bpp::ParameterAliasable Class Reference

Extend the Parametrizable interface with support for parameter aliases. More...

#include <Bpp/Numeric/ParameterAliasable.h>

Inheritance diagram for bpp::ParameterAliasable:

Collaboration diagram for bpp::ParameterAliasable:

Public Member Functions
	ParameterAliasable ()
virtual	~ParameterAliasable ()
virtual size_t	getNumberOfIndependentParameters () const =0
	Get the number of independent parameters. More...
virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0
	Set two parameters as 'aliased'. More...
virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
	alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0
	Detach two parameters previously set as 'aliased'. More...
virtual const ParameterList &	getIndependentParameters () const =0
	Get the minimal list of parameters to set the model. More...
virtual std::vector< std::string >	getAlias (const std::string &name) const =0
virtual std::map< std::string, std::string >	getAliases () const =0
virtual bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name. More...
virtual const ParameterList &	getParameters () const =0
	Get all parameters available. More...
virtual const Parameter &	getParameter (const std::string &name) const =0
	Get the parameter with specified name. More...
virtual double	getParameterValue (const std::string &name) const =0
	Get the value for parameter of name 'name'. More...
virtual void	setAllParametersValues (const ParameterList &parameters)=0
	Set the parameters values to be equals to those of parameters. More...
virtual void	setParameterValue (const std::string &name, double value)=0
	Set the value of parameter with name name to be equal to value. More...
virtual void	setParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...
virtual bool	matchParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...
virtual size_t	getNumberOfParameters () const =0
	Get the number of parameters. More...
virtual void	setNamespace (const std::string &prefix)=0
	Set the namespace for the parameter names. More...
virtual std::string	getNamespace () const =0
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
	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
virtual ParameterList &	getParameters_ ()=0
	Get all parameters available. More...

Detailed Description

Extend the Parametrizable interface with support for parameter aliases.

Parameter aliases allows several parameter to be constrained together, and for instance, be jointly estimated. The alias relationship is not symmetric:

aliasParameters("a","b");

results in the value of "b" being updated when a is modified, but a will not be updated upon modification of "a". "b" will also be removed of the list of "independent" parameters. Furthermore, a parameter can only be aliased with another one:

aliasParameters("a","b");
aliasParameters("c","b"); //ERROR, throws an exception.

However, several parameters can be aliased to the same one:

aliasParameters("a","b");
aliasParameters("a","c");

In this case, modifying "a" will automatically update the values of "b" and "c", and "b" and "c" are removed from the list of indepedent parameters. Finally, parameters can be chained:

aliasParameters("a","b");
aliasParameters("b","c");

is equivallent to the previous example.

Definition at line 84 of file ParameterAliasable.h.

Constructor & Destructor Documentation

ParameterAliasable()

bpp::ParameterAliasable::ParameterAliasable ( )

inline

Definition at line 88 of file ParameterAliasable.h.

~ParameterAliasable()

virtual bpp::ParameterAliasable::~ParameterAliasable ( )

inlinevirtual

Definition at line 89 of file ParameterAliasable.h.

Member Function Documentation

aliasParameters() [1/2]

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

pure 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.

Implemented in bpp::AbstractParameterAliasable.

aliasParameters() [2/2]

virtual void bpp::ParameterAliasable::aliasParameters ( std::map< std::string, std::string > &  unparsedParams, bool  verbose  )

pure 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

Implemented in bpp::AbstractParameterAliasable.

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::TransformedParameter, bpp::MultipleDiscreteDistribution, bpp::DiscreteDistribution, bpp::ParameterListener, bpp::BppNumberI, bpp::HmmLikelihood, bpp::HmmEmissionProbabilities, bpp::Optimizer, bpp::OptimizationStopCondition, bpp::DerivableSecondOrder, bpp::DerivableFirstOrder, bpp::AbstractNumericalDerivative, bpp::Constraint, bpp::OutputStream, bpp::PlaceboTransformedParameter, bpp::IntervalTransformedParameter, bpp::RTransformedParameter, bpp::Table< T >, bpp::PrincipalComponentAnalysis, bpp::DualityDiagram, bpp::CorrespondenceAnalysis, bpp::ContingencyTableTest, bpp::Range< T >, bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::Simplex, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::ConstantDistribution, bpp::BetaDiscreteDistribution, bpp::ParametrizableCollection< N >, bpp::ParameterList, bpp::Parameter, bpp::ParameterEvent, bpp::BppUnsignedInteger, bpp::BppInteger, bpp::BppDouble, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::BppNotANumber, bpp::LinearMatrix< Scalar >, bpp::ColMatrix< Scalar >, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::LogsumHmmLikelihood, bpp::FullHmmTransitionMatrix, bpp::AutoCorrelationTransitionMatrix, bpp::TwoPointsNumericalDerivative, bpp::ThreePointsNumericalDerivative, bpp::SimpleNewtonMultiDimensions, bpp::SimpleMultiDimensions, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::ReparametrizationFunctionWrapper, bpp::PowellMultiDimensions, bpp::PowellMultiDimensions::PMDStopCondition, bpp::FunctionStopCondition, bpp::ParametersStopCondition, bpp::NegativeOperator, bpp::MathOperator, bpp::FunctionOperator< F >, bpp::ConstantOperator, bpp::ComputationTree, bpp::BinaryOperator, bpp::NewtonOneDimension, bpp::NewtonBacktrackOneDimension, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::MetaOptimizer, bpp::MetaOptimizerInfos, bpp::GoldenSectionSearch, bpp::GoldenSectionSearch::GSSStopCondition, bpp::TestFunction, bpp::InfinityDerivableSecondOrderWrapper, bpp::InfinityDerivableFirstOrderWrapper, bpp::InfinityFunctionWrapper, bpp::FivePointsNumericalDerivative, bpp::DownhillSimplexMethod, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::DirectionFunction, bpp::ConjugateGradientMultiDimensions, bpp::BrentOneDimension, bpp::BrentOneDimension::BODStopCondition, bpp::BfgsMultiDimensions, bpp::DataTable, bpp::IntervalConstraint, bpp::AutoParameter, bpp::AliasParameterListener, bpp::StdErr, bpp::StdOut, bpp::StlOutputStreamWrapper, bpp::StlOutputStream, bpp::NullOutputStream, bpp::RGBColor, bpp::Point2D< T >, bpp::Font, bpp::GlobalGraph, bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl >, bpp::BppVector< T >, bpp::BppString, and bpp::BppBoolean.

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

getAlias()

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

pure virtual

Returns

The list of names of the parameters that are aliased with a given parameter. Depending on the implementation, the function may be recursive or not...

Parameters

name	The name of the parameter to look for.

Implemented in bpp::AbstractParameterAliasable.

Referenced by bpp::BppOParametrizableFormat::write().

getAliases()

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

pure virtual

Returns

the map of the aliases.

Implemented in bpp::AbstractParameterAliasable.

getIndependentParameters()

virtual const ParameterList& bpp::ParameterAliasable::getIndependentParameters ( ) const

pure virtual

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.

Implemented in bpp::AbstractParameterAliasable.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

getNamespace()

virtual std::string bpp::Parametrizable::getNamespace ( ) const

pure virtualinherited

Returns

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

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

Referenced by bpp::FunctionWrapper::getNamespace().

getNumberOfIndependentParameters()

virtual size_t bpp::ParameterAliasable::getNumberOfIndependentParameters ( ) const

pure virtual

Get the number of independent parameters.

Returns

The number of independent parameters. If no parameters are aliased, this is equivalent to the getNumberOfParameters() method.

Implemented in bpp::AbstractParameterAliasable.

getNumberOfParameters()

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const

pure virtualinherited

Get the number of parameters.

See also

getNumberOfIndependentParameters If some parameters are aliased.

Returns

The number of parameters.

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

Referenced by bpp::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

getParameter()

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string &  name ) const

pure virtualinherited

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.

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

Referenced by bpp::FunctionWrapper::getParameter().

getParameterNameWithoutNamespace()

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string &  name ) const

pure virtualinherited

Resolves a parameter name according to the current namespace.

Returns

The parameter name without the namespace prefix, if any.

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

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().

getParameters()

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const

pure virtualinherited

Get all parameters available.

See also

getIndependentParameters if some parameters are aliased.

Returns

A list with all parameters available.

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

Referenced by bpp::NewtonOneDimension::doStep(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::FunctionWrapper::getParameters(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

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::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameters_().

getParameterValue()

virtual double bpp::Parametrizable::getParameterValue ( const std::string &  name ) const

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns

the value of parameter name.

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

Referenced by bpp::FunctionWrapper::getParameterValue().

hasParameter()

virtual bool bpp::Parametrizable::hasParameter ( const std::string &  name ) const

pure virtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns

y/n.

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

Referenced by bpp::FunctionWrapper::hasParameter().

matchParametersValues()

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList &  parameters )

pure virtualinherited

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.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

setAllParametersValues()

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList &  parameters )

pure virtualinherited

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.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

setNamespace()

virtual void bpp::Parametrizable::setNamespace ( const std::string &  prefix )

pure virtualinherited

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.

Implemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::AbstractParametrizable, bpp::AbstractParameterAliasable, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::LogsumHmmLikelihood::setNamespace(), bpp::FunctionWrapper::setNamespace(), and bpp::InvariantMixedDiscreteDistribution::setNamespace().

setParametersValues()

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList &  parameters )

pure virtualinherited

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.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

setParameterValue()

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

pure virtualinherited

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.

Implemented in bpp::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().

unaliasParameters()

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

pure 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.

Implemented in bpp::AbstractParameterAliasable.

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

• Bpp/Numeric/ParameterAliasable.h