Inheritance diagram for GroupsExtension:

Detailed Description

groups Base extension class for the package.

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 is the Groups package extension of the SBMLExtension class that is used to facilitate libSBML plug-ins in the implementation of an SBMLLevel 3 package.

Public Member Functions
virtual void	addL2Namespaces (XMLNamespaces *xmlns) const
	Adds the package's Level 2 namespace(s). More...

virtual GroupsExtension *	clone () const
	Creates and returns a deep copy of this GroupsExtension object. More...

virtual void	enableL2NamespaceForDocument (SBMLDocument *doc) const
	Called to enable the package on the SBMLDocument object. More...

virtual unsigned int	getLevel (const std::string &uri) const
	Returns the SBML Level for the given URI of this package. More...

virtual const std::string &	getName () const
	Returns the name of this SBML Level 3 package ("groups"). More...

int	getNumOfSBasePlugins () const
	Returns the number of SBasePluginCreatorBase objects stored in this object. More...

unsigned int	getNumOfSupportedPackageURI () const
	Returns the number of supported package namespace URIs. More...

virtual unsigned int	getPackageVersion (const std::string &uri) const
	Returns the SBML Level 3 package version for the given URI of this package. More...

virtual SBMLNamespaces *	getSBMLExtensionNamespaces (const std::string &uri) const
	Returns a GroupsPkgNamespaces object. More...

virtual const char *	getStringFromTypeCode (int typeCode) const
	Takes a type code of the “groups” package and returns a string describing the code. More...

const std::string &	getSupportedPackageURI (unsigned int n) const
	Returns the nth XML namespace URI. More...

virtual const std::string &	getURI (unsigned int sbmlLevel, unsigned int sbmlVersion, unsigned int pkgVersion) const
	Returns a string representing the SBML XML namespace of this SBML Level 3 package. More...

virtual unsigned int	getVersion (const std::string &uri) const
	Returns the Version within the SBML Level for the given URI of this package. More...

	GroupsExtension ()
	Creates a new GroupsExtension instance. More...

	GroupsExtension (const GroupsExtension &orig)
	Copy constructor for GroupsExtension. More...

bool	isEnabled () const
	Returns `true` if this package is enabled. More...

virtual bool	isInUse (SBMLDocument *doc) const
	Indicates whether this extension is being used by the given SBMLDocument. More...

bool	isSupported (const std::string &uri) const
	Returns `true` if the given XML namespace URI is supported by this package extension. More...

GroupsExtension &	operator= (const GroupsExtension &rhs)
	Assignment operator for GroupsExtension. More...

virtual void	removeL2Namespaces (XMLNamespaces *xmlns) const
	Removes the package's Level 2 namespace(s). More...

bool	setEnabled (bool isEnabled)
	Enable or disable this package. More...

virtual	~GroupsExtension ()
	Destructor for GroupsExtension. More...

Static Public Member Functions
static unsigned int	getDefaultLevel ()
	Returns the default SBML Level implemented by this libSBML extension. More...

static unsigned int	getDefaultPackageVersion ()
	Returns the default version of the SBML Level 3 package implemented by this libSBML extension. More...

static unsigned int	getDefaultVersion ()
	Returns the default SBML Version implemented by this libSBML extension. More...

static const std::string &	getPackageName ()
	Returns the nickname of the SBML Level 3 package implemented by this libSBML extension. More...

static const std::string &	getXmlnsL3V1V1 ()
	Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension. More...

Constructor & Destructor Documentation

GroupsExtension::GroupsExtension ( )

Creates a new GroupsExtension instance.

GroupsExtension::GroupsExtension ( const GroupsExtension & orig )

Copy constructor for GroupsExtension.

Parameters

orig	the GroupsExtension instance to copy.

GroupsExtension::~GroupsExtension ( )

virtual

Destructor for GroupsExtension.

Member Function Documentation

void SBMLExtension::addL2Namespaces ( XMLNamespaces * xmlns ) const

virtualinherited

Adds the package's Level 2 namespace(s).

: This method is related to special facilities designed to support legacy behaviors surrounding SBML Level 2 models. Due to the historical background of the SBML Layout package, libSBML implements special behavior for that package: it always creates a Layout plugin object for any SBML Level 2 document it reads in, regardless of whether that document actually uses Layout constructs. Since Level 2 does not use namespaces on the top level of the SBML document object, libSBML simply keys off the fact that the model is a Level 2 model. To allow the extensions for the Layout and Render (and possibly other) packages to support this behavior, the SBMLExtension class contains special methods to allow packages to hook themselves into the Level 2 parsing apparatus when necessary.

This virtual method should be overridden by all package extensions that want to serialize to an SBML Level 2 annotation. In Level 2, the XML namespace declaration for the package is not placed on the top-level SBML document object but rather inside individual annotations. addL2Namespaces() is invoked automatically for Level 2 documents when an SBMLExtensionNamespace object is created; removeL2Namespaces() is automatically invoked by SBMLDocument to prevent the namespace(s) from being put on the top-level SBML Level 2 element (because Level 2 doesn't support namespaces there); and enableL2NamespaceForDocument() is called automatically when any SBML document (of any Level/Version) is read in.

Parameters

xmlns

an XMLNamespaces object that will be used for the annotation. Implementation should override this method with something that adds the package's namespace(s) to the set of namespaces in xmlns. For instance, here is the code from the Layout package extension:

if (!xmlns->containsUri( LayoutExtension::getXmlnsL2()))

xmlns->add(LayoutExtension::getXmlnsL2(), "layout");

Reimplemented in LayoutExtension, and RenderExtension.

GroupsExtension * GroupsExtension::clone ( ) const

virtual

Creates and returns a deep copy of this GroupsExtension object.

Returns: a (deep) copy of this GroupsExtension object.

Implements SBMLExtension.

void SBMLExtension::enableL2NamespaceForDocument ( SBMLDocument * doc ) const

virtualinherited

Called to enable the package on the SBMLDocument object.

: This method is related to special facilities designed to support legacy behaviors surrounding SBML Level 2 models. Due to the historical background of the SBML Layout package, libSBML implements special behavior for that package: it always creates a Layout plugin object for any SBML Level 2 document it reads in, regardless of whether that document actually uses Layout constructs. Since Level 2 does not use namespaces on the top level of the SBML document object, libSBML simply keys off the fact that the model is a Level 2 model. To allow the extensions for the Layout and Render (and possibly other) packages to support this behavior, the SBMLExtension class contains special methods to allow packages to hook themselves into the Level 2 parsing apparatus when necessary.

This virtual method should be overridden by all package extensions that want to serialize to an SBML Level 2 annotation. In Level 2, the XML namespace declaration for the package is not placed on the top-level SBML document object but rather inside individual annotations. addL2Namespaces() is invoked automatically for Level 2 documents when an SBMLExtensionNamespace object is created; removeL2Namespaces() is automatically invoked by SBMLDocument to prevent the namespace(s) from being put on the top-level SBML Level 2 element (because Level 2 doesn't support namespaces there); and enableL2NamespaceForDocument() is called automatically when any SBML document (of any Level/Version) is read in.

Parameters

doc

the SBMLDocument object for the model. Implementations should override this method with something that enables the package based on the package's namespace(s). For example, here is the code from the Layout package extension:

if (doc->getLevel() == 2)

doc->enablePackage(LayoutExtension::getXmlnsL2(), "layout", true);

Reimplemented in LayoutExtension, and RenderExtension.

unsigned int GroupsExtension::getDefaultLevel ( )

static

Returns the default SBML Level implemented by this libSBML extension.

Returns: the SBML Level, as an unsigned integer.

unsigned int GroupsExtension::getDefaultPackageVersion ( )

static

Returns the default version of the SBML Level 3 package implemented by this libSBML extension.

Returns: the default version number of the SBML Level 3 package definition, as an unsigned integer.

unsigned int GroupsExtension::getDefaultVersion ( )

static

Returns the default SBML Version implemented by this libSBML extension.

Returns: the Version within the default SBML Level, as an unsigned integer.

unsigned int GroupsExtension::getLevel ( const std::string & uri ) const

virtual

Returns the SBML Level for the given URI of this package.

Parameters

uri	the string of the URI that represents one of the versions of the "groups" package.

Returns: the SBML Level for the given URI of this package, or 0 if the given URI is invalid, or for a different package.

Implements SBMLExtension.

const std::string & GroupsExtension::getName ( ) const

virtual

Returns the name of this SBML Level 3 package ("groups").

Returns: a string representing the name of this package ("groups").

Implements SBMLExtension.

int SBMLExtension::getNumOfSBasePlugins ( ) const

inherited

Returns the number of SBasePluginCreatorBase objects stored in this object.

Returns: the total number of SBasePluginCreatorBase objects stored in this SBMLExtension-derived object.

unsigned int SBMLExtension::getNumOfSupportedPackageURI ( ) const

inherited

Returns the number of supported package namespace URIs.

Returns: the number of supported package XML namespace URIs of this package extension.

const std::string & GroupsExtension::getPackageName ( )

static

Returns the nickname of the SBML Level 3 package implemented by this libSBML extension.

Returns: the package nickname, as a string.

unsigned int GroupsExtension::getPackageVersion ( const std::string & uri ) const

virtual

Returns the SBML Level 3 package version for the given URI of this package.

Parameters

uri	the string of the URI that represents one of the versions of the "groups" package.

Returns: the version of the SBML Level 3 package for the given URI of this package, or 0 if the given URI is invalid, or for a different package.

Implements SBMLExtension.

SBMLNamespaces * GroupsExtension::getSBMLExtensionNamespaces ( const std::string & uri ) const

virtual

Returns a GroupsPkgNamespaces object.

Parameters

uri	the string of the URI that represents one of the versions of the "groups" package.

Returns: GroupsPkgNamespaces object corresponding to the given URI of this package, or NULL if the given URI is not defined in the "groups" package.

Implements SBMLExtension.

const char * GroupsExtension::getStringFromTypeCode ( int typeCode ) const

virtual

Takes a type code of the “groups” package and returns a string describing the code.

Parameters

typeCode a libSBML type code defined by the libSBML extension implementing support for the SBML Level 3 “groups” package.

Returns: a text string representing the type code given by typeCode. If the type code is unrecognized for this implementation of the libSBML “groups” package, the string returned will be "(Unknown SBML Groups Type)".

Implements SBMLExtension.

const std::string & SBMLExtension::getSupportedPackageURI ( unsigned int n ) const

inherited

Returns the nth XML namespace URI.

Parameters

n	the index number of the namespace URI being sought.

Returns: a string representing the XML namespace URI understood to be supported by this package. An empty string will be returned if there is no nth URI.

const std::string & GroupsExtension::getURI	(	unsigned int	sbmlLevel,
		unsigned int	sbmlVersion,
		unsigned int	pkgVersion
	)		const

virtual

Returns a string representing the SBML XML namespace of this SBML Level 3 package.

Parameters

sbmlLevel	the level of SBML.
sbmlVersion	the version of SBML.
pkgVersion	the version of this package.

Returns: a string representing the name of this package ("groups").

The namespace URI constructed by this method corresponds to the combination of the Level and Version of SBML, and the Version of the SBML Level 3 package. (At the time of this writing, the only SBML Level that supports packages is Level 3, so the value of sbmlLevel is necessarily always 3.)

Implements SBMLExtension.

unsigned int GroupsExtension::getVersion ( const std::string & uri ) const

virtual

Returns the Version within the SBML Level for the given URI of this package.

Parameters

uri	the string of the URI that represents one of the versions of the "groups" package.

Returns: the SBML Version within the SBML Level for the given URI of this package, or 0 if the given URI is invalid, or for a different package.

Implements SBMLExtension.

const std::string & GroupsExtension::getXmlnsL3V1V1 ( )

static

Returns the XML namespace URI of the SBML Level 3 package implemented by this libSBML extension.

Returns: the XML namespace, as a string.

bool SBMLExtension::isEnabled ( ) const

inherited

Returns true if this package is enabled.

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

bool SBMLExtension::isInUse ( SBMLDocument * doc ) const

virtualinherited

Indicates whether this extension is being used by the given SBMLDocument.

The default implementation returns true. This means that when a document had this extension enabled, it will not be possible to convert it to SBML Level 2 as we cannot make sure that the extension can be converted.

Parameters

doc	the SBML document to test.

Returns: a boolean indicating whether the extension is actually being used by the document.

Reimplemented in LayoutExtension, and RenderExtension.

bool SBMLExtension::isSupported ( const std::string & uri ) const

inherited

Returns true if the given XML namespace URI is supported by this package extension.

Returns: true if the given XML namespace URI (equivalent to a package version) is supported by this package extension, false otherwise.

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

Assignment operator for GroupsExtension.

Parameters

rhs	the GroupsExtension object whose values are to be used as the basis of the assignment.

void SBMLExtension::removeL2Namespaces ( XMLNamespaces * xmlns ) const

virtualinherited

Removes the package's Level 2 namespace(s).

: This method is related to special facilities designed to support legacy behaviors surrounding SBML Level 2 models. Due to the historical background of the SBML Layout package, libSBML implements special behavior for that package: it always creates a Layout plugin object for any SBML Level 2 document it reads in, regardless of whether that document actually uses Layout constructs. Since Level 2 does not use namespaces on the top level of the SBML document object, libSBML simply keys off the fact that the model is a Level 2 model. To allow the extensions for the Layout and Render (and possibly other) packages to support this behavior, the SBMLExtension class contains special methods to allow packages to hook themselves into the Level 2 parsing apparatus when necessary.

This virtual method should be overridden by all package extensions that want to serialize to an SBML Level 2 annotation. In Level 2, the XML namespace declaration for the package is not placed on the top-level SBML document object but rather inside individual annotations. addL2Namespaces() is invoked automatically for Level 2 documents when an SBMLExtensionNamespace object is created; removeL2Namespaces() is automatically invoked by SBMLDocument to prevent the namespace(s) from being put on the top-level SBML Level 2 element (because Level 2 doesn't support namespaces there); and enableL2NamespaceForDocument() is called automatically when any SBML document (of any Level/Version) is read in.

Parameters

xmlns

an XMLNamespaces object that will be used for the annotation. Implementations should override this method with something that removes the package's namespace(s) from the set of namespaces in xmlns. For instance, here is the code from the Layout package extension:

for (int n = 0; n < xmlns->getNumNamespaces(); n++)
{
  if (xmlns->getURI(n) == LayoutExtension::getXmlnsL2())
    xmlns->remove(n);
}

Reimplemented in LayoutExtension, and RenderExtension.

bool SBMLExtension::setEnabled ( bool isEnabled )

inherited

Enable or disable this package.

Parameters

isEnabled flag indicating whether to enable (if true) or disable (false) this package extension.

Returns: true if this call succeeded; false otherwise.

Detailed Description

Public Member Functions

Static Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation