bpp::RTransformedParameter, bpp::NullOutputStream, bpp::ParametrizableCollection< N >, bpp::FirstOrderDerivable, bpp::OptimizerInterface, bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl >, bpp::ThreePointsNumericalDerivative, bpp::DirichletDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::DownhillSimplexMethod, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::FivePointsNumericalDerivative, bpp::ReparametrizationFunctionWrapper, bpp::DataTable, bpp::PrincipalComponentAnalysis, bpp::DualityDiagram, bpp::TruncatedExponentialDiscreteDistribution, bpp::MetaOptimizerInfos, bpp::BrentOneDimension, bpp::NewtonBacktrackOneDimension, bpp::FunctionOperator< F >, bpp::AutoParameter, bpp::GammaDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::AliasParameterListener, bpp::Range< T >, bpp::PowellMultiDimensions, bpp::InvariantMixedDiscreteDistribution, bpp::TwoPointsNumericalDerivative, bpp::ParameterListener, bpp::OutputStream, bpp::GoldenSectionSearch, bpp::DirectionFunction, bpp::Point2D< T >, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ParameterList, bpp::CorrespondenceAnalysis, bpp::HmmLikelihood, bpp::GaussianDiscreteDistribution, bpp::BfgsMultiDimensions, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::FullHmmTransitionMatrix, bpp::BppNotANumber, bpp::UniformDiscreteDistribution, bpp::ContingencyTableTest, bpp::Font, bpp::ConstantDistribution, bpp::DiscreteDistributionInterface, bpp::MultipleDiscreteDistribution, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::MathOperator, bpp::BrentOneDimension::BODStopCondition, bpp::ConjugateGradientMultiDimensions, bpp::OptimizationStopCondition, bpp::AutoCorrelationTransitionMatrix, bpp::ParameterEvent, bpp::ComputationTree, bpp::GoldenSectionSearch::GSSStopCondition, bpp::PowellMultiDimensions::PMDStopCondition, bpp::ConstraintInterface, bpp::HmmStateAlphabet, bpp::RGBColor, bpp::SimpleMultiDimensions, bpp::SimpleNewtonMultiDimensions, bpp::HmmEmissionProbabilities, bpp::BinaryOperator, bpp::BppVector< T >, bpp::TransformedParameter, bpp::BppString, bpp::ConstantOperator, bpp::NegativeOperator, bpp::HmmTransitionMatrix, bpp::BppNumberI, bpp::BppBoolean, and bpp::NewtonOneDimension.

Referenced by bpp::FirstOrderDerivable::~FirstOrderDerivable(), and bpp::SecondOrderDerivable::~SecondOrderDerivable().

deleteParameter_() [1/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( size_t  index )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 237 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), and bpp::ParameterList::hasParameter().

Referenced by bpp::ParametrizableCollection< N >::removeObject().

deleteParameter_() [2/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( std::string &  name )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 245 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), and bpp::ParameterList::hasParameter().

deleteParameters_()

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

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 252 of file AbstractParameterAliasable.h.

fireParameterChanged()

virtual void bpp::AbstractParametrizable::fireParameterChanged ( const ParameterList &  parameters )

inlinevirtualinherited

Notify the class when one or several parameters have changed.

Parameters

parameters

A ParameterList object with parameters that changed.

Reimplemented in bpp::TestFunction, bpp::OrderedSimplex, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::Simplex, bpp::ParametrizableCollection< N >, bpp::ReparametrizationFunctionWrapper, bpp::MixtureOfDiscreteDistributions, bpp::SimpleDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::FullHmmTransitionMatrix, bpp::TruncatedExponentialDiscreteDistribution, bpp::AutoCorrelationTransitionMatrix, bpp::GammaDiscreteDistribution, bpp::InvariantMixedDiscreteDistribution, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::UniformDiscreteDistribution, and bpp::ConstantDistribution.

Definition at line 108 of file AbstractParametrizable.h.

Referenced by bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::DirichletDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::AbstractParametrizable::matchParametersValues(), bpp::AbstractParametrizable::setAllParametersValues(), bpp::AbstractParametrizable::setParametersValues(), and bpp::AbstractParametrizable::setParameterValue().

getAlias()

vector< string > AbstractParameterAliasable::getAlias ( const std::string &  name ) const

virtual

Returns

The list of names of the parameters that are aliased with a given parameter. The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.

Parameters

name	The name of the parameter to look for.

Implements bpp::ParameterAliasable.

Definition at line 204 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, and bpp::VectorTools::append().

Referenced by getAliases(), and bpp::ParametrizableCollection< N >::removeObject().

getAliasedParameters()

ParameterList AbstractParameterAliasable::getAliasedParameters

(

const ParameterList &

pl

)

const

Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list.

Definition at line 244 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), aliasListenersRegister_, bpp::ParameterList::hasParameter(), and bpp::AbstractParametrizable::parameter().

getAliases()

std::map< std::string, std::string > AbstractParameterAliasable::getAliases ( ) const

virtual

Returns

the map of the aliases.

Implements bpp::ParameterAliasable.

Definition at line 225 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, and getAlias().

getFrom()

string AbstractParameterAliasable::getFrom

(

const std::string &

name

)

const

Returns

The name of the parameter from which a given parameter is aliased.

Parameters

name	The name of the parameter to look for.

Definition at line 280 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_.

getFromParameters()

ParameterList AbstractParameterAliasable::getFromParameters

(

const ParameterList &

pl

)

const

Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not).

Definition at line 297 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), aliasListenersRegister_, bpp::ParameterList::hasParameter(), and bpp::AbstractParametrizable::parameter().

getIndependentParameters()

const ParameterList& bpp::AbstractParameterAliasable::getIndependentParameters ( ) const

inlinevirtual

Get the minimal list of parameters to set the model.

If no parameters are aliased, this is the same a getParameters().

Returns

A minimal set of parameters.

Implements bpp::ParameterAliasable.

Definition at line 135 of file AbstractParameterAliasable.h.

getNamespace()

std::string bpp::AbstractParametrizable::getNamespace ( ) const

inlineoverridevirtualinherited

Returns

The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), and bpp::AbstractParametrizable::prefix_.

Referenced by aliasParameters(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), and setNamespace().

getNumberOfIndependentParameters()

size_t bpp::AbstractParameterAliasable::getNumberOfIndependentParameters ( ) const

inlinevirtual

Get the number of independent parameters.

Returns

The number of independent parameters. If no parameters are aliased, this is equivalent to the getNumberOfParameters() method.

Implements bpp::ParameterAliasable.

Definition at line 137 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::getAlias(), bpp::AliasParameterListener::getFrom(), and bpp::ParameterList::size().

getNumberOfParameters()

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also

getNumberOfIndependentParameters If some parameters are aliased.

Returns

The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::setNamespace(), and bpp::ParameterList::size().

Referenced by AbstractParameterAliasable(), aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

getParameter() [1/3]

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

inlineinherited

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

Referenced by AbstractParameterAliasable(), operator=(), and unaliasParameters().

getParameter() [2/3]

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

inlineprotectedinherited

Returns

The shared_ptr parameter at a given position.

Warning

No check is performed on the validity of the index given as input!

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

getParameter() [3/3]

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

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

getParameter_() [1/3]

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

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 164 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::hasParameter(), and bpp::ParameterList::parameter().

Referenced by aliasParameters(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::AbstractParametrizable::removeConstraint(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::AbstractParametrizable::setConstraint(), and unaliasParameters().

getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index )

inlineprotectedinherited

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index ) const

inlineprotectedinherited

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

getParameterNameWithoutNamespace()

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

overridevirtualinherited

Resolves a parameter name according to the current namespace.

Returns

The parameter name without the namespace prefix, if any.

Implements bpp::Parametrizable.

Definition at line 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by AbstractParameterAliasable(), bpp::AbstractParametrizable::getNamespace(), and operator=().

getParameters()

const ParameterList& bpp::AbstractParametrizable::getParameters ( ) const

inlineoverridevirtualinherited

Get all parameters available.

See also

getIndependentParameters if some parameters are aliased.

Returns

A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by aliasParameters(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().

getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtualinherited

Get all parameters available.

See also

getIndependentParameters if some parameters are aliased.

Returns

A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by AbstractParameterAliasable(), aliasParameters(), and operator=().

getParameterValue()

double bpp::AbstractParametrizable::getParameterValue ( const std::string &  name ) const

inlineoverridevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns

the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 53 of file AbstractParametrizable.h.

References bpp::Parameter::getValue(), and bpp::AbstractParametrizable::parameter().

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

getParameterWithNamespace_() [2/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameter().

hasIndependentParameter()

bool bpp::AbstractParameterAliasable::hasIndependentParameter ( const std::string &  name ) const

inline

Definition at line 133 of file AbstractParameterAliasable.h.

References bpp::ParameterList::hasParameter().

hasParameter()

bool bpp::AbstractParametrizable::hasParameter ( const std::string &  name ) const

inlineoverridevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns

y/n.

Implements bpp::Parametrizable.

Definition at line 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

Referenced by aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and unaliasParameters().

includeParameters_()

void bpp::AbstractParameterAliasable::includeParameters_ ( const ParameterList &  parameters )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 227 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::getName(), bpp::AbstractParametrizable::includeParameters_(), bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

matchParametersValues()

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList &  parameters )

inlineoverridevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters

A list of parameters.

Returns

True if at least one parameter value has been changed.

Exceptions

ConstraintException

If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 76 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), and bpp::ParameterList::shareSubList().

Referenced by aliasParameters(), bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

operator=()

AbstractParameterAliasable & AbstractParameterAliasable::operator=

(

const AbstractParameterAliasable &

ap

)

Definition at line 39 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getParameters_(), independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

Referenced by bpp::ParametrizableCollection< N >::operator=(), and bpp::AbstractDiscreteDistribution::operator=().

parameter()

const Parameter& bpp::AbstractParametrizable::parameter ( const std::string &  name ) const

inlineoverridevirtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns

The parameter with given name.

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

Referenced by getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), and bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative().

removeConstraint()

void bpp::AbstractParametrizable::removeConstraint ( const std::string &  name )

inlineoverridevirtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::removeConstraint().

resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotected

Definition at line 262 of file AbstractParameterAliasable.h.

References bpp::ParameterList::reset(), and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::ParametrizableCollection< N >::clear().

setAllParametersValues()

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters )

inlineoverridevirtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

parameters

A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 58 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setAllParametersValues().

setConstraint()

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

inlineoverridevirtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::setConstraint().

Referenced by bpp::SimpleDiscreteDistribution::restrictToConstraint().

setNamespace()

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

virtual

Set the namespace for the parameter names.

Parameters

prefix

The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implements bpp::Parametrizable.

Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 186 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::setNamespace(), and bpp::TextTools::startsWith().

Referenced by bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::MixtureOfDiscreteDistributions::setNamespace().

setParametersValues()

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters )

inlineoverridevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters

A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 70 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParametersValues().

Referenced by bpp::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::LogsumHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().

setParameterValue()

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

inlineoverridevirtualinherited

Set the value of parameter with name name to be equal to value.

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 64 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParameterValue().

shareParameter_()

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

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 212 of file AbstractParameterAliasable.h.

References bpp::ParameterList::shareParameter(), and bpp::AbstractParametrizable::shareParameter_().

shareParameters_()

void bpp::AbstractParameterAliasable::shareParameters_ ( const ParameterList &  parameters )

inlineprotectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 218 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::getName(), bpp::ParameterList::shareParameter(), bpp::AbstractParametrizable::shareParameters_(), and bpp::ParameterList::size().

unaliasParameters()

void AbstractParameterAliasable::unaliasParameters ( const std::string &  p1, const std::string &  p2  )

virtual

Detach two parameters previously set as 'aliased'.

The values of the two parameters will now be independent.

Parameters

p1	Original parameter.
p2	Aliased parameter.

Exceptions

ParameterNotFoundException	if p1 or p2 do not correspond to existing parameters.
Exception	when trying to perform non-valid dissociation.

Implements bpp::ParameterAliasable.

Definition at line 168 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::hasParameter(), independentParameters_, bpp::Parameter::removeParameterListener(), and bpp::ParameterList::shareParameter().

Referenced by bpp::ParametrizableCollection< N >::removeObject().

Member Data Documentation

aliasListenersRegister_

std::map<std::string, std::shared_ptr<AliasParameterListener> > bpp::AbstractParameterAliasable::aliasListenersRegister_

private

Contains all parameter listeners for maintening alias relationships. The registry will be updated appropriately upon cloning and deleting.

Definition at line 115 of file AbstractParameterAliasable.h.

Referenced by AbstractParameterAliasable(), aliasParameters(), getAlias(), getAliasedParameters(), getAliases(), getFrom(), getFromParameters(), operator=(), setNamespace(), and unaliasParameters().

independentParameters_

ParameterList bpp::AbstractParameterAliasable::independentParameters_

mutableprivate

Definition at line 109 of file AbstractParameterAliasable.h.

Referenced by AbstractParameterAliasable(), aliasParameters(), operator=(), and unaliasParameters().

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

• Bpp/Numeric/AbstractParameterAliasable.h
• Bpp/Numeric/AbstractParameterAliasable.cpp