Inheritance diagram for SBMLDocumentPlugin:

Detailed Description

Base class for extending SBMLDocument in packages.

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.

The SBMLDocumentPlugin class is a specialization of SBasePlugin designed specifically for extending SBMLDocument. All package extensions must extend SBMLDocument to implement support for SBML Level 3 packages; these extensions can be subclasses of this class or from a derived class of this class.

All packages must additionally define a required flag named required, which indicates whether that package's constructs can be used to change the core mathematics of the <model> child of the <sbml> element. If they can, this attribute must be set true, and if they cannot, this attribute must be set false.

How to extend SBMLDocumentPlugin for a package implementation

: The following subsections detail the basic steps necessary to use SBMLDocumentPlugin to extend SBMLDocument for a given package extension.

1. Identify the changes necessary to SBMLDocument

The specification for a SBML Level 3 package will define the changes to the SBML <sbml> element. Packages typically do not make any changes beyond adding an attribute named "required" (discussed below), so in most cases, the extension of SBMLDocument is very simple. However, some packages do more. For instance, the Hierarchical Model Composition package adds subobjects for lists of model definitions. SBMLDocumentPlugin supports all these cases.

2. Create the SBMLDocumentPlugin subclass

A package extension will only define one subclass of SBMLDocumentPlugin. Below, we describe in detail the different parts of a subclass definition.

2.1 Override SBasePlugin class-related methods

The derived class must override the constructor, copy constructor, assignment operator (operator=) and clone() methods from SBasePlugin.

2.2 Determine the necessary value of the "required" attribute

At minimum, it is necessary for a package implementation to add the "required" attribute to the SBML <sbml> element mandated by SBML for all Level 3 packages, and this is done using this class as a base. If the 'required' attribute is the only addition necessary for a particular SBML Level 3 package, then the subclass of SBMLDocumentPlugin for the package can have a very simple implementation. Some Level 3 packages add additional attributes or elements to <sbml>, and their implementations would go into the subclassed SBMLDocumentPlugin.

SBMLDocumentPlugin provides methods with default implementations that support managing the "required" attribute, so package extension code does not need to provide implementations—they only need to set the correct value for the SBML Level 3 package based on its specification. The following are the virtual methods for working with the "required" attribute. Package extensions would only need to override them in special circumstances:

setRequired(bool value): This method sets the value of the flag.

getRequired(): This method gets the value of the "required" flag.

isSetRequired(): This method tests if the value has been set.

unsetRequired(): This method unsets the value of the "required" flag.

2.3 Define protected data members

An extended SBMLDocument object may need more than just the "required" attribute, depending on what is defined in the specification for the package being implemented. Data attributes on the extended <sbml> object in an SBML package will have one of the data types std::string, double, int, or bool. Subelements/subobjects will normally be derived from the ListOf class or from SBase.

The additional data members must be properly initialized in the class constructor, and must be properly copied in the copy constructor and assignment operator.

2.4 Override virtual methods for attributes

If the extended component is defined by the SBML Level 3 package to have attributes, then the extended SBMLDocumentPlugin class definition needs to override the following internal methods that come from SBasePlugin (the base class of SBMLDocumentPlugin) and provide appropriate implementations:

addExpectedAttributes(ExpectedAttributes& attributes): This method should add the attributes that are expected to be found on this kind of extended component in an SBML file or data stream.

readAttributes(XMLAttributes& attributes, ExpectedAttributes& expectedAttributes): This method should read the attributes expected to be found on this kind of extended component in an SBML file or data stream.

hasRequiredAttributes(): This method should return true if all of the required attribute for this extended component are present on instance of the object.

writeAttributes(XMLOutputStream& stream): This method should write out the attributes of an extended component. The implementation should use the different kinds of writeAttribute methods defined by XMLOutputStream to achieve this.

2.5 Override virtual methods for subcomponents

If the extended component is defined by the Level 3 package to have subcomponents (i.e., full XML elements rather than mere attributes), then the extended class definition needs to override the following internal methods on SBasePlugin (the base class of SBMLDocumentPlugin) and provide appropriate implementations:

createObject(XMLInputStream& stream): Subclasses must override this method to create, store, and then return an SBML object corresponding to the next XMLToken in the XMLInputStream. To do this, implementations can use methods like peek() on XMLInputStream to test if the next object in the stream is something expected for the package. For example, LayoutModelPlugin uses peek() to examine the next element in the input stream, then tests that element against the Layout namespace and the element name "listOfLayouts" to see if it's the single subcomponent (ListOfLayouts) permitted on a Model object using the Layout package. If it is, it returns the appropriate object.

connectToParent(SBase *sbase): This creates a parent-child relationship between a given extended component and its subcomponent(s).

setSBMLDocument(SBMLDocument* d): This method should set the parent SBMLDocument object on the subcomponent object instances, so that the subcomponent instances know which SBMLDocument contains them.

enablePackageInternal(std::string& pkgURI, std::string& pkgPrefix, bool flag): This method should enable or disable the subcomponent based on whether a given XML namespace is active.

writeElements(XMLOutputStream& stream): This method must be overridden to provide an implementation that will write out the expected subcomponents/subelements to the XML output stream.

readOtherXML(SBase* parentObject, XMLInputStream& stream): This function should be overridden if elements of annotation, notes, MathML content, etc., need to be directly parsed from the given XMLInputStream object.

hasRequiredElements(): This method should return true if a given object contains all the required subcomponents defined by the specification for that SBML Level 3 package.

2.6 Override virtual methods for XML namespaces

If the package needs to add additional xmlns attributes to declare additional XML namespace URIs, the extended class should override the following method coming from SBasePlugin (the parent class of SBMLDocumentPlugin):

writeXMLNS(XMLOutputStream& stream): This method should write out any additional XML namespaces that might be needed by a package implementation.

2.7 Implement additional methods as needed

Extended SBMLDocumentPlugin implementations can add whatever additional utility methods are useful for their implementation.

Examples: convertLayout.cpp.

Public Member Functions
virtual SBMLDocumentPlugin *	clone () const
	Creates and returns a deep copy of this SBMLDocumentPlugin object. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns all child objects of this object. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (const std::string &id)
	Return the first child object found with a given identifier. More...

const std::string &	getElementNamespace () const
	Returns the namespace URI of the package to which this plugin object belongs. More...

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

const std::string &	getPackageName () const
	Returns the short-form name of the package to which this plugin object belongs. More...

unsigned int	getPackageVersion () const
	Returns the package version of the package extension of this plugin object. More...

SBase *	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

const SBase *	getParentSBMLObject () const
	Returns the parent object to which this plugin object is connected. More...

const std::string &	getPrefix () const
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

virtual bool	getRequired () const
	Returns the value of the "required" attribute. More...

SBMLDocument *	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

const SBMLDocument *	getSBMLDocument () const
	Returns the SBMLDocument object containing this object instance. More...

std::string	getURI () const
	Returns the XML namespace URI for the package to which this object belongs. More...

unsigned int	getVersion () const
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

virtual bool	isSetRequired () const
	Returns the value of the "required" attribute. More...

virtual bool	isValidTypeForList (SBase *item) const

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

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)

	SBMLDocumentPlugin (const SBMLDocumentPlugin &orig)
	Copy constructor. More...

	SBMLDocumentPlugin (const std::string &uri, const std::string &prefix, SBMLNamespaces *sbmlns)
	Creates a new SBMLDocumentPlugin object using the given parameters. More...

int	setElementNamespace (const std::string &uri)
	Sets the XML namespace to which this object belongs. More...

virtual int	setRequired (bool value)
	Sets the SBML "required" attribute value. More...

virtual int	unsetRequired ()
	Unsets the value of the "required" attribute of this SBMLDocumentPlugin. More...

virtual	~SBMLDocumentPlugin ()
	Destroy this SBMLDocumentPlugin object. More...

Constructor & Destructor Documentation

◆ SBMLDocumentPlugin() [1/2]

SBMLDocumentPlugin::SBMLDocumentPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		SBMLNamespaces *	sbmlns
	)

Creates a new SBMLDocumentPlugin object using the given parameters.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

: The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
sbmlns	the SBMLNamespaces object for the package.

◆ SBMLDocumentPlugin() [2/2]

SBMLDocumentPlugin::SBMLDocumentPlugin ( const SBMLDocumentPlugin & orig )

Copy constructor.

This creates a copy of this object.

Parameters

orig	the SBMLDocumentPlugin instance to copy.

◆ ~SBMLDocumentPlugin()

SBMLDocumentPlugin::~SBMLDocumentPlugin ( )

virtual

Destroy this SBMLDocumentPlugin object.

Member Function Documentation

◆ clone()

SBMLDocumentPlugin * SBMLDocumentPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this SBMLDocumentPlugin object.

Returns: the (deep) copy of this SBMLDocumentPlugin object.

Reimplemented from SBasePlugin.

Reimplemented in SpatialSBMLDocumentPlugin, RenderSBMLDocumentPlugin, QualSBMLDocumentPlugin, MultiSBMLDocumentPlugin, LayoutSBMLDocumentPlugin, GroupsSBMLDocumentPlugin, FbcSBMLDocumentPlugin, DistribSBMLDocumentPlugin, and CompSBMLDocumentPlugin.

◆ getAllElements()

List * SBasePlugin::getAllElements ( ElementFilter * filter = NULL )

virtualinherited

Returns all child objects of this object.

This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.

Parameters

filter a pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.

Returns: a List of pointers to all children objects.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, RenderListOfLayoutsPlugin, RenderLayoutPlugin, QualModelPlugin, MultiSpeciesReferencePlugin, MultiSpeciesPlugin, MultiSimpleSpeciesReferencePlugin, MultiModelPlugin, MultiCompartmentPlugin, LayoutModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcReactionPlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementByMetaId()

SBase * SBasePlugin::getElementByMetaId ( const std::string & metaid )

virtualinherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

Returns: pointer to the first object found with the given metaid.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementBySId()

SBase * SBasePlugin::getElementBySId ( const std::string & id )

virtualinherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

Reimplemented in SpatialParameterPlugin, SpatialModelPlugin, SpatialCompartmentPlugin, QualModelPlugin, GroupsModelPlugin, FbcSBasePlugin, FbcModelPlugin, DistribSBasePlugin, CompSBMLDocumentPlugin, CompSBasePlugin, and CompModelPlugin.

◆ getElementNamespace()

const std::string & SBasePlugin::getElementNamespace ( ) const

inherited

Returns the namespace URI of the package to which this plugin object belongs.

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

◆ getLevel()

unsigned int SBasePlugin::getLevel ( ) const

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

◆ getPackageName()

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

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

◆ getPackageVersion()

unsigned int SBasePlugin::getPackageVersion ( ) const

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

◆ getPrefix()

const std::string & SBasePlugin::getPrefix ( ) const

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

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

◆ getRequired()

bool SBMLDocumentPlugin::getRequired ( ) const

virtual

Returns the value of the "required" attribute.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: the bool value of "required" attribute for the SBML package.

See also: setRequired(bool value); isSetRequired(); unsetRequired()

◆ getSBMLDocument() [1/2]

SBMLDocument * SBasePlugin::getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

◆ getSBMLDocument() [2/2]

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

inherited

Returns the SBMLDocument object containing this object instance.

: LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

◆ getURI()

std::string SBasePlugin::getURI ( ) const

inherited

Returns the XML namespace URI for the package to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

◆ getVersion()

unsigned int SBasePlugin::getVersion ( ) const

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

◆ isSetRequired()

bool SBMLDocumentPlugin::isSetRequired ( ) const

virtual

Returns the value of the "required" attribute.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Returns: true if the "required" attribute of this SBMLDocument has been set to true, false otherwise.

◆ isValidTypeForList()

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

◆ operator=()

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

Assignment operator for SBMLDocumentPlugin.

Parameters

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

◆ renameMetaIdRefs()

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given meta identifier attribute value with another value.

: In SBML, object "meta" identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as "metaid refs", in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

◆ renameSIdRefs()

virtual void SBasePlugin::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to an identifier", but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

: Replaces all uses of a given UnitSIdRef type attribute value with another value.

: In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as "referring to a unit identifier", but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

◆ setElementNamespace()

int SBasePlugin::setElementNamespace ( const std::string & uri )

inherited

Sets the XML namespace to which this object belongs.

: In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI "http://www.sbml.org/sbml/level3/version1/core". Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace "http://www.sbml.org/sbml/level3/version1/layout/version1/".

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. The value is drawn from the enumeration OperationReturnValues_t. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

Examples: convertLayout.cpp.

◆ setRequired()

int SBMLDocumentPlugin::setRequired ( bool value )

virtual

Sets the SBML "required" attribute value.

: SBML Level 3 requires that every package defines an attribute named "required" on the root <sbml> element in an SBML file or data stream. The attribute, being in the namespace of the Level 3 package in question, must be prefixed by the XML namespace prefix associated with the package. The value of the "required" attribute indicates whether constructs in that package may change the mathematical interpretation of constructs defined in SBML Level 3 Core. A "required" value of true indicates that the package may do so. The value of the attribute is set by the Level 3 package specification, and does not depend on the actual presence or absence of particular package constructs in a given SBML document: in other words, if the package specification defines any construct that can change the model's meaning, the value of the "required" attribute must always be set to true in any SBML document that uses the package.

The XML namespace declaration for an SBML Level 3 package is an indication that a model makes use of features defined by that package, while the "required" attribute indicates whether the features may be ignored without compromising the mathematical meaning of the model. Both are necessary for a complete reference to an SBML Level 3 package.

Parameters

value the value to be assigned to the "required" attribute. The "required" attribute takes a Boolean value, either true or false.

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:

See also: getRequired(); isSetRequired(); unsetRequired()

Reimplemented in CompSBMLDocumentPlugin.

◆ unsetRequired()

int SBMLDocumentPlugin::unsetRequired ( )

virtual

Unsets the value of the "required" attribute of this SBMLDocumentPlugin.

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:

LIBSBML_OPERATION_SUCCESS

Detailed Description

How to extend SBMLDocumentPlugin for a package implementation

1. Identify the changes necessary to SBMLDocument

2. Create the SBMLDocumentPlugin subclass

2.1 Override SBasePlugin class-related methods

2.2 Determine the necessary value of the "required" attribute

2.3 Define protected data members

2.4 Override virtual methods for attributes

2.5 Override virtual methods for subcomponents

2.6 Override virtual methods for XML namespaces

2.7 Implement additional methods as needed

Public Member Functions

Constructor & Destructor Documentation

◆ SBMLDocumentPlugin() [1/2]

◆ SBMLDocumentPlugin() [2/2]

◆ ~SBMLDocumentPlugin()

Member Function Documentation

◆ clone()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getLevel()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getRequired()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getURI()

◆ getVersion()

◆ isSetRequired()

◆ isValidTypeForList()

◆ operator=()

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()

◆ setRequired()

◆ unsetRequired()