Inheritance diagram for CompSBMLDocumentPlugin:

Detailed Description

The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Hierarchical Model Composition (“comp”) package. This extension allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.

The presence of any ModelDefinition or ExternalModelDefinition in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model> child of the <sbml> element that should be simulated.

In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required, which indicates whether “comp” constructs can be used to change the core mathematics of the <model> child of the <sbml> element. Because they can, this attribute must be set true.

Examples: SBMLHttpResolverExample.cpp, spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.

Public Member Functions
int	addExternalModelDefinition (const ExternalModelDefinition *externalModelDefinition)
	Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions. More...

int	addModelDefinition (const ModelDefinition *modelDefinition)
	Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions. More...

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

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

	CompSBMLDocumentPlugin (const std::string &uri, const std::string &prefix, CompPkgNamespaces *compns)
	Creates a new CompSBMLDocumentPlugin object using the given parameters. More...

ExternalModelDefinition *	createExternalModelDefinition ()
	Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object. More...

ModelDefinition *	createModelDefinition ()
	Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object. More...

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Returns the first child element it can find with the given `metaid`, or itself if it has the given `metaid`, or `NULL` if no such object is found. More...

virtual SBase *	getElementBySId (const std::string &id)
	Returns the first child element found that has the given `id` in the model-wide SId namespace, or `NULL` if no such object is found. More...

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

ExternalModelDefinition *	getExternalModelDefinition (const std::string &sid)
	Returns the model definition object based on its identifier. More...

const ExternalModelDefinition *	getExternalModelDefinition (const std::string &sid) const
	Returns the model definition object based on its identifier. More...

ExternalModelDefinition *	getExternalModelDefinition (unsigned int n)
	Returns the ExternalModelDefinition with the given index. More...

const ExternalModelDefinition *	getExternalModelDefinition (unsigned int n) const
	Returns the ExternalModelDefinition with the given index. More...

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

ListOfExternalModelDefinitions *	getListOfExternalModelDefinitions ()
	Returns the ListOf object that holds each ExternalModelDefinition. More...

const ListOfExternalModelDefinitions *	getListOfExternalModelDefinitions () const
	Returns the ListOf object that holds each ExternalModelDefinition. More...

ListOfModelDefinitions *	getListOfModelDefinitions ()
	Returns the ListOf object that holds each ModelDefinition. More...

const ListOfModelDefinitions *	getListOfModelDefinitions () const
	Returns the ListOf object that holds each ModelDefinition. More...

SBase *	getModel (const std::string &sid)
	Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier. More...

const SBase *	getModel (const std::string &sid) const
	Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier. More...

ModelDefinition *	getModelDefinition (const std::string &sid)
	Returns the model definition object based on its identifier. More...

const ModelDefinition *	getModelDefinition (const std::string &sid) const
	Returns the model definition object based on its identifier. More...

ModelDefinition *	getModelDefinition (unsigned int n)
	Returns the ModelDefinition with the given index. More...

const ModelDefinition *	getModelDefinition (unsigned int n) const
	Returns the ModelDefinition with the given index. More...

unsigned int	getNumExternalModelDefinitions () const
	Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin. More...

unsigned int	getNumModelDefinitions () const
	Returns the number of ModelDefinition objects for this SBMLDocumentPlugin. 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

CompSBMLDocumentPlugin &	operator= (const CompSBMLDocumentPlugin &orig)
	Assignment operator for CompSBMLDocumentPlugin. More...

ExternalModelDefinition *	removeExternalModelDefinition (std::string id)
	Removes the ExternalModelDefinition with the given `id`. More...

ExternalModelDefinition *	removeExternalModelDefinition (unsigned int index)
	Removes the ExternalModelDefinition with the given index. More...

ModelDefinition *	removeModelDefinition (std::string id)
	Removes the ModelDefinition with the given `id` from the CompSBMLDocumentPlugin. More...

ModelDefinition *	removeModelDefinition (unsigned int index)
	Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin. 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)

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

virtual int	setRequired (bool value)
	Sets the bool value of "required" attribute of corresponding package in SBMLDocument element. More...

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

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

Private Member Functions
virtual void	clearStoredURIDocuments ()
	Clears the internal list of SBMLDocuments kept when resolving URIs. More...

virtual std::string	getResolvedURI (const std::string &uri)
	Used by getSBMDocumentFromURI to first resolve the URI into its canonical form, for example, from 'model.xml" to "file:/path/to/model.xml". More...

Friends
class	ExternalModelDefinition

Constructor & Destructor Documentation

◆ CompSBMLDocumentPlugin() [1/2]

CompSBMLDocumentPlugin::CompSBMLDocumentPlugin	(	const std::string &	uri,
		const std::string &	prefix,
		CompPkgNamespaces *	compns
	)

Creates a new CompSBMLDocumentPlugin 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.
compns	the namespaces object for the package.

◆ CompSBMLDocumentPlugin() [2/2]

CompSBMLDocumentPlugin::CompSBMLDocumentPlugin ( const CompSBMLDocumentPlugin & orig )

Copy constructor.

Creates a copy of this CompSBMLDocumentPlugin object.

Parameters

orig	the instance to copy.

◆ ~CompSBMLDocumentPlugin()

CompSBMLDocumentPlugin::~CompSBMLDocumentPlugin ( )

virtual

Destroy this object.

Member Function Documentation

◆ addExternalModelDefinition()

int CompSBMLDocumentPlugin::addExternalModelDefinition ( const ExternalModelDefinition * externalModelDefinition )

Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions.

Parameters

externalModelDefinition the ExternalModelDefinition object to be added to the ListOFExternalModelDefinitions. Fails if the added ExternalModelDefinition is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of external model definitions.

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:

◆ addModelDefinition()

int CompSBMLDocumentPlugin::addModelDefinition ( const ModelDefinition * modelDefinition )

Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions.

Parameters

modelDefinition the ModelDefinition object to be added to the ListOfModelDefinitions. Fails if the added ModelDefinition is NULL, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.

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:

◆ clearStoredURIDocuments()

void CompSBMLDocumentPlugin::clearStoredURIDocuments ( )

privatevirtual

Clears the internal list of SBMLDocuments kept when resolving URIs.

May invalidate distributed pointers, and therefore should only be used if a call to getSBMLDocumentFromURI has returned an incorrect document, and the URI resolvers have since been tweaked so as to no longer return the same result.

◆ clone()

CompSBMLDocumentPlugin * CompSBMLDocumentPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this CompSBMLDocumentPlugin object.

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

Reimplemented from SBMLDocumentPlugin.

◆ createExternalModelDefinition()

ExternalModelDefinition * CompSBMLDocumentPlugin::createExternalModelDefinition ( )

Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object.

Returns: a newly created ExternalModelDefinition object.

Examples: SBMLHttpResolverExample.cpp, spec_example2.cpp, and spec_example3.cpp.

◆ createModelDefinition()

ModelDefinition * CompSBMLDocumentPlugin::createModelDefinition ( )

Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object.

Returns: a newly created ModelDefinition object.

Examples: spec_example1.cpp, spec_example3.cpp, and spec_example4.cpp.

◆ getAllElements()

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

virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

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 from SBasePlugin.

◆ getElementByMetaId()

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

virtual

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or NULL if no such object is found.

Parameters

metaid string representing the meta identifier of the object to find.

Returns: a pointer to the SBase element with the given metaid.

Reimplemented from SBasePlugin.

◆ getElementBySId()

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

virtual

Returns the first child element found that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters

id	string representing the identifier of the object to find.

Returns: a pointer to the SBase element with the given id.

Note: The comp SBML document plugin has multiple model-wide SId namespaces, so a valid document may well contain multiple elements with the same SId that reside in separate models. It is not recommended to ever call this function—instead, call the function on the child ModelDefinition objects.

Reimplemented from SBasePlugin.

◆ 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.

◆ getExternalModelDefinition() [1/4]

ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( const std::string & sid )

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or NULL if no such ExternalModelDefinition exists.

See also: getExternalModelDefinition(unsigned int n); getListOfExternalModelDefinitions()

◆ getExternalModelDefinition() [2/4]

const ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( const std::string & sid ) const

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or NULL if no such ExternalModelDefinition exists.

See also: getExternalModelDefinition(unsigned int n); getListOfExternalModelDefinitions()

◆ getExternalModelDefinition() [3/4]

ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( unsigned int n )

Returns the ExternalModelDefinition with the given index.

Parameters

n	the index number of the ExternalModelDefinition to get.

Returns: the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, NULL is returned.

◆ getExternalModelDefinition() [4/4]

const ExternalModelDefinition * CompSBMLDocumentPlugin::getExternalModelDefinition ( unsigned int n ) const

Returns the ExternalModelDefinition with the given index.

Parameters

n	the index number of the ExternalModelDefinition to get.

Returns: the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, NULL is returned.

◆ 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()

◆ getListOfExternalModelDefinitions() [1/2]

ListOfExternalModelDefinitions * CompSBMLDocumentPlugin::getListOfExternalModelDefinitions ( )

Returns the ListOf object that holds each ExternalModelDefinition.

Returns: the ListOf object that each all ExternalModelDefinition.

◆ getListOfExternalModelDefinitions() [2/2]

const ListOfExternalModelDefinitions * CompSBMLDocumentPlugin::getListOfExternalModelDefinitions ( ) const

Returns the ListOf object that holds each ExternalModelDefinition.

Returns: the ListOf object that each all ExternalModelDefinition.

◆ getListOfModelDefinitions() [1/2]

ListOfModelDefinitions * CompSBMLDocumentPlugin::getListOfModelDefinitions ( )

Returns the ListOf object that holds each ModelDefinition.

Returns: the ListOf object that holds each ModelDefinition.

◆ getListOfModelDefinitions() [2/2]

const ListOfModelDefinitions * CompSBMLDocumentPlugin::getListOfModelDefinitions ( ) const

Returns the ListOf object that holds each ModelDefinition.

Returns: the ListOf object that holds each ModelDefinition.

◆ getModel() [1/2]

SBase * CompSBMLDocumentPlugin::getModel ( const std::string & sid )

Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: The SBase* corresponding to the given sid or NULL if no such model exists. If no such model exists, this will return NULL.

◆ getModel() [2/2]

const SBase * CompSBMLDocumentPlugin::getModel ( const std::string & sid ) const

Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: The SBase* corresponding to the given sid or NULL if no such model exists. If no such model exists, this will return NULL.

◆ getModelDefinition() [1/4]

ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( const std::string & sid )

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ModelDefinition in the ListOfModelDefinitions with the given sid or NULL if no such ModelDefinition exists.

See also: getModelDefinition(unsigned int n); getListOfModelDefinitions()

◆ getModelDefinition() [2/4]

const ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( const std::string & sid ) const

Returns the model definition object based on its identifier.

Parameters

sid	a string representing the identifier of the model definition to get.

Returns: ModelDefinition in the ListOfModelDefinitions with the given sid or NULL if no such ModelDefinition exists.

See also: getModelDefinition(unsigned int n); getListOfModelDefinitions()

◆ getModelDefinition() [3/4]

ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( unsigned int n )

Returns the ModelDefinition with the given index.

Parameters

n	the index number of the ModelDefinition to get.

Returns: the nth ModelDefinition in the ListOfModelDefinitions. If the index is invalid, NULL is returned.

◆ getModelDefinition() [4/4]

const ModelDefinition * CompSBMLDocumentPlugin::getModelDefinition ( unsigned int n ) const

Returns the ModelDefinition with the given index.

Parameters

n	the index number of the ModelDefinition to get.

Returns: the nth ModelDefinition in the ListOfModelDefinitions. If the index n is invalid, NULL is returned.

◆ getNumExternalModelDefinitions()

unsigned int CompSBMLDocumentPlugin::getNumExternalModelDefinitions ( ) const

Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.

Returns: the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.

◆ getNumModelDefinitions()

unsigned int CompSBMLDocumentPlugin::getNumModelDefinitions ( ) const

Returns the number of ModelDefinition objects for this SBMLDocumentPlugin.

Returns: the number of ModelDefinition objects.

◆ 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

virtualinherited

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()

◆ getResolvedURI()

std::string CompSBMLDocumentPlugin::getResolvedURI ( const std::string & uri )

privatevirtual

Used by getSBMDocumentFromURI to first resolve the URI into its canonical form, for example, from 'model.xml" to "file:/path/to/model.xml".

◆ 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

virtualinherited

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=()

CompSBMLDocumentPlugin & CompSBMLDocumentPlugin::operator= ( const CompSBMLDocumentPlugin & orig )

Assignment operator for CompSBMLDocumentPlugin.

Parameters

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

◆ removeExternalModelDefinition() [1/2]

ExternalModelDefinition * CompSBMLDocumentPlugin::removeExternalModelDefinition ( std::string id )

Removes the ExternalModelDefinition with the given id.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, NULL is returned.

Parameters

id	the id of the ExternalModelDefinition object to remove.

Returns: the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeExternalModelDefinition() [2/2]

ExternalModelDefinition * CompSBMLDocumentPlugin::removeExternalModelDefinition ( unsigned int index )

Removes the ExternalModelDefinition with the given index.

A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, NULL is returned.

Parameters

index the index of the ExternalModelDefinition object to remove.

Returns: the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeModelDefinition() [1/2]

ModelDefinition * CompSBMLDocumentPlugin::removeModelDefinition ( std::string id )

Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, NULL is returned.

Parameters

id	the id of the ModelDefinition object to remove.

Returns: the ModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ removeModelDefinition() [2/2]

ModelDefinition * CompSBMLDocumentPlugin::removeModelDefinition ( unsigned int index )

Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.

A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, NULL is returned.

Parameters

index the index of the ModelDefinition object to remove.

Returns: the ModelDefinition object removed. As mentioned above, the caller owns the returned object. NULL is returned if the given index is out of range.

◆ 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 CompSBMLDocumentPlugin::setRequired ( bool value )

virtual

Sets the bool value of "required" attribute of corresponding package in SBMLDocument element.

The only legal value is 'true' for the Hierarchical Model Composition package.

Parameters

value the bool value of "required" attribute of corresponding package in SBMLDocument element.

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:

Reimplemented from SBMLDocumentPlugin.

Examples: spec_example1.cpp, spec_example2.cpp, spec_example3.cpp, and spec_example4.cpp.

◆ unsetRequired()

int SBMLDocumentPlugin::unsetRequired ( )

virtualinherited

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

Friends And Related Function Documentation

◆ ExternalModelDefinition

friend class ExternalModelDefinition

friend

Detailed Description

Public Member Functions

Private Member Functions

Friends

Constructor & Destructor Documentation

◆ CompSBMLDocumentPlugin() [1/2]

◆ CompSBMLDocumentPlugin() [2/2]

◆ ~CompSBMLDocumentPlugin()

Member Function Documentation

◆ addExternalModelDefinition()

◆ addModelDefinition()

◆ clearStoredURIDocuments()

◆ clone()

◆ createExternalModelDefinition()

◆ createModelDefinition()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getExternalModelDefinition() [1/4]

◆ getExternalModelDefinition() [2/4]

◆ getExternalModelDefinition() [3/4]

◆ getExternalModelDefinition() [4/4]

◆ getLevel()

◆ getListOfExternalModelDefinitions() [1/2]

◆ getListOfExternalModelDefinitions() [2/2]

◆ getListOfModelDefinitions() [1/2]

◆ getListOfModelDefinitions() [2/2]

◆ getModel() [1/2]

◆ getModel() [2/2]

◆ getModelDefinition() [1/4]

◆ getModelDefinition() [2/4]

◆ getModelDefinition() [3/4]

◆ getModelDefinition() [4/4]

◆ getNumExternalModelDefinitions()

◆ getNumModelDefinitions()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getRequired()

◆ getResolvedURI()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getURI()

◆ getVersion()

◆ isSetRequired()

◆ isValidTypeForList()

◆ operator=()

◆ removeExternalModelDefinition() [1/2]

◆ removeExternalModelDefinition() [2/2]

◆ removeModelDefinition() [1/2]

◆ removeModelDefinition() [2/2]

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()

◆ setRequired()

◆ unsetRequired()

Friends And Related Function Documentation

◆ ExternalModelDefinition