bpp::ParameterAliasableAdapter Class Reference

A low-level implementation of the ParameterAliasable interface with void functions. More...

#include <Bpp/Numeric/ParameterAliasable.h>

Inheritance diagram for bpp::ParameterAliasableAdapter:

Collaboration diagram for bpp::ParameterAliasableAdapter:

Public Member Functions
	ParameterAliasableAdapter ()
virtual	~ParameterAliasableAdapter ()
virtual Clonable *	clone () const =0
	Create a copy of this object and send a pointer to it. More...
The ParameterAliasable interface.
const ParameterList &	getIndependentParameters () const
void	aliasParameters (const std::string &p1, const std::string &p2)
void	unaliasParameters (const std::string &p1, const std::string &p2)
unsigned int	getNumberOfIndependentParameters () const
std::vector< std::string >	getAlias (const std::string &name) const
std::map< std::string, std::string >	getAliases () const
The Parametrizable interface.
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...
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...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0
	Get all parameters available. More...

Protected Attributes
ParameterList	parameters_
Parameter	parameter_

Detailed Description

A low-level implementation of the ParameterAliasable interface with void functions.

See also

Parameter, ParameterList, ParameterAliasable

Definition at line 128 of file ParameterAliasable.h.

Constructor & Destructor Documentation

ParameterAliasableAdapter()

bpp::ParameterAliasableAdapter::ParameterAliasableAdapter ( )

inline

Definition at line 132 of file ParameterAliasable.h.

~ParameterAliasableAdapter()

virtual bpp::ParameterAliasableAdapter::~ParameterAliasableAdapter ( )

inlinevirtual

Definition at line 133 of file ParameterAliasable.h.

Member Function Documentation

aliasParameters()

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

inline

Definition at line 142 of file ParameterAliasable.h.

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().

getAlias()

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

inline

Definition at line 145 of file ParameterAliasable.h.

getAliases()

std::map<std::string, std::string> bpp::ParameterAliasableAdapter::getAliases ( ) const

inline

Definition at line 146 of file ParameterAliasable.h.

getIndependentParameters()

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

inline

Definition at line 141 of file ParameterAliasable.h.

References bpp::Parametrizable::getParameters().

getNamespace()

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

inlineoverridevirtualinherited

Returns

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

Implements bpp::Parametrizable.

Definition at line 204 of file Parametrizable.h.

getNumberOfIndependentParameters()

unsigned int bpp::ParameterAliasableAdapter::getNumberOfIndependentParameters ( ) const

inline

Definition at line 144 of file ParameterAliasable.h.

getNumberOfParameters()

size_t bpp::ParametrizableAdapter::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also

getNumberOfIndependentParameters If some parameters are aliased.

Returns

The number of parameters.

Implements bpp::Parametrizable.

Definition at line 202 of file Parametrizable.h.

getParameterNameWithoutNamespace()

std::string bpp::ParametrizableAdapter::getParameterNameWithoutNamespace ( const std::string &  name ) const

inlineoverridevirtualinherited

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 205 of file Parametrizable.h.

getParameters()

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

inlineoverridevirtualinherited

Get all parameters available.

See also

getIndependentParameters if some parameters are aliased.

Returns

A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 193 of file Parametrizable.h.

getParameters_()

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )

protectedpure virtualinherited

Get all parameters available.

See also

getIndependentParameters if some parameters are aliased.

Returns

A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::Parametrizable::~Parametrizable().

getParameterValue()

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

inlineoverridevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns

the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 195 of file Parametrizable.h.

hasParameter()

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

inlineoverridevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns

y/n.

Implements bpp::Parametrizable.

Definition at line 192 of file Parametrizable.h.

References bpp::ParameterList::hasParameter().

matchParametersValues()

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

inlineoverridevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters

A list of parameters.

Returns

True if at least one parameter value has been changed.

Exceptions

ConstraintException

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

Implements bpp::Parametrizable.

Definition at line 199 of file Parametrizable.h.

parameter()

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

inlineoverridevirtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns

The parameter with given name.

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 194 of file Parametrizable.h.

removeConstraint()

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

inlineoverridevirtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 200 of file Parametrizable.h.

setAllParametersValues()

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

inlineoverridevirtualinherited

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

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

Parameters

parameters

A list with all parameters.

Exceptions

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

Implements bpp::Parametrizable.

Definition at line 196 of file Parametrizable.h.

setConstraint()

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

inlineoverridevirtualinherited

Set/Change the constraint associated with one parameter.

Parameters

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

Exceptions

ParameterNotFoundException

if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 201 of file Parametrizable.h.

setNamespace()

void bpp::ParametrizableAdapter::setNamespace ( const std::string &  prefix )

inlineoverridevirtualinherited

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.

Definition at line 203 of file Parametrizable.h.

setParametersValues()

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

inlineoverridevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters

A list containing all parameters to update.

Exceptions

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

Implements bpp::Parametrizable.

Definition at line 198 of file Parametrizable.h.

setParameterValue()

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

inlineoverridevirtualinherited

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

Parameters

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

Exceptions

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

Implements bpp::Parametrizable.

Definition at line 197 of file Parametrizable.h.

unaliasParameters()

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

inline

Definition at line 143 of file ParameterAliasable.h.

Member Data Documentation

parameter_

Parameter bpp::ParametrizableAdapter::parameter_

protectedinherited

Definition at line 180 of file Parametrizable.h.

parameters_

ParameterList bpp::ParametrizableAdapter::parameters_

protectedinherited

Definition at line 179 of file Parametrizable.h.

---

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

• Bpp/Numeric/ParameterAliasable.h