#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, Constraint *constraint=0, bool attachConstraint=false) throw (ConstraintException)
	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) throw (ConstraintException)
	Set the value of this parameter. More...

virtual void	setMessageHandler (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 const Constraint *	getConstraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual Constraint *	getConstraint ()
	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 const Constraint *	removeConstraint ()
	Remove the constraint associated to this parameter. More...

virtual void	setConstraint (Constraint *constraint, bool attach=false)
	Set a constraint to this parameter. More...

virtual void	addParameterListener (ParameterListener *listener, bool attachListener=true)
	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 IntervalConstraint	R_PLUS

static const IntervalConstraint	R_PLUS_STAR

static const IntervalConstraint	R_MINUS

static const IntervalConstraint	R_MINUS_STAR

static const IntervalConstraint	PROP_CONSTRAINT_IN

static const IntervalConstraint	PROP_CONSTRAINT_EX

Protected Member Functions
void	fireParameterNameChanged (ParameterEvent &event)

void	fireParameterValueChanged (ParameterEvent &event)

Protected Attributes
std::string	name_

double	value_

double	precision_

Constraint *	constraint_

bool	attach_

std::vector< ParameterListener * >	listeners_

std::vector< bool >	listenerAttach_

Private Attributes
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 58 of file AutoParameter.h.

Constructor & Destructor Documentation

◆ AutoParameter() [1/3]

AutoParameter::AutoParameter	(	const std::string &	name = `""`,
		double	value = `0`,
		Constraint *	constraint = `0`,
		bool	attachConstraint = `false`
	)
throw	(	ConstraintException
	)

Build a new AutoParameter.

Parameters

name	The parameter name.
value	The parameter value.
constraint	An optional pointer toward a Constraint object.
attachConstraint	Tell if the constraint must be attached to this parameter, or shared between different objects. See Parameter.

Exceptions

ConstraintException If the parameter value does not match the contraint.

Constructors:

Definition at line 61 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 64 of file AutoParameter.cpp.

◆ AutoParameter() [3/3]

AutoParameter::AutoParameter ( const AutoParameter & param )

Copy constructor.

Parameters

param The parameter to copy.

Definition at line 66 of file AutoParameter.cpp.

◆ ~AutoParameter()

virtual bpp::AutoParameter::~AutoParameter ( )

inlinevirtual

Definition at line 99 of file AutoParameter.h.

Member Function Documentation

◆ addParameterListener()

virtual void bpp::Parameter::addParameterListener	(	ParameterListener *	listener,
		bool	attachListener = `true`
	)

inlinevirtualinherited

Add a new listener to this parameter.

Parameters

listener	The listener to add.
attachListener	Tell if the parameter will own this listener. If so, deep copies will be made when cloning the parameter, and the listener will be destroyed upon destruction of the parameter or upon removal. Alternatively, only superficial copies will be made, and the listener will persist if the parameter is destroyed.

Definition at line 298 of file Parameter.h.

References bpp::Parameter::listenerAttach_, and bpp::Parameter::listeners_.

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 101 of file AutoParameter.h.

References AutoParameter().

◆ fireParameterNameChanged()

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

inlineprotectedinherited

Definition at line 320 of file Parameter.h.

References bpp::Parameter::listeners_.

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

◆ fireParameterValueChanged()

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

inlineprotectedinherited

Definition at line 325 of file Parameter.h.

References bpp::Parameter::listeners_.

◆ getConstraint() [1/2]

virtual const Constraint* bpp::Parameter::getConstraint ( ) const

inlinevirtualinherited

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

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

Definition at line 255 of file Parameter.h.

References bpp::Parameter::constraint_.

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

◆ getConstraint() [2/2]

virtual Constraint* bpp::Parameter::getConstraint ( )

inlinevirtualinherited

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

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

Definition at line 262 of file Parameter.h.

References bpp::Parameter::constraint_.

◆ getName()

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

inlinevirtualinherited

Get the name of this parameter.

Returns: The parameter name.

Definition at line 234 of file Parameter.h.

References bpp::Parameter::name_.

Referenced by bpp::ParameterList::deleteParameter(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::ParameterList::getCommonParametersWith(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), bpp::ParameterList::getParameter(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParametersStopCondition::isToleranceReached(), 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 248 of file Parameter.h.

References bpp::Parameter::precision_.

◆ getValue()

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

inlinevirtualinherited

Get the value of this parameter.

Returns: The parameter value.

Definition at line 241 of file Parameter.h.

References bpp::Parameter::value_.

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 269 of file Parameter.h.

References bpp::Parameter::constraint_.

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 187 of file Parameter.cpp.

References bpp::Parameter::listeners_.

◆ operator=()

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

Assignment operator.

Parameters

param The parameter to copy.

Definition at line 68 of file AutoParameter.cpp.

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

◆ removeConstraint()

const Constraint * 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 163 of file Parameter.cpp.

References bpp::Parameter::constraint_.

Referenced by 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 172 of file Parameter.cpp.

References bpp::Parameter::listenerAttach_, and bpp::Parameter::listeners_.

◆ setConstraint()

void Parameter::setConstraint	(	Constraint *	constraint,
		bool	attach = `false`
	)

virtualinherited

Set a constraint to this parameter.

Parameters

constraint	a pointer to the constraint (may be null)
attach	says if the constraint is attached to the Parameter (default: false).

Constraint:

Definition at line 143 of file Parameter.cpp.

References bpp::Parameter::attach_, bpp::Parameter::constraint_, bpp::Constraint::isCorrect(), and bpp::Parameter::value_.

Referenced by bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ setMessageHandler()

virtual void bpp::AutoParameter::setMessageHandler ( 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 134 of file AutoParameter.h.

References messageHandler_.

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 208 of file Parameter.h.

References bpp::Parameter::fireParameterNameChanged(), and bpp::Parameter::name_.

Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), 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 136 of file Parameter.cpp.

References bpp::Parameter::precision_.

◆ setValue()

void AutoParameter::setValue	(	double	value	)
throw	(	ConstraintException
	)

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.

Exceptions

ConstraintException Never thrown!

Reimplemented from bpp::Parameter.

Definition at line 77 of file AutoParameter.cpp.

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

Member Data Documentation

◆ attach_

bool bpp::Parameter::attach_

protectedinherited

Definition at line 143 of file Parameter.h.

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

◆ constraint_

Constraint* bpp::Parameter::constraint_

protectedinherited

Definition at line 142 of file Parameter.h.

Referenced by bpp::Parameter::getConstraint(), bpp::Parameter::hasConstraint(), bpp::Parameter::operator=(), bpp::Parameter::Parameter(), bpp::Parameter::removeConstraint(), bpp::Parameter::setConstraint(), and bpp::Parameter::~Parameter().

◆ CONSTRAINTS_AUTO

string AutoParameter::CONSTRAINTS_AUTO = "auto"

static

Definition at line 138 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 139 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 140 of file AutoParameter.h.

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

◆ listenerAttach_

std::vector<bool> bpp::Parameter::listenerAttach_

protectedinherited

Definition at line 145 of file Parameter.h.

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

◆ listeners_

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

protectedinherited

Definition at line 144 of file Parameter.h.

Referenced by bpp::Parameter::addParameterListener(), bpp::Parameter::fireParameterNameChanged(), bpp::Parameter::fireParameterValueChanged(), bpp::Parameter::hasParameterListener(), bpp::Parameter::operator=(), bpp::Parameter::Parameter(), bpp::Parameter::removeParameterListener(), and bpp::Parameter::~Parameter().

◆ messageHandler_

OutputStream* bpp::AutoParameter::messageHandler_

private

Definition at line 62 of file AutoParameter.h.

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

◆ name_

std::string bpp::Parameter::name_

protectedinherited

Definition at line 139 of file Parameter.h.

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

◆ precision_

double bpp::Parameter::precision_

protectedinherited

Definition at line 141 of file Parameter.h.

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

◆ PROP_CONSTRAINT_EX

const IntervalConstraint Parameter::PROP_CONSTRAINT_EX

staticinherited

Definition at line 337 of file Parameter.h.

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

◆ PROP_CONSTRAINT_IN

const IntervalConstraint Parameter::PROP_CONSTRAINT_IN

staticinherited

Definition at line 336 of file Parameter.h.

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

◆ R_MINUS

const IntervalConstraint Parameter::R_MINUS

staticinherited

Definition at line 334 of file Parameter.h.

◆ R_MINUS_STAR

const IntervalConstraint Parameter::R_MINUS_STAR

staticinherited

Definition at line 335 of file Parameter.h.

◆ R_PLUS

const IntervalConstraint Parameter::R_PLUS

staticinherited

Definition at line 332 of file Parameter.h.

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

◆ R_PLUS_STAR

const IntervalConstraint Parameter::R_PLUS_STAR

staticinherited

Definition at line 333 of file Parameter.h.

Referenced by bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution().

◆ value_

double bpp::Parameter::value_

protectedinherited

Definition at line 140 of file Parameter.h.

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

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()

◆ fireParameterNameChanged()

◆ fireParameterValueChanged()

◆ getConstraint() [1/2]

◆ getConstraint() [2/2]

◆ getName()

◆ getPrecision()

◆ getValue()

◆ hasConstraint()

◆ hasParameterListener()

◆ operator=()

◆ removeConstraint()

◆ removeParameterListener()

◆ setConstraint()

◆ setMessageHandler()

◆ setName()

◆ setPrecision()

◆ setValue()

Member Data Documentation

◆ attach_

◆ constraint_

◆ CONSTRAINTS_AUTO

◆ CONSTRAINTS_IGNORE

◆ CONSTRAINTS_KEEP

◆ listenerAttach_

◆ listeners_

◆ messageHandler_

◆ name_

◆ precision_

◆ PROP_CONSTRAINT_EX

◆ PROP_CONSTRAINT_IN

◆ R_MINUS

◆ R_MINUS_STAR

◆ R_PLUS

◆ R_PLUS_STAR

◆ value_