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
	Tell if there is a parameter with specified name. More...
const ParameterList &	getParameters () const
	Get all parameters available. More...
const Parameter &	getParameter (const std::string &name) const throw (ParameterNotFoundException)
	Get the parameter with specified name. More...
double	getParameterValue (const std::string &name) const throw (ParameterNotFoundException)
	Get the value for parameter of name 'name'. More...
void	setAllParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Set the parameters values to be equals to those of parameters. More...
void	setParameterValue (const std::string &name, double value) throw (ParameterNotFoundException, ConstraintException)
	Set the value of parameter with name name to be equal to value. More...
void	setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters. More...
bool	matchParametersValues (const ParameterList &parameters) throw (ConstraintException)
	Update the parameters from parameters. More...
size_t	getNumberOfParameters () const
	Get the number of parameters. More...
void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names. More...
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
	Resolves a parameter name according to the current namespace. More...
virtual void	fireParameterChanged (const ParameterList &parameters)=0
	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	deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name) throw (ParameterNotFoundException)
Parameter &	getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)
Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)
const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)
ParameterList &	getParameters_ ()

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 62 of file AbstractParametrizable.h.

Constructor & Destructor Documentation

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

inline

Definition at line 70 of file AbstractParametrizable.h.

virtual bpp::AbstractParametrizable::~AbstractParametrizable ( )

inlinevirtual

Definition at line 72 of file AbstractParametrizable.h.

Member Function Documentation

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

inlineprotected

Definition at line 136 of file AbstractParametrizable.h.

References parameters_.

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

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

inlineprotected

Definition at line 142 of file AbstractParametrizable.h.

References parameters_.

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

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::StdErr, bpp::FunctionStopCondition, bpp::StdOut, bpp::LinearMatrix< Scalar >, bpp::PlaceboTransformedParameter, bpp::StlOutputStreamWrapper, bpp::ParametersStopCondition, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::IntervalTransformedParameter, bpp::MetaOptimizer, bpp::StlOutputStream, bpp::DerivableSecondOrder, bpp::Parameter, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::IntervalConstraint, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::LowMemoryRescaledHmmLikelihood, bpp::NullOutputStream, bpp::LogsumHmmLikelihood, bpp::Simplex, bpp::RTransformedParameter, bpp::RescaledHmmLikelihood, bpp::DerivableFirstOrder, bpp::Optimizer, bpp::DownhillSimplexMethod, bpp::AbstractNumericalDerivative, bpp::SimpleDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::DualityDiagram, bpp::ReparametrizationFunctionWrapper, bpp::PrincipalComponentAnalysis, bpp::TruncatedExponentialDiscreteDistribution, bpp::DataTable, bpp::MetaOptimizerInfos, bpp::MixtureOfDiscreteDistributions, bpp::NewtonBacktrackOneDimension, bpp::AutoParameter, bpp::FivePointsNumericalDerivative, bpp::ParameterListener, bpp::ThreePointsNumericalDerivative, bpp::UNode, bpp::InvariantMixedDiscreteDistribution, bpp::PowellMultiDimensions, bpp::Range< T >, bpp::OutputStream, bpp::AliasParameterListener, bpp::BrentOneDimension, bpp::GammaDiscreteDistribution, bpp::GoldenSectionSearch, bpp::DirectionFunction, bpp::TwoPointsNumericalDerivative, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::BppVector< TYPE >, bpp::CorrespondenceAnalysis, bpp::Point2D< T >, bpp::Number< T >, bpp::BppString, bpp::BasicTNode, bpp::ParameterList, bpp::ContingencyTableTest, bpp::Font, bpp::BfgsMultiDimensions, bpp::BppBoolean, bpp::TNode, bpp::HmmLikelihood, bpp::GaussianDiscreteDistribution, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::OptimizationStopCondition, bpp::ParameterEvent, bpp::UniformDiscreteDistribution, bpp::DiscreteDistribution, bpp::MultipleDiscreteDistribution, bpp::ConstantDistribution, bpp::ConjugateGradientMultiDimensions, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::RGBColor, bpp::BrentOneDimension::BODStopCondition, bpp::ONode, bpp::GoldenSectionSearch::GSSStopCondition, bpp::PowellMultiDimensions::PMDStopCondition, bpp::SimpleMultiDimensions, bpp::SimpleNewtonMultiDimensions, bpp::HmmEmissionProbabilities, bpp::Constraint, bpp::TransformedParameter, and bpp::NewtonOneDimension.

void bpp::AbstractParametrizable::deleteParameter_ ( size_t  index ) throw (IndexOutOfBoundsException)

inlineprotected

Definition at line 147 of file AbstractParametrizable.h.

References parameters_, parameters_, and parameters_.

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

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

pure virtual

Notify the class when one or several parameters have changed.

Parameters

parameters

A ParameterList object with parameters that changed.

Implemented in bpp::TestFunction, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::AbstractParameterAliasable, bpp::RescaledHmmLikelihood, bpp::Simplex, bpp::MixtureOfDiscreteDistributions, bpp::ReparametrizationFunctionWrapper, bpp::SimpleDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::InvariantMixedDiscreteDistribution, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::UniformDiscreteDistribution, and bpp::ConstantDistribution.

Referenced by matchParametersValues(), setAllParametersValues(), setParametersValues(), and setParameterValue().

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

inlinevirtual

Returns

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

Implements bpp::Parametrizable.

Definition at line 124 of file AbstractParametrizable.h.

References prefix_.

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

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlinevirtual

Get the number of parameters.

See Also

getNumberOfIndependentParameters If some parameters are aliased.

Returns

The number of parameters.

Implements bpp::Parametrizable.

Definition at line 120 of file AbstractParametrizable.h.

References parameters_.

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

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string &  name ) const throw (ParameterNotFoundException)

inlinevirtual

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 79 of file AbstractParametrizable.h.

References parameters_.

Referenced by bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), getParameterValue(), getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::TestFunction::getValue(), and bpp::TestFunction::getValue().

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

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 parameters_.

Referenced by bpp::AbstractParameterAliasable::deleteParameter_(), getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

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

inlineprotected

Definition at line 188 of file AbstractParametrizable.h.

References parameters_, parameters_, and parameters_.

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

inlineprotected

Definition at line 194 of file AbstractParametrizable.h.

References parameters_, parameters_, and parameters_.

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

virtual

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 63 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

inlinevirtual

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 77 of file AbstractParametrizable.h.

References parameters_.

Referenced by bpp::AbstractParameterAliasable::fireParameterChanged(), and bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions().

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotected

Definition at line 201 of file AbstractParametrizable.h.

References parameters_.

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

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

inlinevirtual

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 84 of file AbstractParametrizable.h.

References getParameter(), and bpp::Parameter::getValue().

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

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

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 174 of file AbstractParametrizable.h.

References getParameter_().

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

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 183 of file AbstractParametrizable.h.

References getParameter().

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

inlinevirtual

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 75 of file AbstractParametrizable.h.

References parameters_.

Referenced by bpp::ConstantDistribution::fireParameterChanged().

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

inlinevirtual

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 111 of file AbstractParametrizable.h.

References fireParameterChanged(), and parameters_.

Referenced by bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::TestFunction::setParameters().

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotected

Definition at line 154 of file AbstractParametrizable.h.

References parameters_.

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

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters ) throw (ParameterNotFoundException, ConstraintException)

inlinevirtual

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 90 of file AbstractParametrizable.h.

References fireParameterChanged(), and parameters_.

void AbstractParametrizable::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 45 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters ) throw (ParameterNotFoundException, ConstraintException)

inlinevirtual

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 104 of file AbstractParametrizable.h.

References fireParameterChanged(), and parameters_.

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

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

inlinevirtual

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 97 of file AbstractParametrizable.h.

References fireParameterChanged(), and parameters_.

Member Data Documentation

ParameterList bpp::AbstractParametrizable::parameters_

private

Definition at line 66 of file AbstractParametrizable.h.

Referenced by addParameter_(), addParameters_(), deleteParameter_(), deleteParameter_(), deleteParameter_(), getNumberOfParameters(), getParameter(), getParameter_(), getParameter_(), getParameter_(), getParameter_(), getParameter_(), getParameter_(), getParameter_(), getParameters(), getParameters_(), hasParameter(), matchParametersValues(), resetParameters_(), setAllParametersValues(), setParametersValues(), setParameterValue(), and setParameterValue().

std::string bpp::AbstractParametrizable::prefix_

private

Definition at line 67 of file AbstractParametrizable.h.

Referenced by getNamespace(), getParameter(), getParameter_(), hasParameter(), setParameterValue(), and setParameterValue().

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

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