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:

List of all members.

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.
const ParameterList &	getParameters () const
	Get all parameters available.
const Parameter &	getParameter (const std::string &name) const throw (ParameterNotFoundException)
	Get the parameter with specified name.
double	getParameterValue (const std::string &name) const throw (ParameterNotFoundException)
	Get the value for parameter of name 'name'.
void	setAllParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Set the parameters values to be equals to those of parameters.
void	setParameterValue (const std::string &name, double value) throw (ParameterNotFoundException, ConstraintException)
	Set the value of parameter with name name to be equal to value.
void	setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters.
bool	matchParametersValues (const ParameterList &parameters) throw (ConstraintException)
	Update the parameters from parameters.
size_t	getNumberOfParameters () const
	Get the number of parameters.
void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names.
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
	Resolves a parameter name according to the current namespace.
virtual void	fireParameterChanged (const ParameterList &parameters)=0
	Notify the class when one or several parameters have changed.
virtual Clonable *	clone () const =0
	Create a copy of this object and send a pointer to it.
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_

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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.

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Constructor & Destructor Documentation

bpp::AbstractParametrizable::AbstractParametrizable

(

const std::string &

prefix

)

[inline]

Definition at line 70 of file AbstractParametrizable.h.

virtual bpp::AbstractParametrizable::~AbstractParametrizable

(

)

[inline, virtual]

Definition at line 72 of file AbstractParametrizable.h.

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Member Function Documentation

void bpp::AbstractParametrizable::addParameter_

(

Parameter *

parameter

)

[inline, protected]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 136 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter(), and parameters_.

Referenced by bpp::TestFunction::TestFunction().

void bpp::AbstractParametrizable::addParameters_

(

const ParameterList &

parameters

)

[inline, protected]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 142 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters(), and parameters_.

virtual Clonable* bpp::Clonable::clone

(

)

const [pure virtual, inherited]

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::AliasParameterListener, bpp::PowellMultiDimensions, bpp::Range< T >, bpp::OutputStream, 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::ConstantDistribution, bpp::DiscreteDistribution, bpp::MultipleDiscreteDistribution, 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) [inline, protected]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 147 of file AbstractParametrizable.h.

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

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::AbstractParameterAliasable, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, 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 [inline, virtual]

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::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::write().

size_t bpp::AbstractParametrizable::getNumberOfParameters

(

)

const [inline, virtual]

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

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) [inline, virtual]

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 bpp::ParameterList::getParameter(), parameters_, and prefix_.

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

Parameter& bpp::AbstractParametrizable::getParameter_

(

const std::string &

name

)

throw (ParameterNotFoundException) [inline, protected]

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::ParameterList::getParameter(), parameters_, and prefix_.

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

Parameter& bpp::AbstractParametrizable::getParameter_

(

size_t

index

)

throw (IndexOutOfBoundsException) [inline, protected]

Definition at line 188 of file AbstractParametrizable.h.

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

const Parameter& bpp::AbstractParametrizable::getParameter_

(

size_t

index

)

const throw (IndexOutOfBoundsException) [inline, protected]

Definition at line 194 of file AbstractParametrizable.h.

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

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 [inline, virtual]

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_

(

)

[inline, protected]

Definition at line 201 of file AbstractParametrizable.h.

References parameters_.

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

double bpp::AbstractParametrizable::getParameterValue

(

const std::string &

name

)

const throw (ParameterNotFoundException) [inline, virtual]

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::GammaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_

(

const std::string &

name

)

throw (ParameterNotFoundException) [inline, protected]

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) [inline, protected]

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 [inline, virtual]

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 bpp::ParameterList::hasParameter(), parameters_, and prefix_.

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

bool bpp::AbstractParametrizable::matchParametersValues

(

const ParameterList &

parameters

)

throw (ConstraintException) [inline, virtual]

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(), bpp::ParameterList::matchParametersValues(), and parameters_.

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

void bpp::AbstractParametrizable::resetParameters_

(

)

[inline, protected]

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 154 of file AbstractParametrizable.h.

References parameters_, and bpp::ParameterList::reset().

void bpp::AbstractParametrizable::setAllParametersValues

(

const ParameterList &

parameters

)

throw (ParameterNotFoundException, ConstraintException) [inline, virtual]

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

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::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 45 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

void bpp::AbstractParametrizable::setParametersValues

(

const ParameterList &

parameters

)

throw (ParameterNotFoundException, ConstraintException) [inline, virtual]

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

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) [inline, virtual]

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(), parameters_, prefix_, bpp::ParameterList::setParameterValue(), and bpp::ParameterList::subList().

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Member Data Documentation

ParameterList bpp::AbstractParametrizable::parameters_ [private]

Definition at line 66 of file AbstractParametrizable.h.

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

std::string bpp::AbstractParametrizable::prefix_ [private]

Definition at line 67 of file AbstractParametrizable.h.

Referenced by getNamespace(), getParameter(), getParameter_(), hasParameter(), 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