ListOfGroups_t Class Reference

Detailed Description

groups A list of Group_t objects.

The SBML Level 3 Groups package provides a means of defining a group of entities: a simple mechanism for indicating that particular components of an SBML model are related in some way. A group is defined using a Group_t class object, and all the Group_t objects in a model are stored in the parent Model_t object within a ListOfGroups_t object.

A ListOfGroups_t is optional, but, if present, must contain at least one Group_t object. In common with other ListOf___ classes in SBML, ListOfGroups_t is derived from SBase_t. It inherits SBase_t's attributes "metaid" and "sboTerm", as well as the subcomponents for Annotation and Notes, but does not add any new attributes of its own.

The various ListOf___ structures in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ data structures are derived from the intermediate utility structure ListOf_t, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf_t is itself is in turn derived from SBase_t, which provides all of the various ListOf___ data structures with common features defined by the SBML specification, such as "metaid" attributes and annotations.

The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase_t means that software tools can add information about the lists themselves into each list container's "annotation".

See also

ListOfFunctionDefinitions_t

ListOfUnitDefinitions_t

ListOfCompartmentTypes_t

ListOfSpeciesTypes_t

ListOfCompartments_t

ListOfSpecies_t

ListOfParameters_t

ListOfInitialAssignments_t

ListOfRules_t

ListOfConstraints_t

ListOfReactions_t

ListOfEvents_t

Note

In the C API for libSBML, functions that in other language APIs would be inherited by the various ListOf___ structures not shown in the pages for the individual ListOf___'s. Instead, the functions are defined on ListOf_t. Please consult the documentation for ListOf_t for the many common functions available for manipulating ListOf___ structures. The documentation for the individual ListOf___ structures (ListOfCompartments_t, ListOfReactions_t, etc.) does not reveal all of the functionality available.

Public Member Functions
Group_t *	ListOfGroups_getById (ListOf_t *lo, const char *sid)
	Get a Group_t from the ListOf_t based on its identifier. More...
Group_t *	ListOfGroups_getGroup (ListOf_t *lo, unsigned int n)
	Get a Group_t from the ListOf_t. More...
Group_t *	ListOfGroups_remove (ListOf_t *lo, unsigned int n)
	Removes the nth Group_t from this ListOf_t and returns a pointer to it. More...
Group_t *	ListOfGroups_removeById (ListOf_t *lo, const char *sid)
	Removes the Group_t from this ListOf_t based on its identifier and returns a pointer to it. More...

Member Function Documentation

Group_t * ListOfGroups_getById	(	ListOf_t *	lo,
		const char *	sid
	)

Get a Group_t from the ListOf_t based on its identifier.

Parameters

lo	the ListOf_t structure to search.
sid	a string representing the identifier of the Group_t to retrieve.

Returns

the Group_t in this ListOf_t with the given sid or NULL if no such Group_t exists.

Note

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

Group_t * ListOfGroups_getGroup	(	ListOf_t *	lo,
		unsigned int	n
	)

Get a Group_t from the ListOf_t.

Parameters

lo	the ListOf_t structure to search.
n	an unsigned int representing the index of the Group_t to retrieve.

Returns

the nth Group_t in this ListOf_t. If the index n is invalid, NULL is returned.

Note

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

Group_t * ListOfGroups_remove	(	ListOf_t *	lo,
		unsigned int	n
	)

Removes the nth Group_t from this ListOf_t and returns a pointer to it.

Parameters

lo	the ListOf_t structure to search.
n	an unsigned int representing the index of the Group_t to remove.

Returns

a pointer to the nth Group_t in this ListOf_t.

Warning

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf_appendAndOwn() or ListOf_insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

Group_t * ListOfGroups_removeById	(	ListOf_t *	lo,
		const char *	sid
	)

Removes the Group_t from this ListOf_t based on its identifier and returns a pointer to it.

Parameters

lo	the ListOf_t structure to search.
sid	a string representing the identifier of the Group_t to remove.

Returns

the Group_t in this ListOf_t based on the identifier or NULL if no such Group_t exists.

Warning

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf_appendAndOwn() or ListOf_insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.