#include <Bpp/Numeric/Function/DirectionFunction.h>

Inheritance diagram for bpp::DirectionFunction:

Collaboration diagram for bpp::DirectionFunction:

Public Member Functions
	DirectionFunction (Function *function=0)

	DirectionFunction (const DirectionFunction &df)

DirectionFunction &	operator= (const DirectionFunction &df)

virtual	~DirectionFunction ()

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

void	setParameters (const ParameterList &parameters)
	Set the point where the function must be computed. More...

double	getValue () const
	Get the value of the function at the current point. More...

const ParameterList &	getParameters () const
	Get all parameters available. More...

void	init (const ParameterList &p, const std::vector< double > &xi)

void	autoParameter ()

void	ignoreConstraints ()

void	setConstraintPolicy (const std::string &constraintPolicy)

std::string	getConstraintPolicy () const

void	setMessageHandler (OutputStream *messenger)

Function *	getFunction () const

ParameterList	getFunctionParameters () const

size_t	getNumberOfParameters () const
	Get the number of parameters. More...

virtual double	f (const ParameterList &parameters)
	Get the value of the function according to a given set of parameters. More...

virtual bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name. 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 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...

The Parametrizable interface.
bool	hasParameter (const std::string &name) const
	Tell if there is a parameter with specified name. More...

const Parameter &	getParameter (const std::string &name) const
	Get the parameter with specified name. More...

double	getParameterValue (const std::string &name) const
	Get the value for parameter of name 'name'. More...

void	setAllParametersValues (const ParameterList &parameters)
	Set the parameters values to be equals to those of parameters. More...

void	setParameterValue (const std::string &name, double value)
	Set the value of parameter with name name to be equal to value. More...

void	setParametersValues (const ParameterList &parameters)
	Update the parameters from parameters. More...

bool	matchParametersValues (const ParameterList &parameters)
	Update the parameters from 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...

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

Protected Attributes
ParameterList	parameters_

Parameter	parameter_

Private Attributes
ParameterList	params_

ParameterList	p_

ParameterList	xt_

std::vector< double >	xi_

Function *	function_

std::string	constraintPolicy_

OutputStream *	messenger_

Detailed Description

Definition at line 53 of file DirectionFunction.h.

Constructor & Destructor Documentation

◆ DirectionFunction() [1/2]

bpp::DirectionFunction::DirectionFunction ( Function * function = 0 )

inline

Definition at line 65 of file DirectionFunction.h.

Referenced by clone().

◆ DirectionFunction() [2/2]

bpp::DirectionFunction::DirectionFunction ( const DirectionFunction & df )

inline

Definition at line 70 of file DirectionFunction.h.

◆ ~DirectionFunction()

virtual bpp::DirectionFunction::~DirectionFunction ( )

inlinevirtual

Definition at line 87 of file DirectionFunction.h.

Member Function Documentation

◆ autoParameter()

void DirectionFunction::autoParameter ( )

Definition at line 95 of file DirectionFunction.cpp.

References bpp::AutoParameter::setMessageHandler().

◆ clone()

DirectionFunction* bpp::DirectionFunction::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 89 of file DirectionFunction.h.

References DirectionFunction().

◆ f()

virtual double bpp::Function::f ( const ParameterList & parameters )

inlinevirtualinherited

Get the value of the function according to a given set of parameters.

Parameters

parameters The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, and bpp::AbstractNumericalDerivative.

Definition at line 117 of file Functions.h.

References bpp::Function::getValue(), and bpp::Function::setParameters().

Referenced by bpp::BrentOneDimension::doInit(), bpp::DownhillSimplexMethod::doInit(), bpp::GoldenSectionSearch::doInit(), bpp::NewtonBacktrackOneDimension::doInit(), bpp::NewtonOneDimension::doInit(), bpp::PowellMultiDimensions::doInit(), bpp::BfgsMultiDimensions::doStep(), bpp::BrentOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::FunctionWrapper::f(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::PowellMultiDimensions::optimize(), bpp::AbstractOptimizer::step(), bpp::DownhillSimplexMethod::tryExtrapolation(), and bpp::NumTools::uniRoot().

◆ getConstraintPolicy()

std::string bpp::DirectionFunction::getConstraintPolicy ( ) const

inline

Definition at line 103 of file DirectionFunction.h.

References constraintPolicy_.

◆ getFunction()

Function* bpp::DirectionFunction::getFunction ( ) const

inline

Definition at line 105 of file DirectionFunction.h.

References function_.

◆ getFunctionParameters()

ParameterList bpp::DirectionFunction::getFunctionParameters ( ) const

inline

Returns: The set of parameters associated to the function, as specified by the init() method.

Definition at line 109 of file DirectionFunction.h.

References p_.

◆ getNamespace() [1/2]

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

inlinevirtualinherited

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

Implements bpp::Parametrizable.

Definition at line 222 of file Parametrizable.h.

◆ getNamespace() [2/2]

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().

◆ getNumberOfParameters()

size_t bpp::DirectionFunction::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 110 of file DirectionFunction.h.

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

◆ getParameter() [1/2]

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

inlinevirtualinherited

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 214 of file Parametrizable.h.

References bpp::ParametrizableAdapter::parameter_.

◆ getParameter() [2/2]

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() [1/2]

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

inlinevirtualinherited

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 223 of file Parametrizable.h.

◆ getParameterNameWithoutNamespace() [2/2]

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()

const ParameterList & DirectionFunction::getParameters ( ) const

virtual

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 70 of file DirectionFunction.cpp.

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

◆ getParameters_()

ParameterList & DirectionFunction::getParameters_ ( )

protectedvirtual

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 75 of file DirectionFunction.cpp.

◆ getParameterValue() [1/2]

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

inlinevirtualinherited

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 215 of file Parametrizable.h.

◆ getParameterValue() [2/2]

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().

◆ getValue()

double DirectionFunction::getValue ( ) const

virtual

Get the value of the function at the current point.

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 63 of file DirectionFunction.cpp.

◆ hasParameter() [1/2]

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

inlinevirtualinherited

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 212 of file Parametrizable.h.

References bpp::ParameterList::hasParameter(), and bpp::ParametrizableAdapter::parameters_.

◆ hasParameter() [2/2]

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().

◆ ignoreConstraints()

void DirectionFunction::ignoreConstraints ( )

Definition at line 107 of file DirectionFunction.cpp.

◆ init()

void DirectionFunction::init	(	const ParameterList &	p,
		const std::vector< double > &	xi
	)

Definition at line 82 of file DirectionFunction.cpp.

References bpp::AutoParameter::CONSTRAINTS_AUTO, and bpp::AutoParameter::CONSTRAINTS_IGNORE.

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

◆ matchParametersValues() [1/2]

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

inlinevirtualinherited

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 219 of file Parametrizable.h.

◆ matchParametersValues() [2/2]

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().

◆ operator=()

DirectionFunction& bpp::DirectionFunction::operator= ( const DirectionFunction & df )

inline

Definition at line 74 of file DirectionFunction.h.

References constraintPolicy_, function_, messenger_, p_, params_, xi_, and xt_.

◆ setAllParametersValues() [1/2]

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

inlinevirtualinherited

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 216 of file Parametrizable.h.

◆ setAllParametersValues() [2/2]

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().

◆ setConstraintPolicy()

void bpp::DirectionFunction::setConstraintPolicy ( const std::string & constraintPolicy )

inline

Definition at line 102 of file DirectionFunction.h.

References constraintPolicy_.

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

◆ setMessageHandler()

void bpp::DirectionFunction::setMessageHandler ( OutputStream * messenger )

inline

Definition at line 104 of file DirectionFunction.h.

References messenger_.

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

◆ setNamespace() [1/2]

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

inlinevirtualinherited

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 221 of file Parametrizable.h.

◆ setNamespace() [2/2]

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().

◆ setParameters()

void DirectionFunction::setParameters ( const ParameterList & parameters )

virtual

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implements bpp::Function.

Definition at line 49 of file DirectionFunction.cpp.

References bpp::ParameterList::setParameters().

◆ setParametersValues() [1/2]

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

inlinevirtualinherited

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 218 of file Parametrizable.h.

◆ setParametersValues() [2/2]

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() [1/2]

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

inlinevirtualinherited

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 217 of file Parametrizable.h.

◆ setParameterValue() [2/2]

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().

Member Data Documentation

◆ constraintPolicy_

std::string bpp::DirectionFunction::constraintPolicy_

private

Definition at line 61 of file DirectionFunction.h.

Referenced by getConstraintPolicy(), operator=(), and setConstraintPolicy().

◆ function_

Function* bpp::DirectionFunction::function_

private

Definition at line 60 of file DirectionFunction.h.

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

◆ messenger_

OutputStream* bpp::DirectionFunction::messenger_

private

Definition at line 62 of file DirectionFunction.h.

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

◆ p_

ParameterList bpp::DirectionFunction::p_

private

Definition at line 58 of file DirectionFunction.h.

Referenced by getFunctionParameters(), getNumberOfParameters(), and operator=().

◆ parameter_

Parameter bpp::ParametrizableAdapter::parameter_

protectedinherited

Definition at line 200 of file Parametrizable.h.

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

◆ parameters_

ParameterList bpp::ParametrizableAdapter::parameters_

protectedinherited

Definition at line 199 of file Parametrizable.h.

Referenced by bpp::ParametrizableAdapter::getParameters(), and bpp::ParametrizableAdapter::hasParameter().

◆ params_

ParameterList bpp::DirectionFunction::params_

mutableprivate

Definition at line 58 of file DirectionFunction.h.

Referenced by operator=().

◆ xi_

std::vector<double> bpp::DirectionFunction::xi_

private

Definition at line 59 of file DirectionFunction.h.

Referenced by operator=().

◆ xt_

ParameterList bpp::DirectionFunction::xt_

private

Definition at line 58 of file DirectionFunction.h.

Referenced by operator=().

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

Bpp/Numeric/Function/DirectionFunction.h
Bpp/Numeric/Function/DirectionFunction.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DirectionFunction() [1/2]

◆ DirectionFunction() [2/2]

◆ ~DirectionFunction()

Member Function Documentation

◆ autoParameter()

◆ clone()

◆ f()

◆ getConstraintPolicy()

◆ getFunction()

◆ getFunctionParameters()

◆ getNamespace() [1/2]

◆ getNamespace() [2/2]

◆ getNumberOfParameters()

◆ getParameter() [1/2]

◆ getParameter() [2/2]

◆ getParameterNameWithoutNamespace() [1/2]

◆ getParameterNameWithoutNamespace() [2/2]

◆ getParameters()

◆ getParameters_()

◆ getParameterValue() [1/2]

◆ getParameterValue() [2/2]

◆ getValue()

◆ hasParameter() [1/2]

◆ hasParameter() [2/2]

◆ ignoreConstraints()

◆ init()

◆ matchParametersValues() [1/2]

◆ matchParametersValues() [2/2]

◆ operator=()

◆ setAllParametersValues() [1/2]

◆ setAllParametersValues() [2/2]

◆ setConstraintPolicy()

◆ setMessageHandler()

◆ setNamespace() [1/2]

◆ setNamespace() [2/2]

◆ setParameters()

◆ setParametersValues() [1/2]

◆ setParametersValues() [2/2]

◆ setParameterValue() [1/2]

◆ setParameterValue() [2/2]

Member Data Documentation

◆ constraintPolicy_

◆ function_

◆ messenger_

◆ p_

◆ parameter_

◆ parameters_

◆ params_

◆ xi_

◆ xt_