Detailed Description

fbc Association_t of a gene product with a Reaction_t

In the SBML Level 3 Flux Balance Constraints (“fbc”) package representation format, a GeneProduct_t object represents a single gene or implied gene product. The gene or gene product is identified using the required attribute "label", which is a text string. (This attribute is separate from the usual SBML "id" attribute, which is used to cross-reference entities within an SBML model.) A GeneProduct_t object can also possess an optional "associatedSpecies" attribute; if this a attribute is defined, it should have a value of type SIdRef and be the identifier of a Species_t object defined in the enclosing Model_t. An "associatedSpecies", if it exists, is interpreted to be a species associated with the gene or gene product that is represented by the GeneProduct_t object.

Note: This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (“fbc”) specification. In Version 1 of “fbc”, the information encoded by this class can be stored instead using the Association_t and GeneAssociation_t annotation classes. Please see the Version 1 and Version 2 “fbc” specifications for more details.

Public Member Functions
GeneProduct_t *	GeneProduct_clone (GeneProduct_t *gp)
	Creates a deep copy of the given GeneProduct_t structure. More...

GeneProduct_t *	GeneProduct_create (unsigned int level, unsigned int version, unsigned int pkgVersion)
	Creates a new GeneProduct_t structure using the given SBML `level` and `version`, and the `pkgVersion` package version. More...

void	GeneProduct_free (GeneProduct_t *gp)
	Frees the given GeneProduct_t structure. More...

const char *	GeneProduct_getAssociatedSpecies (const GeneProduct_t *gp)
	Returns the value of the "associatedSpecies" attribute of the given GeneProduct_t structure. More...

const char *	GeneProduct_getId (const GeneProduct_t *gp)
	Returns the value of the "id" attribute of the given GeneProduct_t structure. More...

const char *	GeneProduct_getLabel (const GeneProduct_t *gp)
	Returns the value of the "label" attribute of the given GeneProduct_t structure. More...

const char *	GeneProduct_getName (const GeneProduct_t *gp)
	Returns the value of the "name" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_hasRequiredAttributes (const GeneProduct_t *gp)
	Predicate returning `1` (true) or `0` (false) depending on whether all the required attributes of the given GeneProduct_t structure have been set. More...

int	GeneProduct_isSetAssociatedSpecies (const GeneProduct_t *gp)
	Predicate returning `1` (true) if the given GeneProduct_t structure's "associatedSpecies" is set. More...

int	GeneProduct_isSetId (const GeneProduct_t *gp)
	Predicate returning `1` (true) if the given GeneProduct_t structure's "id" is set. More...

int	GeneProduct_isSetLabel (const GeneProduct_t *gp)
	Predicate returning `1` (true) if the given GeneProduct_t structure's "label" is set. More...

int	GeneProduct_isSetName (const GeneProduct_t *gp)
	Predicate returning `1` (true) if the given GeneProduct_t structure's "name" is set. More...

int	GeneProduct_setAssociatedSpecies (GeneProduct_t gp, const char associatedSpecies)
	Sets the "associatedSpecies" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_setId (GeneProduct_t gp, const char id)
	Sets the "id" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_setLabel (GeneProduct_t gp, const char label)
	Sets the "label" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_setName (GeneProduct_t gp, const char name)
	Sets the "name" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_unsetAssociatedSpecies (GeneProduct_t *gp)
	Unsets the value of the "associatedSpecies" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_unsetId (GeneProduct_t *gp)
	Unsets the value of the "id" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_unsetLabel (GeneProduct_t *gp)
	Unsets the value of the "label" attribute of the given GeneProduct_t structure. More...

int	GeneProduct_unsetName (GeneProduct_t *gp)
	Unsets the value of the "name" attribute of the given GeneProduct_t structure. More...

Member Function Documentation

GeneProduct_t * GeneProduct_clone ( GeneProduct_t * gp )

Creates a deep copy of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure to be copied.

Returns: a (deep) copy of the given GeneProduct_t structure, or a null pointer if a failure occurred.

GeneProduct_t * GeneProduct_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new GeneProduct_t structure using the given SBML level and version, and the pkgVersion package version.

Parameters

level	an unsigned int, the SBML level to assign to this GeneProduct_t structure.
version	an unsigned int, the SBML version to assign to this GeneProduct_t structure.
pkgVersion	an unsigned int, the version of the package to assign to this GeneProduct_t structure.

Returns: the newly-created GeneProduct_t structure, or a null pointer if an error occurred during construction.

Note: Attempting to add an object to an SBMLDocument_t having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument_t), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.

void GeneProduct_free ( GeneProduct_t * gp )

Frees the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure to be freed.

const char * GeneProduct_getAssociatedSpecies ( const GeneProduct_t * gp )

Returns the value of the "associatedSpecies" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure.

Returns: the associatedSpecies of this structure.

const char * GeneProduct_getId ( const GeneProduct_t * gp )

Returns the value of the "id" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure.

Returns: the id of this structure.

const char * GeneProduct_getLabel ( const GeneProduct_t * gp )

Returns the value of the "label" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure.

Returns: the label of this structure.

const char * GeneProduct_getName ( const GeneProduct_t * gp )

Returns the value of the "name" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_t structure.

Returns: the name of this structure.

int GeneProduct_hasRequiredAttributes ( const GeneProduct_t * gp )

Predicate returning 1 (true) or 0 (false) depending on whether all the required attributes of the given GeneProduct_t structure have been set.

Parameters

gp	the GeneProduct_t structure to check.

Returns: 1 (true) if all the required attributes for this structure have been defined, 0 (false) otherwise.

int GeneProduct_isSetAssociatedSpecies ( const GeneProduct_t * gp )

Predicate returning 1 (true) if the given GeneProduct_t structure's "associatedSpecies" is set.

Parameters

gp	the GeneProduct_t structure.

Returns: 1 (true) if the "associatedSpecies" of this GeneProduct_t structure is set, 0 (false) otherwise.

int GeneProduct_isSetId ( const GeneProduct_t * gp )

Predicate returning 1 (true) if the given GeneProduct_t structure's "id" is set.

Parameters

gp	the GeneProduct_t structure.

Returns: 1 (true) if the "id" of this GeneProduct_t structure is set, 0 (false) otherwise.

int GeneProduct_isSetLabel ( const GeneProduct_t * gp )

Predicate returning 1 (true) if the given GeneProduct_t structure's "label" is set.

Parameters

gp	the GeneProduct_t structure.

Returns: 1 (true) if the "label" of this GeneProduct_t structure is set, 0 (false) otherwise.

int GeneProduct_isSetName ( const GeneProduct_t * gp )

Predicate returning 1 (true) if the given GeneProduct_t structure's "name" is set.

Parameters

gp	the GeneProduct_t structure.

Returns: 1 (true) if the "name" of this GeneProduct_t structure is set, 0 (false) otherwise.

int GeneProduct_setAssociatedSpecies	(	GeneProduct_t *	gp,
		const char *	associatedSpecies
	)

Sets the "associatedSpecies" attribute of the given GeneProduct_t structure.

This function copies the string given in associatedSpecies. If the string is a null pointer, this function is equivalent to calling GeneProduct_unsetAssociatedSpecies().

Parameters

gp	the GeneProduct_t structure.
associatedSpecies	the string to which the structures "associatedSpecies" attribute should 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:

Note: Using this function with a null pointer for associatedSpecies is equivalent to unsetting the value of the "associatedSpecies" attribute.

int GeneProduct_setId	(	GeneProduct_t *	gp,
		const char *	id
	)

Sets the "id" attribute of the given GeneProduct_t structure.

This function copies the string given in id. If the string is a null pointer, this function is equivalent to calling GeneProduct_unsetId().

Parameters

gp	the GeneProduct_t structure.
id	the string to which the structures "id" attribute should 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:

Note: Using this function with a null pointer for id is equivalent to unsetting the value of the "id" attribute.

int GeneProduct_setLabel	(	GeneProduct_t *	gp,
		const char *	label
	)

Sets the "label" attribute of the given GeneProduct_t structure.

This function copies the string given in label. If the string is a null pointer, this function is equivalent to calling GeneProduct_unsetLabel().

Parameters

gp	the GeneProduct_t structure.
label	the string to which the structures "label" attribute should 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:

Note: Using this function with a null pointer for label is equivalent to unsetting the value of the "label" attribute.

int GeneProduct_setName	(	GeneProduct_t *	gp,
		const char *	name
	)

Sets the "name" attribute of the given GeneProduct_t structure.

This function copies the string given in name. If the string is a null pointer, this function is equivalent to calling GeneProduct_unsetName().

Parameters

gp	the GeneProduct_t structure.
name	the string to which the structures "name" attribute should 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:

Note: Using this function with a null pointer for name is equivalent to unsetting the value of the "name" attribute.

int GeneProduct_unsetAssociatedSpecies ( GeneProduct_t * gp )

Unsets the value of the "associatedSpecies" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_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:

int GeneProduct_unsetId ( GeneProduct_t * gp )

Unsets the value of the "id" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_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:

int GeneProduct_unsetLabel ( GeneProduct_t * gp )

Unsets the value of the "label" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_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:

int GeneProduct_unsetName ( GeneProduct_t * gp )

Unsets the value of the "name" attribute of the given GeneProduct_t structure.

Parameters

gp	the GeneProduct_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:

Detailed Description

Public Member Functions

Member Function Documentation