bpp::AbstractParametrizable Class Reference

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

#include <Bpp/Numeric/AbstractParametrizable.h>

Inheritance diagram for bpp::AbstractParametrizable:

Collaboration diagram for bpp::AbstractParametrizable:

Public Member Functions
	AbstractParametrizable (const std::string &prefix)
virtual	~AbstractParametrizable ()
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...
void	setNamespace (const std::string &prefix) override
	Set the namespace for the parameter names. 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
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 &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
ParameterList &	getParameters_ () override
	Get all parameters available. More...
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)

Private Attributes
ParameterList	parameters_
std::string	prefix_

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 26 of file AbstractParametrizable.h.

Constructor & Destructor Documentation

AbstractParametrizable()

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

inline

Definition at line 34 of file AbstractParametrizable.h.

~AbstractParametrizable()

virtual bpp::AbstractParametrizable::~AbstractParametrizable ( )

inlinevirtual

Definition at line 36 of file AbstractParametrizable.h.

Member Function Documentation

addParameter_()

virtual void bpp::AbstractParametrizable::addParameter_ ( Parameter *  parameter )

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 111 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter().

Referenced by bpp::AbstractParameterAliasable::addParameter_(), and bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix().

addParameters_()

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

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 117 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters().

Referenced by bpp::AbstractParameterAliasable::addParameters_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().

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]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( size_t  index )

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::deleteParameter_().

deleteParameter_() [2/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( std::string &  name )

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 144 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter().

deleteParameters_()

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

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 149 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters().

fireParameterChanged()

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

inlinevirtual

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

getNamespace()

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

inlineoverridevirtual

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 getParameterNameWithoutNamespace(), and prefix_.

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

getNumberOfParameters()

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtual

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

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

getParameter() [1/3]

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

inline

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

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

getParameter() [2/3]

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

inlineprotected

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 )

inlineprotected

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

getParameter_() [1/3]

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

inlineprotected

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

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

getParameter_() [2/3]

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

inlineprotected

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

getParameter_() [3/3]

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

inlineprotected

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

getParameterNameWithoutNamespace()

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

overridevirtual

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 bpp::AbstractParameterAliasable::AbstractParameterAliasable(), getNamespace(), and bpp::AbstractParameterAliasable::operator=().

getParameters()

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

inlineoverridevirtual

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 parameters_.

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

getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtual

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 parameters_.

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

getParameterValue()

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

inlineoverridevirtual

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 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::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

getParameterWithNamespace_() [1/2]

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

inlineprotected

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 getParameter_().

getParameterWithNamespace_() [2/2]

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

inlineprotected

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 parameter().

hasParameter()

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

inlineoverridevirtual

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 bpp::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().

includeParameters_()

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

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 132 of file AbstractParametrizable.h.

References bpp::ParameterList::includeParameters().

Referenced by bpp::AbstractParameterAliasable::includeParameters_().

matchParametersValues()

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

inlineoverridevirtual

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

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

parameter()

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

inlineoverridevirtual

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 bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), getParameterValue(), getParameterWithNamespace_(), and bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative().

removeConstraint()

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

inlineoverridevirtual

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

resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotected

Definition at line 154 of file AbstractParametrizable.h.

References bpp::ParameterList::reset().

Referenced by bpp::AbstractParameterAliasable::resetParameters_().

setAllParametersValues()

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

inlineoverridevirtual

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

setConstraint()

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

inlineoverridevirtual

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

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

setNamespace()

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

overridevirtual

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::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 10 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by getNumberOfParameters(), bpp::AbstractParameterAliasable::setNamespace(), bpp::LowMemoryRescaledHmmLikelihood::setNamespace(), bpp::LogsumHmmLikelihood::setNamespace(), and bpp::RescaledHmmLikelihood::setNamespace().

setParametersValues()

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

inlineoverridevirtual

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

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

setParameterValue()

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

inlineoverridevirtual

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(), fireParameterChanged(), and bpp::ParameterList::setParameterValue().

shareParameter_()

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

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 122 of file AbstractParametrizable.h.

References bpp::ParameterList::shareParameter().

Referenced by bpp::AbstractParameterAliasable::shareParameter_().

shareParameters_()

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

inlineprotectedvirtual

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 127 of file AbstractParametrizable.h.

References bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractParameterAliasable::shareParameters_().

Member Data Documentation

parameters_

ParameterList bpp::AbstractParametrizable::parameters_

private

Definition at line 30 of file AbstractParametrizable.h.

Referenced by getParameters(), and getParameters_().

prefix_

std::string bpp::AbstractParametrizable::prefix_

private

Definition at line 31 of file AbstractParametrizable.h.

Referenced by getNamespace().

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

• Bpp/Numeric/AbstractParametrizable.h
• Bpp/Numeric/AbstractParametrizable.cpp