bpp-core  2.2.0
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
bpp::AbstractParametrizable Class Referenceabstract

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 deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
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

◆ AbstractParametrizable()

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

Definition at line 70 of file AbstractParametrizable.h.

◆ ~AbstractParametrizable()

virtual bpp::AbstractParametrizable::~AbstractParametrizable ( )
inlinevirtual

Definition at line 72 of file AbstractParametrizable.h.

Member Function Documentation

◆ addParameter_()

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

Definition at line 137 of file AbstractParametrizable.h.

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

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

◆ addParameters_()

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

Definition at line 143 of file AbstractParametrizable.h.

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

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

◆ 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::AbstractParametrizable::deleteParameter_ ( size_t  index)
throw (IndexOutOfBoundsException
)
inlineprotected

Definition at line 148 of file AbstractParametrizable.h.

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

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

◆ deleteParameter_() [2/2]

void bpp::AbstractParametrizable::deleteParameter_ ( std::string &  name)
inlineprotected

Definition at line 155 of file AbstractParametrizable.h.

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

◆ deleteParameters_()

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

Definition at line 160 of file AbstractParametrizable.h.

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

◆ fireParameterChanged()

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

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

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

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

◆ getNamespace()

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 125 of file AbstractParametrizable.h.

References prefix_.

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

◆ getNumberOfParameters()

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 121 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().

◆ getParameter()

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

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif 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::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), getParameterValue(), getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotected
Parameters
nameThe name of the parameter.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 175 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::deleteParameter_(), 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
)
inlineprotected

Definition at line 199 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

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

Definition at line 205 of file AbstractParametrizable.h.

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

◆ getParameterNameWithoutNamespace()

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().

◆ getParameters()

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

◆ getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )
inlineprotected

Definition at line 212 of file AbstractParametrizable.h.

References parameters_.

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

◆ getParameterValue()

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

Get the value for parameter of name 'name'.

Parameters
nameThe 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::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::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotected
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name) const
throw (ParameterNotFoundException
)
inlineprotected
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 194 of file AbstractParametrizable.h.

References getParameter().

◆ hasParameter()

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

Tell if there is a parameter with specified name.

Parameters
nameThe 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_.

◆ matchParametersValues()

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

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf 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::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), bpp::TestFunction::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )
inlineprotected

Definition at line 165 of file AbstractParametrizable.h.

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

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

◆ setAllParametersValues()

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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf 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().

◆ setNamespace()

void AbstractParametrizable::setNamespace ( const std::string &  prefix)
virtual

Set the namespace for the parameter names.

Parameters
prefixThe '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().

◆ setParametersValues()

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
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf 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::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::LogsumHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().

◆ setParameterValue()

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
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf 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().

Member Data Documentation

◆ parameters_

ParameterList bpp::AbstractParametrizable::parameters_
private

Definition at line 66 of file AbstractParametrizable.h.

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

◆ prefix_

std::string bpp::AbstractParametrizable::prefix_
private

Definition at line 67 of file AbstractParametrizable.h.

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

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