MultiCompartmentPlugin_t Class Reference

Detailed Description

multi Extension of Compartment_t for the "multi" package.

The MultiCompartmentPlugin_t object is used to extend the standard SBML Compartment_t base object with an optional "compartmentType" attribute, a required "isType" Boolean attribute, and a child ListOfCompartmentReferences_t. The "isType" attribute flags whether this Compartment_t should be treated as a standard SBML Compartment_t (if false), or as a more generic rule-based "type" of Compartment_t (if true). A compartment "type" is a template (in the sense of prototype) for all Compartment_t objects referencing it (via "compartmentType" attributes). A Species_t object directly referencing a compartment type is not a "fully defined" species, but rather a "template" species. If the value of the "isType" attribute is false, the Compartment_t object is a "not-a-type" compartment, and it is similar to a SBML core Compartment_t except it can reference a compartment type and can have a ListOfCompartmentReferences_t child. Each child CompartmentReference_t in the ListOfCompartmentReferences_t defines a subcompartment of the parent Compartment_t. The "compartmentType" attribute identifies this Compartment_t as the CompartmentType_t defined elsewhere in the Model_t. If the "compartmentType" attribute is set, the "isType" attribute must be true.

Public Member Functions
int	MultiCompartmentPlugin_addCompartmentReference (MultiCompartmentPlugin_t *mcp, const CompartmentReference_t *cr)
	Adds a copy of the given CompartmentReference_t to this MultiCompartmentPlugin_t. More...
CompartmentReference_t *	MultiCompartmentPlugin_createCompartmentReference (MultiCompartmentPlugin_t *mcp)
	Creates a new CompartmentReference_t object, adds it to this MultiCompartmentPlugin_t object and returns the CompartmentReference_t object created. More...
CompartmentReference_t *	MultiCompartmentPlugin_getCompartmentReference (MultiCompartmentPlugin_t *mcp, unsigned int n)
	Get a CompartmentReference_t from the MultiCompartmentPlugin_t. More...
CompartmentReference_t *	MultiCompartmentPlugin_getCompartmentReferenceById (MultiCompartmentPlugin_t *mcp, const char *sid)
	Get a CompartmentReference_t from the MultiCompartmentPlugin_t based on its identifier. More...
char *	MultiCompartmentPlugin_getCompartmentType (const MultiCompartmentPlugin_t *mcp)
	Returns the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t. More...
int	MultiCompartmentPlugin_getIsType (const MultiCompartmentPlugin_t *mcp)
	Returns the value of the "isType" attribute of this MultiCompartmentPlugin_t. More...
ListOf_t *	MultiCompartmentPlugin_getListOfCompartmentReferences (MultiCompartmentPlugin_t *mcp)
	Returns a ListOf_t * containing CompartmentReference_t objects from this MultiCompartmentPlugin_t. More...
unsigned int	MultiCompartmentPlugin_getNumCompartmentReferences (MultiCompartmentPlugin_t *mcp)
	Get the number of CompartmentReference_t objects in this MultiCompartmentPlugin_t. More...
int	MultiCompartmentPlugin_isSetCompartmentType (const MultiCompartmentPlugin_t *mcp)
	Predicate returning 1 (true) if this MultiCompartmentPlugin_t's "compartmentType" attribute is set. More...
int	MultiCompartmentPlugin_isSetIsType (const MultiCompartmentPlugin_t *mcp)
	Predicate returning 1 (true) if this MultiCompartmentPlugin_t's "isType" attribute is set. More...
CompartmentReference_t *	MultiCompartmentPlugin_removeCompartmentReference (MultiCompartmentPlugin_t *mcp, unsigned int n)
	Removes the nth CompartmentReference_t from this MultiCompartmentPlugin_t and returns a pointer to it. More...
CompartmentReference_t *	MultiCompartmentPlugin_removeCompartmentReferenceById (MultiCompartmentPlugin_t *mcp, const char *sid)
	Removes the CompartmentReference_t from this MultiCompartmentPlugin_t based on its identifier and returns a pointer to it. More...
int	MultiCompartmentPlugin_setCompartmentType (MultiCompartmentPlugin_t *mcp, const char *compartmentType)
	Sets the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t. More...
int	MultiCompartmentPlugin_setIsType (MultiCompartmentPlugin_t *mcp, int isType)
	Sets the value of the "isType" attribute of this MultiCompartmentPlugin_t. More...
int	MultiCompartmentPlugin_unsetCompartmentType (MultiCompartmentPlugin_t *mcp)
	Unsets the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t. More...
int	MultiCompartmentPlugin_unsetIsType (MultiCompartmentPlugin_t *mcp)
	Unsets the value of the "isType" attribute of this MultiCompartmentPlugin_t. More...

Member Function Documentation

int MultiCompartmentPlugin_addCompartmentReference	(	MultiCompartmentPlugin_t *	mcp,
		const CompartmentReference_t *	cr
	)

Adds a copy of the given CompartmentReference_t to this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure to which the CompartmentReference_t should be added.
cr	the CompartmentReference_t object to add.

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
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_DUPLICATE_OBJECT_ID

CompartmentReference_t * MultiCompartmentPlugin_createCompartmentReference

(

MultiCompartmentPlugin_t *

mcp

)

Creates a new CompartmentReference_t object, adds it to this MultiCompartmentPlugin_t object and returns the CompartmentReference_t object created.

Parameters

mcp	the MultiCompartmentPlugin_t structure to which the CompartmentReference_t should be added.

Returns

a new CompartmentReference_t object instance.

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.

CompartmentReference_t * MultiCompartmentPlugin_getCompartmentReference	(	MultiCompartmentPlugin_t *	mcp,
		unsigned int	n
	)

Get a CompartmentReference_t from the MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure to search.
n	an unsigned int representing the index of the CompartmentReference_t to retrieve.

Returns

the nth CompartmentReference_t in the ListOfCompartmentReferences_t within this MultiCompartmentPlugin_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.

CompartmentReference_t * MultiCompartmentPlugin_getCompartmentReferenceById	(	MultiCompartmentPlugin_t *	mcp,
		const char *	sid
	)

Get a CompartmentReference_t from the MultiCompartmentPlugin_t based on its identifier.

Parameters

mcp	the MultiCompartmentPlugin_t structure to search.
sid	a string representing the identifier of the CompartmentReference_t to retrieve.

Returns

the CompartmentReference_t in the ListOfCompartmentReferences_t within this MultiCompartmentPlugin_t with the given sid or NULL if no such CompartmentReference_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.

char * MultiCompartmentPlugin_getCompartmentType

(

const MultiCompartmentPlugin_t *

mcp

)

Returns the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure whose compartmentType is sought.

Returns

the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t as a pointer to a string.

Warning

The string returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the string will not be reflected in any resulting SBML document unless the string is added to an SBML Document. Even in this case, the string should be deleted, as adding a string to an SBML Document adds a copy of the string, and does not transfer ownership of that string.

int MultiCompartmentPlugin_getIsType

(

const MultiCompartmentPlugin_t *

mcp

)

Returns the value of the "isType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure whose isType is sought.

Returns

the value of the "isType" attribute of this MultiCompartmentPlugin_t as a boolean.

ListOf_t * MultiCompartmentPlugin_getListOfCompartmentReferences

(

MultiCompartmentPlugin_t *

mcp

)

Returns a ListOf_t * containing CompartmentReference_t objects from this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure whose ListOfCompartmentReferences_t is sought.

Returns

the ListOfCompartmentReferences_t from this MultiCompartmentPlugin_t as a ListOf_t *.

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.

See also

MultiCompartmentPlugin_addCompartmentReference()

MultiCompartmentPlugin_createCompartmentReference()

MultiCompartmentPlugin_getCompartmentReferenceById()

MultiCompartmentPlugin_getCompartmentReference()

MultiCompartmentPlugin_getNumCompartmentReferences()

MultiCompartmentPlugin_removeCompartmentReferenceById()

MultiCompartmentPlugin_removeCompartmentReference()

unsigned int MultiCompartmentPlugin_getNumCompartmentReferences

(

MultiCompartmentPlugin_t *

mcp

)

Get the number of CompartmentReference_t objects in this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure to query.

Returns

the number of CompartmentReference_t objects in this MultiCompartmentPlugin_t.

int MultiCompartmentPlugin_isSetCompartmentType

(

const MultiCompartmentPlugin_t *

mcp

)

Predicate returning 1 (true) if this MultiCompartmentPlugin_t's "compartmentType" attribute is set.

Parameters

mcp	the MultiCompartmentPlugin_t structure.

Returns

1 (true) if this MultiCompartmentPlugin_t's "compartmentType" attribute has been set, otherwise 0 (false) is returned.

int MultiCompartmentPlugin_isSetIsType

(

const MultiCompartmentPlugin_t *

mcp

)

Predicate returning 1 (true) if this MultiCompartmentPlugin_t's "isType" attribute is set.

Parameters

mcp	the MultiCompartmentPlugin_t structure.

Returns

1 (true) if this MultiCompartmentPlugin_t's "isType" attribute has been set, otherwise 0 (false) is returned.

CompartmentReference_t * MultiCompartmentPlugin_removeCompartmentReference	(	MultiCompartmentPlugin_t *	mcp,
		unsigned int	n
	)

Removes the nth CompartmentReference_t from this MultiCompartmentPlugin_t and returns a pointer to it.

Parameters

mcp	the MultiCompartmentPlugin_t structure to search.
n	an unsigned int representing the index of the CompartmentReference_t to remove.

Returns

a pointer to the nth CompartmentReference_t in this MultiCompartmentPlugin_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.

CompartmentReference_t * MultiCompartmentPlugin_removeCompartmentReferenceById	(	MultiCompartmentPlugin_t *	mcp,
		const char *	sid
	)

Removes the CompartmentReference_t from this MultiCompartmentPlugin_t based on its identifier and returns a pointer to it.

Parameters

mcp	the MultiCompartmentPlugin_t structure to search.
sid	a string representing the identifier of the CompartmentReference_t to remove.

Returns

the CompartmentReference_t in this MultiCompartmentPlugin_t based on the identifier or NULL if no such CompartmentReference_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.

int MultiCompartmentPlugin_setCompartmentType	(	MultiCompartmentPlugin_t *	mcp,
		const char *	compartmentType
	)

Sets the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure.
compartmentType	const char * value of the "compartmentType" attribute to be set.

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
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_INVALID_OBJECT

int MultiCompartmentPlugin_setIsType	(	MultiCompartmentPlugin_t *	mcp,
		int	isType
	)

Sets the value of the "isType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure.
isType	int value of the "isType" attribute to be set.

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
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_INVALID_OBJECT

int MultiCompartmentPlugin_unsetCompartmentType

(

MultiCompartmentPlugin_t *

mcp

)

Unsets the value of the "compartmentType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure.

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
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT

int MultiCompartmentPlugin_unsetIsType

(

MultiCompartmentPlugin_t *

mcp

)

Unsets the value of the "isType" attribute of this MultiCompartmentPlugin_t.

Parameters

mcp	the MultiCompartmentPlugin_t structure.

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
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT