Detailed Description

fbc An objective function for a flux.

An integral component in a complete description of a steady-state model is the so-called objective function, which generally consists of a linear combination of model variables (fluxes) and a sense (direction). In the SBML Level 3 Flux Balance Constraints (“fbc”) package, this concept is succinctly captured in the Objective_t class. An Objective_t object includes a list of flux objectives, each in the form of a FluxObjective_t object.

The FluxObjective_t class is a relatively simple container for a model variable weighted by a signed linear coefficient. In addition to the common SBML object attributes of "id" and "name" (both of which are optional), it adds two required attributes: "reaction" and "coefficient".

The "reaction" attribute must have a value of type SIdRef, and its value is restricted to the identifier of a Reaction_t object in the model. The "reaction" attribute identifiers the reaction to which the FluxObjective_t applies. The "coefficient" attribute must have a value of type double, and refers to the coefficient that this FluxObjective_t takes in the enclosing Objective_t. Its unit of measurement is dimensionless. The meaning of these two attributes together is given by the formula coefficient × reaction-flux. Since reactions in SBML Level 3 are in units of extent, the units of a flux objective are thus extent per time.

The following example * illustrates the use of these attributes in an example of a * ListOfObjectives_t:

<fbc:listOfObjectives fbc:activeObjective="obj1">
 <fbc:objective fbc:id="obj1" fbc:type="maximize">
  <fbc:listOfFluxObjectives>
   <fbc:fluxObjective fbc:reaction="R1" fbc:coefficient="1"/>
   <fbc:fluxObjective fbc:reaction="R2" fbc:coefficient="2"/>
  </fbc:listOfFluxObjectives>
 </fbc:objective>
</fbc:listOfObjectives>

See also: Objective_t; ListOfObjectives_t; ListOfFluxObjectives_t

Public Member Functions
FluxObjective_t *	FluxObjective_clone (FluxObjective_t *fo)
	Creates a deep copy of the given FluxObjective_t structure. More...

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

void	FluxObjective_free (FluxObjective_t *fo)
	Frees the given FluxObjective_t structure. More...

double	FluxObjective_getCoefficient (const FluxObjective_t *fo)
	Returns the value of the "coefficient" attribute of the given FluxObjective_t structure. More...

const char *	FluxObjective_getId (const FluxObjective_t *fo)
	Returns the value of the "id" attribute of the given FluxObjective_t structure. More...

const char *	FluxObjective_getName (const FluxObjective_t *fo)
	Returns the value of the "name" attribute of the given FluxObjective_t structure. More...

const char *	FluxObjective_getReaction (const FluxObjective_t *fo)
	Returns the value of the "reaction" attribute of the given FluxObjective_t structure. More...

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

int	FluxObjective_isSetCoefficient (const FluxObjective_t *fo)
	Predicate returning `1` (true) if the given FluxObjective_t structure's "coefficient" is set. More...

int	FluxObjective_isSetId (const FluxObjective_t *fo)
	Predicate returning `1` (true) if the given FluxObjective_t structure's "id" is set. More...

int	FluxObjective_isSetName (const FluxObjective_t *fo)
	Predicate returning `1` (true) if the given FluxObjective_t structure's "name" is set. More...

int	FluxObjective_isSetReaction (const FluxObjective_t *fo)
	Predicate returning `1` (true) if the given FluxObjective_t structure's "reaction" is set. More...

int	FluxObjective_setCoefficient (FluxObjective_t *fo, double coefficient)
	Sets the "coefficient" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_setId (FluxObjective_t fo, const char id)
	Sets the "id" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_setName (FluxObjective_t fo, const char name)
	Sets the "name" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_setReaction (FluxObjective_t fo, const char reaction)
	Sets the "reaction" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_unsetCoefficient (FluxObjective_t *fo)
	Unsets the value of the "coefficient" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_unsetId (FluxObjective_t *fo)
	Unsets the value of the "id" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_unsetName (FluxObjective_t *fo)
	Unsets the value of the "name" attribute of the given FluxObjective_t structure. More...

int	FluxObjective_unsetReaction (FluxObjective_t *fo)
	Unsets the value of the "reaction" attribute of the given FluxObjective_t structure. More...

FluxObjective_t *	ListOfFluxObjectives_getById (ListOf_t lo, const char sid)
	Return the structure indicated by the given `sid`. More...

FluxObjective_t *	ListOfFluxObjectives_removeById (ListOf_t lo, const char sid)
	Removes the structure with the given `sid` from the given ListOf_t structure and returns a pointer to it. More...

Member Function Documentation

FluxObjective_t * FluxObjective_clone ( FluxObjective_t * fo )

Creates a deep copy of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_t structure to be copied.

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

FluxObjective_t * FluxObjective_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new FluxObjective_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 FluxObjective_t structure.
version	an unsigned int, the SBML version to assign to this FluxObjective_t structure.
pkgVersion	an unsigned int, the version of the package to assign to this FluxObjective_t structure.

Returns: the newly-created FluxObjective_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 FluxObjective_free ( FluxObjective_t * fo )

Frees the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_t structure to be freed.

double FluxObjective_getCoefficient ( const FluxObjective_t * fo )

Returns the value of the "coefficient" attribute of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_t structure.

Returns: the coefficient of this structure.

const char * FluxObjective_getId ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

Returns: the id of this structure.

const char * FluxObjective_getName ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

Returns: the name of this structure.

const char * FluxObjective_getReaction ( const FluxObjective_t * fo )

Returns the value of the "reaction" attribute of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_t structure.

Returns: the reaction of this structure.

int FluxObjective_hasRequiredAttributes ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure to check.

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

int FluxObjective_isSetCoefficient ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

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

int FluxObjective_isSetId ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

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

int FluxObjective_isSetName ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

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

int FluxObjective_isSetReaction ( const FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_t structure.

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

int FluxObjective_setCoefficient	(	FluxObjective_t *	fo,
		double	coefficient
	)

Sets the "coefficient" attribute of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_t structure.
coefficient	the string to which the structures "coefficient" 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:

int FluxObjective_setId	(	FluxObjective_t *	fo,
		const char *	id
	)

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

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

Parameters

fo	the FluxObjective_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 FluxObjective_setName	(	FluxObjective_t *	fo,
		const char *	name
	)

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

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

Parameters

fo	the FluxObjective_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 FluxObjective_setReaction	(	FluxObjective_t *	fo,
		const char *	reaction
	)

Sets the "reaction" attribute of the given FluxObjective_t structure.

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

Parameters

fo	the FluxObjective_t structure.
reaction	the string to which the structures "reaction" 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 reaction is equivalent to unsetting the value of the "reaction" attribute.

int FluxObjective_unsetCoefficient ( FluxObjective_t * fo )

Unsets the value of the "coefficient" attribute of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_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 FluxObjective_unsetId ( FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_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 FluxObjective_unsetName ( FluxObjective_t * fo )

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

Parameters

fo	the FluxObjective_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 FluxObjective_unsetReaction ( FluxObjective_t * fo )

Unsets the value of the "reaction" attribute of the given FluxObjective_t structure.

Parameters

fo	the FluxObjective_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:

FluxObjective_t * ListOfFluxObjectives_getById	(	ListOf_t *	lo,
		const char *	sid
	)

Return the structure indicated by the given sid.

Parameters

lo	the ListOf_t structure to use.
sid	a string matching the "id" attribute of the element sought.

Returns: the structure for the given variable, or NULL if no such object exists in the list.

FluxObjective_t * ListOfFluxObjectives_removeById	(	ListOf_t *	lo,
		const char *	sid
	)

Removes the structure with the given sid from the given ListOf_t structure and returns a pointer to it.

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

Parameters

lo	the ListOf_t structure.
sid	the string of the "id" attribute of the sought structure.

Returns: the structure removed. As mentioned above, the caller owns the returned structure. NULL is returned if no structure with the "id" attribute exists in the given ListOf_t structure.

Detailed Description

Public Member Functions

Member Function Documentation