#include <Bpp/Numeric/AutoParameter.h>

Inheritance diagram for bpp::AutoParameter:

Collaboration diagram for bpp::AutoParameter:

Public Member Functions
	AutoParameter (const std::string &name="", double value=0, std::shared_ptr< ConstraintInterface > constraint=nullptr)
	Build a new AutoParameter. More...

	AutoParameter (const Parameter &param)
	Copy constructor. More...

	AutoParameter (const AutoParameter &param)
	Copy constructor. More...

AutoParameter &	operator= (const AutoParameter &param)
	Assignment operator. More...

virtual	~AutoParameter ()

AutoParameter *	clone () const
	Create a copy of this object and send a pointer to it. More...

virtual void	setValue (double value)
	Set the value of this parameter. More...

virtual void	setMessageHandler (std::shared_ptr< OutputStream > mh)
	Set the message handler for this AutoParameter. More...

virtual void	setName (const std::string &name)
	Set the name of this parameter. More...

void	setPrecision (double precision)
	Set the precision of this parameter. More...

virtual const std::string &	getName () const
	Get the name of this parameter. More...

virtual double	getValue () const
	Get the value of this parameter. More...

virtual double	getPrecision () const
	Get the precision of this parameter. More...

virtual std::shared_ptr< const ConstraintInterface >	getConstraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual std::shared_ptr< ConstraintInterface >	getConstraint ()
	Return the constraint associated to this parameter if there is one. More...

virtual const ConstraintInterface &	constraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual ConstraintInterface &	constraint ()
	Return the constraint associated to this parameter if there is one. More...

virtual bool	hasConstraint () const
	Tells if this parameter has a constraint. More...

virtual std::shared_ptr< ConstraintInterface >	removeConstraint ()
	Remove the constraint associated to this parameter. More...

virtual void	setConstraint (std::shared_ptr< ConstraintInterface > constraint)
	Set a constraint to this parameter. More...

virtual void	addParameterListener (std::shared_ptr< ParameterListener > listener)
	Add a new listener to this parameter. More...

virtual void	removeParameterListener (const std::string &listenerId)
	Remove all listeners with a given id from this parameter. More...

virtual bool	hasParameterListener (const std::string &listenerId)
	Tell is there is a listener with a given id from this parameter. More...

Static Public Attributes
static std::string	CONSTRAINTS_AUTO = "auto"

static std::string	CONSTRAINTS_IGNORE = "ignore"

static std::string	CONSTRAINTS_KEEP = "keep"

static const std::shared_ptr< IntervalConstraint >	R_PLUS

static const std::shared_ptr< IntervalConstraint >	R_PLUS_STAR

static const std::shared_ptr< IntervalConstraint >	R_MINUS

static const std::shared_ptr< IntervalConstraint >	R_MINUS_STAR

static const std::shared_ptr< IntervalConstraint >	PROP_CONSTRAINT_IN

static const std::shared_ptr< IntervalConstraint >	PROP_CONSTRAINT_EX

Protected Member Functions
void	fireParameterNameChanged (ParameterEvent &event)

void	fireParameterValueChanged (ParameterEvent &event)

void	fireParameterConstraintChanged (ParameterEvent &event)

Protected Attributes
std::string	name_

double	value_

double	precision_

std::shared_ptr< ConstraintInterface >	constraint_

std::vector< std::shared_ptr< ParameterListener > >	listeners_

Private Attributes
std::shared_ptr< OutputStream >	messageHandler_

Detailed Description

The AutoParameter class.

This class overides the setValue() method of class Parameter so that no Exception is thrown. This allows to perform optimization under constraint.

Definition at line 23 of file AutoParameter.h.

Constructor & Destructor Documentation

◆ AutoParameter() [1/3]

AutoParameter::AutoParameter	(	const std::string &	name = `""`,
		double	value = `0`,
		std::shared_ptr< ConstraintInterface >	constraint = `nullptr`
	)

Build a new AutoParameter.

Parameters

name	The parameter name.
value	The parameter value.
constraint	An optional shared pointer toward a Constraint object.

Exceptions

ConstraintException If the parameter value does not match the contraint.

Constructors:

Definition at line 26 of file AutoParameter.cpp.

Referenced by clone().

◆ AutoParameter() [2/3]

AutoParameter::AutoParameter ( const Parameter & param )

Copy constructor.

Parameters

param The parameter to copy.

Definition at line 29 of file AutoParameter.cpp.

◆ AutoParameter() [3/3]

AutoParameter::AutoParameter ( const AutoParameter & param )

Copy constructor.

Parameters

param The parameter to copy.

Definition at line 31 of file AutoParameter.cpp.

◆ ~AutoParameter()

virtual bpp::AutoParameter::~AutoParameter ( )

inlinevirtual

Definition at line 61 of file AutoParameter.h.

Member Function Documentation

◆ addParameterListener()

virtual void bpp::Parameter::addParameterListener ( std::shared_ptr< ParameterListener > listener )

inlinevirtualinherited

Add a new listener to this parameter.

Parameters

listener The listener to add.

Definition at line 261 of file Parameter.h.

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

◆ clone()

AutoParameter* bpp::AutoParameter::clone ( ) const

inlinevirtual

Create a copy of this object and send a pointer to it.

Returns: A pointer toward the copy object.

Implements bpp::Clonable.

Definition at line 63 of file AutoParameter.h.

References AutoParameter(), and setValue().

◆ constraint() [1/2]

virtual const ConstraintInterface& bpp::Parameter::constraint ( ) const

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A referec toward the constraint if there is one, otherwise throw an exception.

Definition at line 203 of file Parameter.h.

Referenced by bpp::Parameter::setConstraint().

◆ constraint() [2/2]

virtual ConstraintInterface& bpp::Parameter::constraint ( )

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A referec toward the constraint if there is one, otherwise throw an exception.

Definition at line 225 of file Parameter.h.

◆ fireParameterConstraintChanged()

void bpp::Parameter::fireParameterConstraintChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 298 of file Parameter.h.

◆ fireParameterNameChanged()

void bpp::Parameter::fireParameterNameChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 282 of file Parameter.h.

◆ fireParameterValueChanged()

void bpp::Parameter::fireParameterValueChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 290 of file Parameter.h.

Referenced by bpp::Parameter::setValue().

◆ getConstraint() [1/2]

virtual std::shared_ptr<const ConstraintInterface> bpp::Parameter::getConstraint ( ) const

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A shared pointer toward the constraint, or NULL if there is no constraint.

Definition at line 196 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParameterList::matchParametersValues(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ getConstraint() [2/2]

virtual std::shared_ptr<ConstraintInterface> bpp::Parameter::getConstraint ( )

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A shared pointer toward the constraint, or NULL if there is no constraint.

Definition at line 218 of file Parameter.h.

◆ getName()

virtual const std::string& bpp::Parameter::getName ( ) const

inlinevirtualinherited

Get the name of this parameter.

Returns: The parameter name.

Definition at line 174 of file Parameter.h.

Referenced by bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::getCommonParametersWith(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParametersStopCondition::isToleranceReached(), bpp::ParameterList::parameter(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::AliasParameterListener::parameterValueChanged(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ getPrecision()

virtual double bpp::Parameter::getPrecision ( ) const

inlinevirtualinherited

Get the precision of this parameter.

Returns: The precision value.

Definition at line 188 of file Parameter.h.

◆ getValue()

virtual double bpp::Parameter::getValue ( ) const

inlinevirtualinherited

Get the value of this parameter.

Returns: The parameter value.

Definition at line 181 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), bpp::RTransformedParameter::getFirstOrderDerivative(), bpp::IntervalTransformedParameter::getFirstOrderDerivative(), bpp::RTransformedParameter::getOriginalValue(), bpp::IntervalTransformedParameter::getOriginalValue(), bpp::PlaceboTransformedParameter::getOriginalValue(), bpp::AbstractParametrizable::getParameterValue(), bpp::ParameterList::getParameterValue(), bpp::RTransformedParameter::getSecondOrderDerivative(), bpp::IntervalTransformedParameter::getSecondOrderDerivative(), bpp::TestFunction::getValue(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParametersStopCondition::isToleranceReached(), bpp::ParameterList::matchParametersValues(), bpp::ParameterList::setAllParametersValues(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ hasConstraint()

virtual bool bpp::Parameter::hasConstraint ( ) const

inlinevirtualinherited

Tells if this parameter has a constraint.

Returns: True if this parameter has a contraint.

Definition at line 238 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParameterList::matchParametersValues(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ hasParameterListener()

bool Parameter::hasParameterListener ( const std::string & listenerId )

virtualinherited

Tell is there is a listener with a given id from this parameter.

Parameters

listenerId The id of listener to remove.

Returns: True if at list one listener with the given id was found.

Definition at line 104 of file Parameter.cpp.

References bpp::Parameter::listeners_, bpp::Parameter::PROP_CONSTRAINT_EX, bpp::Parameter::PROP_CONSTRAINT_IN, bpp::Parameter::R_MINUS, bpp::Parameter::R_MINUS_STAR, bpp::Parameter::R_PLUS, and bpp::Parameter::R_PLUS_STAR.

◆ operator=()

AutoParameter & AutoParameter::operator= ( const AutoParameter & param )

Assignment operator.

Parameters

param The parameter to copy.

Definition at line 33 of file AutoParameter.cpp.

References messageHandler_, and bpp::Parameter::operator=().

◆ removeConstraint()

std::shared_ptr< ConstraintInterface > Parameter::removeConstraint ( )

virtualinherited

Remove the constraint associated to this parameter.

Warning! The contraint objet is not deleted.

Returns: A pointer toward the formerly used contraint.

Definition at line 85 of file Parameter.cpp.

References bpp::Parameter::constraint_.

Referenced by bpp::AbstractParametrizable::removeConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ removeParameterListener()

void Parameter::removeParameterListener ( const std::string & listenerId )

virtualinherited

Remove all listeners with a given id from this parameter.

Parameters

listenerId The id of listener to remove.

Definition at line 94 of file Parameter.cpp.

References bpp::Parameter::listeners_.

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

◆ setConstraint()

void Parameter::setConstraint ( std::shared_ptr< ConstraintInterface > constraint )

virtualinherited

Set a constraint to this parameter.

Parameters

constraint A pointer to the constraint (may be null)

Constraint:

Definition at line 76 of file Parameter.cpp.

References bpp::Parameter::constraint(), bpp::Parameter::constraint_, and bpp::Parameter::value_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and bpp::AbstractParametrizable::setConstraint().

◆ setMessageHandler()

virtual void bpp::AutoParameter::setMessageHandler ( std::shared_ptr< OutputStream > mh )

inlinevirtual

Set the message handler for this AutoParameter.

The message handler keeps all messages that the parameter may send. The default handler is set to standard output, but you can pass any ostream object (cerr, ofstream, etc.).

A NULL pointer disable message output.

Parameters

mh	The message handler to use.

Definition at line 95 of file AutoParameter.h.

Referenced by bpp::DirectionFunction::autoParameter(), bpp::AbstractOptimizer::autoParameter(), and bpp::BppODiscreteDistributionFormat::initialize_().

◆ setName()

virtual void bpp::Parameter::setName ( const std::string & name )

inlinevirtualinherited

Set the name of this parameter.

Parameters

name	the new parameter name.

Definition at line 148 of file Parameter.h.

Referenced by bpp::ParametrizableCollection< N >::addObject(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ setPrecision()

void Parameter::setPrecision ( double precision )

inherited

Set the precision of this parameter.

Parameters

precision the new parameter precision.

Precision:

Definition at line 69 of file Parameter.cpp.

References bpp::Parameter::precision_.

Referenced by bpp::Parameter::Parameter().

◆ setValue()

void AutoParameter::setValue ( double value )

virtual

Set the value of this parameter.

This method is redefined so that no constraintException is thrown! When a Constraint is match, we automatically apply a correct value instead. This correct value is the nearest limit reached by the value, or a value next to the limit if the limit is not reachable.

This allow to perform optimization under constraint whith algorithms that are not initially built for this.

Parameters

value the new parameter value.

Reimplemented from bpp::Parameter.

Definition at line 42 of file AutoParameter.cpp.

References bpp::Parameter::constraint_, bpp::ConstraintException::getBadValue(), messageHandler_, bpp::Parameter::name_, bpp::Parameter::setValue(), and bpp::NumConstants::TINY().

Referenced by clone().

Member Data Documentation

◆ constraint_

std::shared_ptr<ConstraintInterface> bpp::Parameter::constraint_

protectedinherited

Definition at line 104 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::removeConstraint(), bpp::Parameter::setConstraint(), setValue(), and bpp::Parameter::setValue().

◆ CONSTRAINTS_AUTO

string AutoParameter::CONSTRAINTS_AUTO = "auto"

static

Definition at line 98 of file AutoParameter.h.

Referenced by bpp::AbstractOptimizer::AbstractOptimizer(), bpp::DirectionFunction::init(), bpp::AbstractOptimizer::init(), bpp::OneDimensionOptimizationTools::lineMinimization(), bpp::OneDimensionOptimizationTools::lineSearch(), and bpp::AbstractOptimizer::operator=().

◆ CONSTRAINTS_IGNORE

string AutoParameter::CONSTRAINTS_IGNORE = "ignore"

static

Definition at line 99 of file AutoParameter.h.

Referenced by bpp::AbstractOptimizer::AbstractOptimizer(), bpp::DirectionFunction::init(), bpp::AbstractOptimizer::init(), and bpp::AbstractOptimizer::operator=().

◆ CONSTRAINTS_KEEP

string AutoParameter::CONSTRAINTS_KEEP = "keep"

static

Definition at line 100 of file AutoParameter.h.

Referenced by bpp::OneDimensionOptimizationTools::lineMinimization(), and bpp::OneDimensionOptimizationTools::lineSearch().

◆ listeners_

std::vector< std::shared_ptr<ParameterListener> > bpp::Parameter::listeners_

protectedinherited

Definition at line 105 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener(), bpp::Parameter::operator=(), and bpp::Parameter::removeParameterListener().

◆ messageHandler_

std::shared_ptr<OutputStream> bpp::AutoParameter::messageHandler_

private

Definition at line 27 of file AutoParameter.h.

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

◆ name_

std::string bpp::Parameter::name_

protectedinherited

Definition at line 101 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), and setValue().

◆ precision_

double bpp::Parameter::precision_

protectedinherited

Definition at line 103 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::setPrecision(), and bpp::Parameter::setValue().

◆ PROP_CONSTRAINT_EX

const std::shared_ptr< IntervalConstraint > Parameter::PROP_CONSTRAINT_EX

staticinherited

Definition at line 312 of file Parameter.h.

Referenced by bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), bpp::Parameter::hasParameterListener(), and bpp::Simplex::Simplex().

◆ PROP_CONSTRAINT_IN

const std::shared_ptr< IntervalConstraint > Parameter::PROP_CONSTRAINT_IN

staticinherited

Definition at line 311 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), and bpp::Simplex::Simplex().

◆ R_MINUS

const std::shared_ptr< IntervalConstraint > Parameter::R_MINUS

staticinherited

Definition at line 309 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener().

◆ R_MINUS_STAR

const std::shared_ptr< IntervalConstraint > Parameter::R_MINUS_STAR

staticinherited

Definition at line 310 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener().

◆ R_PLUS

const std::shared_ptr< IntervalConstraint > Parameter::R_PLUS

staticinherited

Definition at line 307 of file Parameter.h.

Referenced by bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::Parameter::hasParameterListener(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().

◆ R_PLUS_STAR

const std::shared_ptr< IntervalConstraint > Parameter::R_PLUS_STAR

staticinherited

Definition at line 308 of file Parameter.h.

Referenced by bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), and bpp::Parameter::hasParameterListener().

◆ value_

double bpp::Parameter::value_

protectedinherited

Definition at line 102 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::setConstraint(), and bpp::Parameter::setValue().

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

Bpp/Numeric/AutoParameter.h
Bpp/Numeric/AutoParameter.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AutoParameter() [1/3]

◆ AutoParameter() [2/3]

◆ AutoParameter() [3/3]

◆ ~AutoParameter()

Member Function Documentation

◆ addParameterListener()

◆ clone()

◆ constraint() [1/2]

◆ constraint() [2/2]

◆ fireParameterConstraintChanged()

◆ fireParameterNameChanged()

◆ fireParameterValueChanged()

◆ getConstraint() [1/2]

◆ getConstraint() [2/2]

◆ getName()

◆ getPrecision()

◆ getValue()

◆ hasConstraint()

◆ hasParameterListener()

◆ operator=()

◆ removeConstraint()

◆ removeParameterListener()

◆ setConstraint()

◆ setMessageHandler()

◆ setName()

◆ setPrecision()

◆ setValue()

Member Data Documentation

◆ constraint_

◆ CONSTRAINTS_AUTO

◆ CONSTRAINTS_IGNORE

◆ CONSTRAINTS_KEEP

◆ listeners_

◆ messageHandler_

◆ name_

◆ precision_

◆ PROP_CONSTRAINT_EX

◆ PROP_CONSTRAINT_IN

◆ R_MINUS

◆ R_MINUS_STAR

◆ R_PLUS

◆ R_PLUS_STAR

◆ value_