bpp::ParametrizableCollection< N > Class Template Reference

Plain collection of parametrizable objects. More...

#include <Bpp/Numeric/ParametrizableCollection.h>

Inheritance diagram for bpp::ParametrizableCollection< N >:

Collaboration diagram for bpp::ParametrizableCollection< N >:

Public Member Functions
	ParametrizableCollection ()
	Create an empty object set. More...
	ParametrizableCollection (const ParametrizableCollection< N > &set)
ParametrizableCollection< N > &	operator= (const ParametrizableCollection< N > &set)
void	clear ()
	Resets all the information contained in this object. More...
	~ParametrizableCollection ()
ParametrizableCollection< N > *	clone () const
	Create a copy of this object and send a pointer to it. More...
void	fireParameterChanged (const ParameterList &parameters)
std::vector< size_t >	hasChanged () const
void	clearChanged ()
size_t	getNumberOfObjects () const
const bool	hasObject (size_t objectIndex) const
	Says if there is a object with a given index. More...
const std::vector< size_t >	keys () const
	Returns the keys of the set. More...
const N *	operator[] (size_t objectIndex) const
	Get one object from the set knowing its index. More...
N *	operator[] (size_t objectIndex)
void	addObject (N *object, size_t objectIndex)
	Add a new object to the set with a given number. More...
N *	removeObject (size_t objectIndex)
	Remove a object from the set, and all corresponding parameters. More...
N *	replaceObject (N *object, size_t objectIndex)
	Replace a object in the set, and returns the replaced one. More...
void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names. More...
const ParameterList &	getIndependentParameters () const
	Get the minimal list of parameters to set the model. More...
size_t	getNumberOfIndependentParameters () const
	Get the number of independent parameters. More...
void	aliasParameters (const std::string &p1, const std::string &p2) throw (ParameterNotFoundException, Exception)
	Set two parameters as 'aliased'. More...
void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
	alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
void	unaliasParameters (const std::string &p1, const std::string &p2) throw (ParameterNotFoundException, Exception)
	Detach two parameters previously set as 'aliased'. More...
ParameterList	getAliasedParameters (const ParameterList &pl) const
	Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More...
std::vector< std::string >	getAlias (const std::string &name) const
std::string	getFrom (const std::string &name) const
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...
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
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)
void	deleteParameter_ (std::string &name) throw (IndexOutOfBoundsException)
void	deleteParameters_ (const std::vector< std::string > &names)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name) throw (ParameterNotFoundException)
Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)
const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)
Parameter &	getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)
ParameterList &	getParameters_ ()

Protected Attributes
std::map< size_t, N *>	objectsSet_
	Contains all objects used. More...
std::vector< size_t >	vChanged_
	A vector of the numbers of objects that have changed during the last fireParameterChanged. More...

Detailed Description

template<class N>
class bpp::ParametrizableCollection< N >

Plain collection of parametrizable objects.

The collection is a map from unsigned integers to Parametrizables.

The access to the parameters of the objects will be done through this collection.

Definition at line 63 of file ParametrizableCollection.h.

Constructor & Destructor Documentation

ParametrizableCollection() [1/2]

template<class N>

bpp::ParametrizableCollection< N >::ParametrizableCollection ( )

inline

Create an empty object set.

Definition at line 87 of file ParametrizableCollection.h.

ParametrizableCollection() [2/2]

template<class N>

bpp::ParametrizableCollection< N >::ParametrizableCollection ( const ParametrizableCollection< N > &  set )

inline

Definition at line 94 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

~ParametrizableCollection()

template<class N>

bpp::ParametrizableCollection< N >::~ParametrizableCollection ( )

inline

Definition at line 136 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::clear().

Member Function Documentation

addObject()

template<class N>

void bpp::ParametrizableCollection< N >::addObject ( N *  object, size_t  objectIndex  )

inline

Add a new object to the set with a given number.

Exceptions

Exception

if the number is already used. See replace function instead.

Parameters

object

A pointer toward an object, that will added to the set.

WARNING! The set will now be the owner of the pointer, and will destroy it if needed! Copy the object first if you don't want it to be lost!

Parameters

objectIndex

The number of the object in the Collection

Definition at line 261 of file ParametrizableCollection.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParameterAliasable::getAlias(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::Parameter::setName(), and bpp::TextTools::toString().

Referenced by bpp::ParametrizableCollection< N >::replaceObject().

addParameter_()

void bpp::AbstractParameterAliasable::addParameter_ ( Parameter *  parameter )

inlineprotectedinherited

Definition at line 212 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameter(), bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::clone(), and bpp::AbstractParameterAliasable::independentParameters_.

Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ConstantDistribution::ConstantDistribution(), bpp::DirichletDiscreteDistribution::DirichletDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::Simplex::Simplex(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().

addParameters_()

void bpp::AbstractParameterAliasable::addParameters_ ( const ParameterList &  parameters )

inlineprotectedinherited

Definition at line 218 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameters(), bpp::AbstractParametrizable::addParameters_(), and bpp::AbstractParameterAliasable::independentParameters_.

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

aliasParameters() [1/2]

void AbstractParameterAliasable::aliasParameters ( const std::string &  p1, const std::string &  p2  ) throw ( ParameterNotFoundException, Exception )

virtualinherited

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.

Implements bpp::ParameterAliasable.

Definition at line 103 of file AbstractParameterAliasable.cpp.

References bpp::Parameter::addParameterListener(), bpp::Parameter::getConstraint(), bpp::Constraint::getDescription(), and bpp::Parameter::hasConstraint().

Referenced by bpp::ParametrizableCollection< N >::addObject().

aliasParameters() [2/2]

void AbstractParameterAliasable::aliasParameters ( std::map< std::string, std::string > &  unparsedParams, bool  verbose  )

virtualinherited

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

Implements bpp::ParameterAliasable.

Definition at line 151 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParameterList::clone(), bpp::Parameter::clone(), bpp::ApplicationTools::displayResult(), bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::matchParametersValues(), bpp::ParameterList::size(), and bpp::TextTools::toString().

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

clear()

template<class N>

void bpp::ParametrizableCollection< N >::clear ( )

inline

Resets all the information contained in this object.

Definition at line 125 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_, bpp::AbstractParameterAliasable::resetParameters_(), and bpp::ParametrizableCollection< N >::vChanged_.

Referenced by bpp::ParametrizableCollection< N >::operator=(), and bpp::ParametrizableCollection< N >::~ParametrizableCollection().

clearChanged()

template<class N>

void bpp::ParametrizableCollection< N >::clearChanged ( )

inline

Definition at line 182 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::vChanged_.

clone()

template<class N>

ParametrizableCollection<N>* bpp::ParametrizableCollection< N >::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 141 of file ParametrizableCollection.h.

deleteParameter_() [1/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( size_t  index ) throw ( IndexOutOfBoundsException )

inlineprotectedinherited

Definition at line 224 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameter_(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.

Referenced by bpp::AbstractParameterAliasable::deleteParameters_(), and bpp::ParametrizableCollection< N >::removeObject().

deleteParameter_() [2/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( std::string &  name ) throw ( IndexOutOfBoundsException )

inlineprotectedinherited

Definition at line 232 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.

deleteParameters_()

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

inlineprotectedinherited

Definition at line 239 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::deleteParameter_().

fireParameterChanged()

template<class N>

void bpp::ParametrizableCollection< N >::fireParameterChanged ( const ParameterList &  parameters )

inlinevirtual

To be called when a parameter has changed. Depending on parameters, this will actualize the corresponding objects in the set.

Parameters

parameters

The modified parameters.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 150 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::hasObject(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::ParameterList::size(), and bpp::ParametrizableCollection< N >::vChanged_.

getAlias()

vector< string > AbstractParameterAliasable::getAlias ( const std::string &  name ) const

virtualinherited

Returns

The list of names of the parameters that are aliased with a given parameter. The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.

Parameters

name	The name of the parameter to look for.

Implements bpp::ParameterAliasable.

Definition at line 245 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::VectorTools::append().

Referenced by bpp::ParametrizableCollection< N >::removeObject().

getAliasedParameters()

ParameterList AbstractParameterAliasable::getAliasedParameters ( const ParameterList &  pl ) const

inherited

Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list.

Definition at line 266 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getParameter(), and bpp::ParameterList::hasParameter().

getFrom()

string AbstractParameterAliasable::getFrom ( const std::string &  name ) const

inherited

Returns

The name of the parameter from which a given parameter is aliased.

Parameters

name	The name of the parameter to look for.

Definition at line 306 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

getIndependentParameters()

const ParameterList& bpp::AbstractParameterAliasable::getIndependentParameters ( ) const

inlinevirtualinherited

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.

Implements bpp::ParameterAliasable.

Definition at line 162 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_.

getNamespace()

std::string bpp::AbstractParametrizable::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 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

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

getNumberOfIndependentParameters()

size_t bpp::AbstractParameterAliasable::getNumberOfIndependentParameters ( ) const

inlinevirtualinherited

Get the number of independent parameters.

Returns

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

Implements bpp::ParameterAliasable.

Definition at line 164 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::size().

getNumberOfObjects()

template<class N>

size_t bpp::ParametrizableCollection< N >::getNumberOfObjects ( ) const

inline

Returns

The current number of distinct discrete objects in this set.

Definition at line 191 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

getNumberOfParameters()

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlinevirtualinherited

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 bpp::AbstractParametrizable::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 )

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 79 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::TestFunction::getValue().

getParameter_() [1/3]

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

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 175 of file AbstractParametrizable.h.

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

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

inlineprotectedinherited

Definition at line 199 of file AbstractParametrizable.h.

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

getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 205 of file AbstractParametrizable.h.

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

getParameterNameWithoutNamespace()

std::string AbstractParametrizable::getParameterNameWithoutNamespace ( const std::string &  name ) const

virtualinherited

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

inlinevirtualinherited

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 bpp::AbstractParametrizable::parameters_.

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

getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotectedinherited

Definition at line 212 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

getParameterValue()

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

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 84 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::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::GammaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

getParameterWithNamespace_() [2/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns

A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException

If no parameter with that name is found in the list.

Definition at line 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

hasChanged()

template<class N>

std::vector<size_t> bpp::ParametrizableCollection< N >::hasChanged ( ) const

inline

Definition at line 177 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::vChanged_.

hasObject()

template<class N>

const bool bpp::ParametrizableCollection< N >::hasObject ( size_t  objectIndex ) const

inline

Says if there is a object with a given index.

Parameters

objectIndex

Index of the object in the set.

Returns

true or false.

Definition at line 200 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

Referenced by bpp::ParametrizableCollection< N >::fireParameterChanged().

hasParameter()

bool bpp::AbstractParametrizable::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 75 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

keys()

template<class N>

const std::vector<size_t> bpp::ParametrizableCollection< N >::keys ( ) const

inline

Returns the keys of the set.

Definition at line 210 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

matchParametersValues()

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

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 111 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), and bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), bpp::TestFunction::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

operator=()

template<class N>

ParametrizableCollection<N>& bpp::ParametrizableCollection< N >::operator= ( const ParametrizableCollection< N > &  set )

inline

Definition at line 105 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::AbstractParameterAliasable::operator=(), and bpp::ParametrizableCollection< N >::vChanged_.

operator[]() [1/2]

template<class N>

const N* bpp::ParametrizableCollection< N >::operator[] ( size_t  objectIndex ) const

inline

Get one object from the set knowing its index.

Parameters

objectIndex

Index of the object in the set.

Returns

A pointer toward the corresponding object.

Definition at line 229 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

operator[]() [2/2]

template<class N>

N* bpp::ParametrizableCollection< N >::operator[] ( size_t  objectIndex )

inline

Definition at line 238 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::objectsSet_.

removeObject()

template<class N>

N* bpp::ParametrizableCollection< N >::removeObject ( size_t  objectIndex )

inline

Remove a object from the set, and all corresponding parameters.

Parameters

objectIndex

The index of the object in the set.

Returns

the removed N*.

Definition at line 301 of file ParametrizableCollection.h.

References bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParameterAliasable::getAlias(), bpp::AbstractParametrizable::getParameters(), bpp::ParametrizableCollection< N >::objectsSet_, bpp::ParameterList::size(), and bpp::AbstractParameterAliasable::unaliasParameters().

Referenced by bpp::ParametrizableCollection< N >::replaceObject().

replaceObject()

template<class N>

N* bpp::ParametrizableCollection< N >::replaceObject ( N *  object, size_t  objectIndex  )

inline

Replace a object in the set, and returns the replaced one.

Parameters

objectIndex	The index of the object to be replaced in the set.
object	the replacing N

Returns

the replaced N*.

Definition at line 344 of file ParametrizableCollection.h.

References bpp::ParametrizableCollection< N >::addObject(), and bpp::ParametrizableCollection< N >::removeObject().

resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 249 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::reset(), and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::ParametrizableCollection< N >::clear().

setAllParametersValues()

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters ) throw ( ParameterNotFoundException, ConstraintException )

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 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::setAllParametersValues().

setNamespace()

void AbstractParameterAliasable::setNamespace ( const std::string &  prefix )

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.

Implements bpp::Parametrizable.

Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 218 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParameterAliasable::independentParameters_, bpp::AbstractParametrizable::setNamespace(), bpp::ParameterList::size(), and bpp::TextTools::startsWith().

Referenced by bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::MixtureOfDiscreteDistributions::setNamespace().

setParametersValues()

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters ) throw ( ParameterNotFoundException, ConstraintException )

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 104 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::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 )

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 97 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, bpp::ParameterList::setParameterValue(), and bpp::ParameterList::subList().

unaliasParameters()

void AbstractParameterAliasable::unaliasParameters ( const std::string &  p1, const std::string &  p2  ) throw ( ParameterNotFoundException, Exception )

virtualinherited

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.

Implements bpp::ParameterAliasable.

Definition at line 198 of file AbstractParameterAliasable.cpp.

Referenced by bpp::ParametrizableCollection< N >::removeObject().

Member Data Documentation

objectsSet_

template<class N>

std::map<size_t, N* > bpp::ParametrizableCollection< N >::objectsSet_

protected

Contains all objects used.

Definition at line 71 of file ParametrizableCollection.h.

Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::fireParameterChanged(), bpp::ParametrizableCollection< N >::getNumberOfObjects(), bpp::ParametrizableCollection< N >::hasObject(), bpp::ParametrizableCollection< N >::keys(), bpp::ParametrizableCollection< N >::operator=(), bpp::ParametrizableCollection< N >::operator[](), bpp::ParametrizableCollection< N >::ParametrizableCollection(), and bpp::ParametrizableCollection< N >::removeObject().

vChanged_

template<class N>

std::vector<size_t> bpp::ParametrizableCollection< N >::vChanged_

protected

A vector of the numbers of objects that have changed during the last fireParameterChanged.

Definition at line 79 of file ParametrizableCollection.h.

Referenced by bpp::ParametrizableCollection< N >::clear(), bpp::ParametrizableCollection< N >::clearChanged(), bpp::ParametrizableCollection< N >::fireParameterChanged(), bpp::ParametrizableCollection< N >::hasChanged(), and bpp::ParametrizableCollection< N >::operator=().

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

• Bpp/Numeric/ParametrizableCollection.h