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...
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) throw (ParameterNotFoundException, Exception)
	Set two parameters as 'aliased'. More...
void	unaliasParameters (const std::string &p1, const std::string &p2) throw (ParameterNotFoundException, Exception)
	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...
std::vector< std::string >	getAlias (const std::string &name) const
std::string	getFrom (const std::string &name) const
void	fireParameterChanged (const ParameterList &parameters)
	Notify the class when one or several parameters have changed. More...
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...
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
	Resolves a parameter name according to the current namespace. 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	deleteParameter_ (std::string &name) throw (IndexOutOfBoundsException)
void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name) throw (ParameterNotFoundException)
Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)
const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)
Parameter &	getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)
ParameterList &	getParameters_ ()

Private Attributes
ParameterList	independentParameters_
std::map< std::string, 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 132 of file AbstractParameterAliasable.h.

Constructor & Destructor Documentation

AbstractParameterAliasable() [1/2]

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

inline

Definition at line 147 of file AbstractParameterAliasable.h.

AbstractParameterAliasable() [2/2]

AbstractParameterAliasable::AbstractParameterAliasable

(

const AbstractParameterAliasable &

ap

)

Definition at line 46 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AliasParameterListener::clone(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameters_(), and bpp::AliasParameterListener::setParameterList().

~AbstractParameterAliasable()

AbstractParameterAliasable::~AbstractParameterAliasable ( )

virtual

Definition at line 92 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_.

Member Function Documentation

addParameter_()

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

inlineprotected

Definition at line 212 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameter(), bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::clone(), and independentParameters_.

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 )

inlineprotected

Definition at line 218 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameters(), bpp::AbstractParametrizable::addParameters_(), and independentParameters_.

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

aliasParameters() [1/2]

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

virtual

Set two parameters as 'aliased'.

The values of the two parameters will be synchronized, so that setting the value of one parameter will automatically set the value of the other one accordingly.

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 association.

Implements bpp::ParameterAliasable.

Definition at line 103 of file AbstractParameterAliasable.cpp.

References bpp::Parameter::addParameterListener(), bpp::Parameter::getConstraint(), bpp::Constraint::getDescription(), and bpp::Parameter::hasConstraint().

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

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 151 of file AbstractParameterAliasable.cpp.

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

Referenced by aliasParameters().

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::StdErr, bpp::FunctionStopCondition, bpp::StdOut, bpp::PlaceboTransformedParameter, bpp::ColMatrix< Scalar >, bpp::StlOutputStreamWrapper, bpp::ParametersStopCondition, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::IntervalTransformedParameter, bpp::BppUnsignedInteger, bpp::MetaOptimizer, bpp::StlOutputStream, bpp::IntervalConstraint, bpp::DerivableSecondOrder, bpp::Parameter, bpp::RescaledHmmLikelihood, bpp::BppInteger, bpp::LogsumHmmLikelihood, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::BppDouble, bpp::LowMemoryRescaledHmmLikelihood, bpp::Simplex, bpp::NullOutputStream, bpp::RTransformedParameter, bpp::ParametrizableCollection< N >, bpp::DerivableFirstOrder, bpp::Optimizer, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::DownhillSimplexMethod, bpp::AbstractNumericalDerivative, bpp::SimpleDiscreteDistribution, bpp::ThreePointsNumericalDerivative, bpp::DirichletDiscreteDistribution, bpp::FivePointsNumericalDerivative, bpp::DualityDiagram, bpp::ReparametrizationFunctionWrapper, bpp::PrincipalComponentAnalysis, bpp::TruncatedExponentialDiscreteDistribution, bpp::MetaOptimizerInfos, bpp::MixtureOfDiscreteDistributions, bpp::NewtonBacktrackOneDimension, bpp::AutoParameter, bpp::DataTable, bpp::ParameterListener, bpp::UNode, bpp::InvariantMixedDiscreteDistribution, bpp::AliasParameterListener, bpp::PowellMultiDimensions, bpp::Range< T >, bpp::OutputStream, bpp::BrentOneDimension, bpp::TwoPointsNumericalDerivative, bpp::GammaDiscreteDistribution, bpp::GoldenSectionSearch, bpp::DirectionFunction, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::BppVector< TYPE >, bpp::CorrespondenceAnalysis, bpp::Point2D< T >, bpp::BppNotANumber, bpp::BppString, bpp::BasicTNode, bpp::HmmLikelihood, bpp::ParameterList, bpp::ContingencyTableTest, bpp::Font, bpp::BfgsMultiDimensions, bpp::FullHmmTransitionMatrix, bpp::BppBoolean, bpp::TNode, bpp::GaussianDiscreteDistribution, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::OptimizationStopCondition, bpp::ParameterEvent, bpp::UniformDiscreteDistribution, bpp::AutoCorrelationTransitionMatrix, 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::Constraint, bpp::HmmEmissionProbabilities, bpp::TransformedParameter, bpp::BppNumberI, and bpp::NewtonOneDimension.

deleteParameter_() [1/2]

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

inlineprotected

Definition at line 224 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameter_(), bpp::ParameterList::hasParameter(), and independentParameters_.

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

deleteParameter_() [2/2]

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

inlineprotected

Definition at line 232 of file AbstractParameterAliasable.h.

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

deleteParameters_()

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

inlineprotected

Definition at line 239 of file AbstractParameterAliasable.h.

References deleteParameter_().

fireParameterChanged()

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

inlinevirtual

Notify the class when one or several parameters have changed.

Parameters

parameters

A ParameterList object with parameters that changed.

Implements bpp::AbstractParametrizable.

Reimplemented in bpp::Simplex, bpp::ParametrizableCollection< N >, bpp::MixtureOfDiscreteDistributions, bpp::SimpleDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::InvariantMixedDiscreteDistribution, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::ConstantDistribution, and bpp::UniformDiscreteDistribution.

Definition at line 206 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::getParameters(), independentParameters_, and bpp::ParameterList::matchParametersValues().

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

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 245 of file AbstractParameterAliasable.cpp.

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

Referenced by 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 266 of file AbstractParameterAliasable.cpp.

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

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 306 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_.

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 162 of file AbstractParameterAliasable.h.

References independentParameters_.

getNamespace()

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

inlinevirtualinherited

Returns

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

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

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

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 164 of file AbstractParameterAliasable.h.

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

getNumberOfParameters()

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlinevirtualinherited

Get the number of parameters.

See also

getNumberOfIndependentParameters If some parameters are aliased.

Returns

The number of parameters.

Implements bpp::Parametrizable.

Definition at line 121 of file AbstractParametrizable.h.

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

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

getParameter()

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

inlinevirtualinherited

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(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

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

getParameter_() [1/3]

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

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 175 of file AbstractParametrizable.h.

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

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

getParameter_() [2/3]

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

inlineprotectedinherited

Definition at line 199 of file AbstractParametrizable.h.

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

getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 205 of file AbstractParametrizable.h.

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

getParameterNameWithoutNamespace()

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

virtualinherited

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().

getParameters()

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

inlinevirtualinherited

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 bpp::AbstractParametrizable::parameters_.

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

getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotectedinherited

Definition at line 212 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

getParameterValue()

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

inlinevirtualinherited

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

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

getParameterWithNamespace_() [1/2]

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

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::getParameter_().

getParameterWithNamespace_() [2/2]

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

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 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

hasParameter()

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

inlinevirtualinherited

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(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

matchParametersValues()

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

inlinevirtualinherited

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

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

operator=()

AbstractParameterAliasable & AbstractParameterAliasable::operator=

(

const AbstractParameterAliasable &

ap

)

Definition at line 69 of file AbstractParameterAliasable.cpp.

References aliasListenersRegister_, bpp::AliasParameterListener::clone(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameters_(), independentParameters_, and bpp::AliasParameterListener::setParameterList().

Referenced by bpp::ConstantDistribution::operator=(), bpp::UniformDiscreteDistribution::operator=(), bpp::GaussianDiscreteDistribution::operator=(), bpp::ExponentialDiscreteDistribution::operator=(), bpp::BetaDiscreteDistribution::operator=(), bpp::InvariantMixedDiscreteDistribution::operator=(), bpp::GammaDiscreteDistribution::operator=(), bpp::TruncatedExponentialDiscreteDistribution::operator=(), bpp::MixtureOfDiscreteDistributions::operator=(), bpp::ParametrizableCollection< N >::operator=(), bpp::SimpleDiscreteDistribution::operator=(), and bpp::AbstractDiscreteDistribution::operator=().

resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotected

Definition at line 249 of file AbstractParameterAliasable.h.

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

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

setAllParametersValues()

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

inlinevirtualinherited

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

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 218 of file AbstractParameterAliasable.cpp.

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

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

setParametersValues()

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

inlinevirtualinherited

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 bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, 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  ) throw ( ParameterNotFoundException, ConstraintException )

inlinevirtualinherited

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

unaliasParameters()

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

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 198 of file AbstractParameterAliasable.cpp.

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

Member Data Documentation

aliasListenersRegister_

std::map<std::string, 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 144 of file AbstractParameterAliasable.h.

Referenced by AbstractParameterAliasable(), getAlias(), getAliasedParameters(), getFrom(), operator=(), setNamespace(), and ~AbstractParameterAliasable().

independentParameters_

ParameterList bpp::AbstractParameterAliasable::independentParameters_

mutableprivate

Definition at line 138 of file AbstractParameterAliasable.h.

Referenced by addParameter_(), addParameters_(), deleteParameter_(), fireParameterChanged(), getIndependentParameters(), getNumberOfIndependentParameters(), operator=(), resetParameters_(), and setNamespace().

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

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