Inheritance diagram for libsbmlcs.GroupsModelPlugin:

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Public Member Functions
int	addGroup (Group group)
	Adds a copy of the given Group object to the list of groups. More...

SBasePlugin	clone ()
	Creates and returns a deep copy of this GroupsModelPlugin object. More...

void	connectToParent (SBase sbase)
	Sets the parent SBML object of this plugin object to this object and child elements (if any). More...

Group	createGroup ()
	Creates a new groups object and adds it to the list of groups objects and returns it. More...

SBase	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 if they have their specific elements. More...

override void	Dispose ()

void	divideAssignmentsToSIdByFunction (string id, ASTNode function)
	If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function). More...

void	enablePackageInternal (string pkgURI, string pkgPrefix, bool flag)
	Enables/Disables the given package with child elements in this plugin object (if any). More...

long	getColumn ()
	Returns the column number on which this object first appears in the XML representation of the SBML document. More...

SBase	getElementByMetaId (string metaid)
	Returns the first child element it can find with the given `metaid`, or `null` if no such object is found. More...

SBase	getElementBySId (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...

string	getElementNamespace ()
	Returns the XML namespace (URI) of the package extension of this plugin object. More...

Group	getGroup (long n)
	Returns the Group object that belongs to the given index. More...

Group	getGroup (string sid)
	Returns the group object based on its identifier. More...

long	getLevel ()
	Returns the SBML level of the package extension of this plugin object. More...

long	getLine ()
	Returns the line number on which this object first appears in the XML representation of the SBML document. More...

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

ListOfGroups	getListOfGroups ()
	Returns the ListOfGroups in this plugin object. More...

long	getNumGroups ()
	Returns the number of Group object in this plugin object. More...

string	getPackageName ()
	Returns the package name of this plugin object. More...

long	getPackageVersion ()
	Returns the package version of the package extension of this plugin object. More...

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

string	getPrefix ()
	Returns the prefix of the package extension of this plugin object. More...

SBMLDocument	getSBMLDocument ()
	Returns the parent SBMLDocument of this plugin object. More...

SBMLNamespaces	getSBMLNamespaces ()

string	getURI ()
	Gets the URI to which this element belongs to. More...

long	getVersion ()
	Returns the SBML version of the package extension of this plugin object. More...

	GroupsModelPlugin (string uri, string prefix, GroupsPkgNamespaces groupsns)
	Creates a new GroupsModelPlugin. More...

	GroupsModelPlugin (GroupsModelPlugin orig)
	Copy constructor for GroupsModelPlugin. More...

bool	hasIdentifierBeginningWith (string prefix)
	Check to see if the given prefix is used by any of the IDs defined by extension elements. More...

bool	hasRequiredElements ()
	Checks if this plugin object has all the required elements. More...

void	logUnknownElement (string element, long sbmlLevel, long sbmlVersion, long pkgVersion)
	Helper to log a common type of error for elements. More...

void	multiplyAssignmentsToSIdByFunction (string id, ASTNode function)
	If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function). More...

int	prependStringToAllIdentifiers (string prefix)
	Add the given string to all identifiers in the object. More...

Group	removeGroup (long n)
	Removes the nth Group object from this plugin object and returns a pointer to it. More...

Group	removeGroup (string sid)
	Removes the Group object with the given id attribute from this plugin object and returns a pointer to it. More...

void	replaceSIDWithFunction (string id, ASTNode function)
	If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function. More...

int	setElementNamespace (string uri)
	Sets the XML namespace to which this element belongs to. More...

bool	stripPackage (string pkgPrefix, bool flag)

int	transformIdentifiers (IdentifierTransformer sidTransformer)

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.GroupsModelPlugin.GroupsModelPlugin	(	string	uri,
		string	prefix,
		GroupsPkgNamespaces	groupsns
	)

Creates a new GroupsModelPlugin.

libsbmlcs.GroupsModelPlugin.GroupsModelPlugin ( GroupsModelPlugin orig )

Copy constructor for GroupsModelPlugin.

Parameters

orig; the GroupsModelPlugin instance to copy.

Member Function Documentation

int libsbmlcs.GroupsModelPlugin.addGroup ( Group group )

Adds a copy of the given Group object to the list of groups.

Parameters

group the Group object to be added to the list of groups.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

SBasePlugin libsbmlcs.GroupsModelPlugin.clone ( )

Creates and returns a deep copy of this GroupsModelPlugin object.

Returns: a (deep) copy of this SBase object

void libsbmlcs.GroupsModelPlugin.connectToParent ( SBase sbase )

Sets the parent SBML object of this plugin object to this object and child elements (if any).

(Creates a child-parent relationship by this plugin object)

This function is called when this object is created by the parent element. Subclasses must override this this function if they have one or more child elements.Also, SBasePlugin::connectToParent() must be called in the overridden function.

Parameters

sbase the SBase object to use

See also: setSBMLDocument; enablePackageInternal

Group libsbmlcs.GroupsModelPlugin.createGroup ( )

Creates a new groups object and adds it to the list of groups objects and returns it.

Returns: a newly created Group object

SBase libsbmlcs.GroupsModelPlugin.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 if they have their specific elements.

Returns: the SBML object corresponding to next XMLToken in the XMLInputStream or null if the token was not recognized.

override void libsbmlcs.GroupsModelPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

void libsbmlcs.SBasePlugin.divideAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If the function of this object is to assign a value has a child 'math' object (or anything with ASTNodes in general), replace the 'math' object with the function (existing/function).

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

void libsbmlcs.GroupsModelPlugin.enablePackageInternal	(	string	pkgURI,
		string	pkgPrefix,
		bool	flag
	)

Enables/Disables the given package with child elements in this plugin object (if any).

(This is an internal implementation invoked from SBase::enablePakcageInternal() function)

Note: Subclasses in which one or more SBase derived elements are defined must override this function.

See also: setSBMLDocument; connectToParent

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

Returns the column number on which this object first appears in the XML representation of the SBML document.

Returns: the column number of the underlying SBML object.

Note: The column number for each construct in an SBML model is set upon reading the model. The accuracy of the column number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real column number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getLine()

SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

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

Parameters

metaid string representing the metaid of objects to find

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

SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

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 id of objects to find

Returns: pointer to the first element found with the given id.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

inherited

Returns the XML namespace (URI) of the package extension of this plugin object.

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

Group libsbmlcs.GroupsModelPlugin.getGroup ( long n )

Returns the Group object that belongs to the given index.

If the index is invalid, null is returned.

Parameters

n	the index number of the Group to get.

Returns: the nth Group in the ListOfGroups.

Group libsbmlcs.GroupsModelPlugin.getGroup ( string sid )

Returns the group object based on its identifier.

Parameters

sid	a string representing the identifier of the Group to get.

Returns: Group in the ListOfGroups with the given id or null if no such Group exists.

See also: get(long n); size()

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

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

Returns: the SBML level of the package extension of this plugin object.

long libsbmlcs.SBasePlugin.getLine ( )

inherited

Returns the line number on which this object first appears in the XML representation of the SBML document.

Returns: the line number of the underlying SBML object.

Note: The line number for each construct in an SBML model is set upon reading the model. The accuracy of the line number depends on the correctness of the XML representation of the model, and on the particular XML parser library being used. The former limitation relates to the following problem: if the model is actually invalid XML, then the parser may not be able to interpret the data correctly and consequently may not be able to establish the real line number. The latter limitation is simply that different parsers seem to have their own accuracy limitations, and out of all the parsers supported by libSBML, none have been 100% accurate in all situations. (At this time, libSBML supports the use of libxml2, Expat and Xerces.)

See also: getColumn()

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

ListOfGroups libsbmlcs.GroupsModelPlugin.getListOfGroups ( )

Returns the ListOfGroups in this plugin object.

Returns: ListOfGroups object in this plugin object.

long libsbmlcs.GroupsModelPlugin.getNumGroups ( )

Returns the number of Group object in this plugin object.

Returns: the number of Group object in this plugin object.

string libsbmlcs.SBasePlugin.getPackageName ( )

inherited

Returns the package name of this plugin object.

Returns: the package name of this plugin object.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

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.

SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

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

Returns: the parent SBase object to which this plugin object connected.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

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

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

SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument ( )

inherited

Returns the parent SBMLDocument of this plugin object.

Returns: the parent SBMLDocument object of this plugin object.

SBMLNamespaces libsbmlcs.SBasePlugin.getSBMLNamespaces ( )

inherited

string libsbmlcs.SBasePlugin.getURI ( )

inherited

Gets the URI to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns: the URI this elements

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

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

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

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

bool libsbmlcs.SBasePlugin.hasIdentifierBeginningWith ( string prefix )

inherited

Check to see if the given prefix is used by any of the IDs defined by extension elements.

A package that defines its own 'id' attribute for a core element would check that attribute here.

bool libsbmlcs.GroupsModelPlugin.hasRequiredElements ( )

Checks if this plugin object has all the required elements.

Subclasses should override this function if they have their specific elements.

Returns: true if this pugin object has all the required elements, otherwise false will be returned.

void libsbmlcs.SBasePlugin.logUnknownElement	(	string	element,
		long	sbmlLevel,
		long	sbmlVersion,
		long	pkgVersion
	)

inherited

Helper to log a common type of error for elements.

void libsbmlcs.SBasePlugin.multiplyAssignmentsToSIdByFunction	(	string	id,
		ASTNode	function
	)

inherited

If this assignment assigns a value to the 'id' element, replace the 'math' object with the function (existing*function).

int libsbmlcs.SBasePlugin.prependStringToAllIdentifiers ( string prefix )

inherited

Add the given string to all identifiers in the object.

If the string is added to anything other than an id or a metaid, this code is responsible for tracking down and renaming all *idRefs in the package extention that identifier comes from.

Group libsbmlcs.GroupsModelPlugin.removeGroup ( long n )

Removes the nth Group object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters

n	the index of the Group object to remove

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

Group libsbmlcs.GroupsModelPlugin.removeGroup ( string sid )

Removes the Group object with the given id attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters

sid	the id attribute of the Group object to remove

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

void libsbmlcs.SBasePlugin.replaceSIDWithFunction	(	string	id,
		ASTNode	function
	)

inherited

If this object has a child 'math' object (or anything with ASTNodes in general), replace all nodes with the name 'id' with the provided function.

Note: This function does nothing itself–subclasses with ASTNode subelements must override this function.

int libsbmlcs.SBasePlugin.setElementNamespace ( string uri )

inherited

Sets the XML namespace to which this element belongs to.

For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

bool libsbmlcs.SBasePlugin.stripPackage	(	string	pkgPrefix,
		bool	flag
	)

inherited

int libsbmlcs.SBasePlugin.transformIdentifiers ( IdentifierTransformer sidTransformer )

inherited

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation