Detailed Description

Registry where package extensions are registered.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

This class provides a central registry of all extensions known to libSBML. Each package extension must be registered with the registry. The registry class is accessed by various classes to retrieve information about known package extensions and to create additional attributes and/or elements by factory objects of the package extensions.

: The package extension registry is implemented as a singleton instance of SBMLExtensionRegistry. The class provides only utility functionality; implementations of SBML packages do not need to implement any subclasses or methods of this class. SBMLExtensionRegistry is useful for its facilities to query the known packages, and to enable or disable packages selectively.

Public Member Functions
int	addExtension (const SBMLExtension *ext)
	Add the given SBMLExtension object to this SBMLExtensionRegistry. More...

void	addL2Namespaces (XMLNamespaces *xmlns) const
	Adds SBML Level 2 namespaces to the namespace list. More...

void	disableUnusedPackages (SBMLDocument *doc)
	Disables unused packages. More...

void	enableL2NamespaceForDocument (SBMLDocument *doc) const
	Enables package extensions that support serialization to SBML annotations. More...

const ASTBasePlugin *	getASTPlugin (unsigned int i)

std::vector< ASTBasePlugin * >	getASTPlugins ()

SBMLExtension *	getExtension (const std::string &package)
	Returns an SBMLExtension object with the given package URI or package name. More...

unsigned int	getNumASTPlugins ()

unsigned int	getNumExtension (const SBaseExtensionPoint &extPoint)
	Returns the number of extensions that have a given extension point. More...

bool	isEnabled (const std::string &uri)
	Returns `true` if the given extension is enabled. More...

bool	isRegistered (const std::string &uri)
	Returns `true` if a package extension is registered for the corresponding package URI. More...

void	removeL2Namespaces (XMLNamespaces *xmlns) const
	Removes SBML Level 2 namespaces from the namespace list. More...

bool	setEnabled (const std::string &uri, bool isEnabled)
	Enables or disable the package with the given URI. More...

Static Public Member Functions
static void	disablePackage (const std::string &package)
	Disables the package with the given URI or name. More...

static void	enablePackage (const std::string &package)
	Enables the package with the given URI / name. More...

static std::vector< std::string >	getAllRegisteredPackageNames ()
	Returns a list of registered packages. More...

static SBMLExtensionRegistry &	getInstance ()
	Returns a singleton instance of the registry. More...

static unsigned int	getNumRegisteredPackages ()
	Returns the number of registered packages. More...

static std::string	getRegisteredPackageName (unsigned int index)
	Returns the nth registered package. More...

static List *	getRegisteredPackageNames ()
	Returns a list of registered packages. More...

static bool	isPackageEnabled (const std::string &package)
	Returns `true` if the named package is enabled. More...

Private Member Functions
const SBMLExtension *	getExtensionInternal (const std::string &package)
	Returns an SBMLExtension object with the given package URI or package name (string). More...

SBMLExtensionRegistry &	operator= (const SBMLExtensionRegistry &rhs)

	SBMLExtensionRegistry ()

	SBMLExtensionRegistry (const SBMLExtensionRegistry &orig)

	~SBMLExtensionRegistry ()

Static Private Attributes
static bool	registered

Constructor & Destructor Documentation

◆ SBMLExtensionRegistry() [1/2]

SBMLExtensionRegistry::SBMLExtensionRegistry ( )

private

◆ SBMLExtensionRegistry() [2/2]

SBMLExtensionRegistry::SBMLExtensionRegistry ( const SBMLExtensionRegistry & orig )

private

◆ ~SBMLExtensionRegistry()

SBMLExtensionRegistry::~SBMLExtensionRegistry ( )

private

Member Function Documentation

◆ addExtension()

int SBMLExtensionRegistry::addExtension ( const SBMLExtension * ext )

Add the given SBMLExtension object to this SBMLExtensionRegistry.

Parameters

ext	the SBMLExtension object to be added.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

◆ addL2Namespaces()

void SBMLExtensionRegistry::addL2Namespaces ( XMLNamespaces * xmlns ) const

Adds SBML Level 2 namespaces to the namespace list.

This will call all overridden SBMLExtension::addL2Namespaces() methods.

Parameters

xmlns an XMLNamespaces object providing one or more namespaces to be added.

◆ disablePackage()

void SBMLExtensionRegistry::disablePackage ( const std::string & package )

static

Disables the package with the given URI or name.

Parameters

package a string representing the URI or name of the SBML package whose package extension is to be disabled.

◆ disableUnusedPackages()

void SBMLExtensionRegistry::disableUnusedPackages ( SBMLDocument * doc )

Disables unused packages.

This method walks through all extensions in the list of plugins of the given SBML document doc, and disables all that are not being used.

Parameters

doc	the SBMLDocument object whose unused package extensions should be disabled.

◆ enableL2NamespaceForDocument()

void SBMLExtensionRegistry::enableL2NamespaceForDocument ( SBMLDocument * doc ) const

Enables package extensions that support serialization to SBML annotations.

SBML Level 2 does not have a package mechanism in the way that SBML Level 3 does. However, SBML annotations can be used to store SBML constructs. In fact, a widely-used approach to developing SBML Level 3 packages involves first using them as annotations.

Parameters

doc	the SBMLDocument object for which this should be enabled.

◆ enablePackage()

void SBMLExtensionRegistry::enablePackage ( const std::string & package )

static

Enables the package with the given URI / name.

Parameters

package the name or URI of a package to enable.

◆ getAllRegisteredPackageNames()

std::vector< std::string > SBMLExtensionRegistry::getAllRegisteredPackageNames ( )

static

Returns a list of registered packages.

This method returns a vector of strings containing the nicknames of the SBML packages for which package extensions are registered with this copy of libSBML. The vector will contain std::string objects.

Returns: a vector of strings of the registered package names.

◆ getASTPlugin()

const ASTBasePlugin * SBMLExtensionRegistry::getASTPlugin ( unsigned int i )

◆ getASTPlugins()

std::vector< ASTBasePlugin * > SBMLExtensionRegistry::getASTPlugins ( )

◆ getExtension()

SBMLExtension* SBMLExtensionRegistry::getExtension ( const std::string & package )

Returns an SBMLExtension object with the given package URI or package name.

Parameters

package a string representing the URI or name of the SBML package whose package extension is being sought.

Returns: a clone of the SBMLExtension object with the given package URI or name.

Note: The caller is responsible for freeing the object returned. Since the object is a clone, freeing it will not result in the deletion of the original package extension object.

◆ getExtensionInternal()

const SBMLExtension* SBMLExtensionRegistry::getExtensionInternal ( const std::string & package )

private

Returns an SBMLExtension object with the given package URI or package name (string).

Parameters

package the URI or name of the package extension.

Returns: the SBMLExtension object with the given package URI or name. The returned extension is NOT ALLOWED to be freed (i.e.: deleted)!

◆ getInstance()

static SBMLExtensionRegistry& SBMLExtensionRegistry::getInstance ( )

static

Returns a singleton instance of the registry.

Callers need to obtain a copy of the package extension registry before they can invoke its methods. The registry is implemented as a singleton, and this is the method callers can use to get a copy of it.

Returns: the instance of the SBMLExtensionRegistry object.

◆ getNumASTPlugins()

unsigned int SBMLExtensionRegistry::getNumASTPlugins ( )

◆ getNumExtension()

unsigned int SBMLExtensionRegistry::getNumExtension ( const SBaseExtensionPoint & extPoint )

Returns the number of extensions that have a given extension point.

Parameters

extPoint the SBaseExtensionPoint object.

Returns: the number of SBMLExtension-derived objects with the given extension point.

◆ getNumRegisteredPackages()

unsigned int SBMLExtensionRegistry::getNumRegisteredPackages ( )

static

Returns the number of registered packages.

Returns: a count of the registered package extensions.

See also: getRegisteredPackageNames()

Examples: printRegisteredPackages.cpp.

◆ getRegisteredPackageName()

std::string SBMLExtensionRegistry::getRegisteredPackageName ( unsigned int index )

static

Returns the nth registered package.

Parameters

index zero-based index of the package name to return.

Returns: the package name with the given index, or NULL if none such exists.

See also: getNumRegisteredPackages()

Examples: printRegisteredPackages.cpp.

◆ getRegisteredPackageNames()

List * SBMLExtensionRegistry::getRegisteredPackageNames ( )

static

Returns a list of registered packages.

This method returns a List object containing the nicknames of the SBML packages for which package extensions are registered with this copy of libSBML. The list will contain strings (e.g., "layout", "fbc", etc.) and has to be freed by the caller.

Returns: a list of strings representing the names of the registered packages.

◆ isEnabled()

bool SBMLExtensionRegistry::isEnabled ( const std::string & uri )

Returns true if the given extension is enabled.

Parameters

uri	the URI of the target package.

Returns: false if the given package is disabled or not registered, true otherwise.

◆ isPackageEnabled()

bool SBMLExtensionRegistry::isPackageEnabled ( const std::string & package )

static

Returns true if the named package is enabled.

Parameters

package the name or URI of a package to test.

Returns: true if the package is enabled, false otherwise.

Examples: flattenModel.cpp.

◆ isRegistered()

bool SBMLExtensionRegistry::isRegistered ( const std::string & uri )

Returns true if a package extension is registered for the corresponding package URI.

Parameters

uri	the URI of the target package.

Returns: true if the package with the given URI is registered, otherwise returns false.

◆ operator=()

SBMLExtensionRegistry& SBMLExtensionRegistry::operator= ( const SBMLExtensionRegistry & rhs )

private

◆ removeL2Namespaces()

void SBMLExtensionRegistry::removeL2Namespaces ( XMLNamespaces * xmlns ) const

Removes SBML Level 2 namespaces from the namespace list.

This will call all overridden SBMLExtension::removeL2Namespaces() methods.

Parameters

xmlns an XMLNamespaces object listing one or more namespaces to be removed.

◆ setEnabled()

bool SBMLExtensionRegistry::setEnabled	(	const std::string &	uri,
		bool	isEnabled
	)

Enables or disable the package with the given URI.

Parameters

uri	the URI of the target package.
isEnabled	`true` to enable the package, `false` to disable.

Returns: false if isEnabled is false or the given package is not registered, otherwise this method returns true.

Member Data Documentation

◆ registered

bool SBMLExtensionRegistry::registered

staticprivate

Detailed Description

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Attributes

Constructor & Destructor Documentation

◆ SBMLExtensionRegistry() [1/2]

◆ SBMLExtensionRegistry() [2/2]

◆ ~SBMLExtensionRegistry()

Member Function Documentation

◆ addExtension()

◆ addL2Namespaces()

◆ disablePackage()

◆ disableUnusedPackages()

◆ enableL2NamespaceForDocument()

◆ enablePackage()

◆ getAllRegisteredPackageNames()

◆ getASTPlugin()

◆ getASTPlugins()

◆ getExtension()

◆ getExtensionInternal()

◆ getInstance()

◆ getNumASTPlugins()

◆ getNumExtension()

◆ getNumRegisteredPackages()

◆ getRegisteredPackageName()

◆ getRegisteredPackageNames()

◆ isEnabled()

◆ isPackageEnabled()

◆ isRegistered()

◆ operator=()

◆ removeL2Namespaces()

◆ setEnabled()

Member Data Documentation

◆ registered