ListOfSpecies_t Class Reference

Detailed Description

A list of Species_t objects.

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
Species_t *	ListOfSpecies_getById (ListOf_t *lo, const char *sid)
	Returns the Species_t structure having a given identifier. More...
Species_t *	ListOfSpecies_removeById (ListOf_t *lo, const char *sid)
	Removes a Species_t structure based on its identifier. More...

Member Function Documentation

Species_t * ListOfSpecies_getById	(	ListOf_t *	lo,
		const char *	sid
	)

Returns the Species_t structure having a given identifier.

Parameters

lo	the ListOfSpecies_t structure to search.
sid	the "id" attribute value being sought.

Returns

item in the lo ListOfSpecies_t with the given sid or a null pointer if no such item exists.

See also

ListOf_t

Species_t * ListOfSpecies_removeById	(	ListOf_t *	lo,
		const char *	sid
	)

Removes a Species_t structure based on its identifier.

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

Parameters

lo	the list of Species_t structures to search.
sid	the "id" attribute value of the structure to remove.

Returns

The Species_t structure removed, or a null pointer if no such item exists in lo.

See also

ListOf_t