Detailed Description

fbc Max or min value for a reaction flux.

The FluxBound_t class of objects is used in Version 1 of the SBML Level 3 Flux Balance Constraints (“fbc”) package to express a single (in)equality that provides the maximum or minimum value that a reaction flux can obtain at steady state. (This same information is encoded differently in Version 2 of “fbc”; see the "upperFluxBound" and "lowerFluxBound" attributes on FbcReactionPlugin_t.)

Attributes on FluxBound_t

In addition to the common optional attributes "id" and "name", FluxBound_t takes three required attributes: "reaction", "operation" and "value". These three attributes define the meaning of the FluxBound_t, and are interpreted using the following expression:

reaction operator value

The "reaction" attribute takes a value of SIdRef. The value must be the identifier of a Reaction_t object defined within the enclosing model.

The "operation" attribute takes a value from the enumeration FluxBoundOperation_t representing different mathematical inequalities. Possible values for "operation" include "greaterEqual", "equal", and others.

The "value" attribute takes a numerical value of type double, and represents the value of the flux bound. The permitted values include positive infinity ("INF") and negative infinity ("-INF").

The following is an example of a set of flux bounds encoded in this form; it also demonstrates the use of ListOfFluxBounds_t.

<fbc:listOfFluxBounds>
    <fbc:fluxBound fbc:id="R1b" fbc:reaction="R1" fbc:operation="greaterEqual" fbc:value="1.2"/>
    <fbc:fluxBound fbc:id="R2b" fbc:reaction="R2" fbc:operation="lessEqual" fbc:value="-1.2"/>
    <fbc:fluxBound fbc:id="R3b" fbc:reaction="R3" fbc:operation="greaterEqual" fbc:value="-INF"/>
    <fbc:fluxBound fbc:id="R4b" fbc:reaction="R4" fbc:operation="lessEqual" fbc:value="INF"/>
    <fbc:fluxBound fbc:id="R5b" fbc:reaction="R5" fbc:operation="equal" fbc:value="1"/>
</fbc:listOfFluxBounds>

Note: This class is only defined for Version 1 of the “fbc” package specification. It was replaced in Version 2 by a Parameter_t referenced by the "upperFluxBound" or "lowerFluxBound" attributes on an FbcReactionPlugin_t. FluxBound_t is therefore not used for Version 2 “fbc” models.

See also: ListOfFluxBounds_t

Public Member Functions
FluxBound_t *	FluxBound_create (unsigned int level, unsigned int version, unsigned int pkgVersion)
	Creates a new FluxBound_t structure using the given SBML `level` and `version`, and the `pkgVersion` package version. More...

const char *	FluxBound_getId (FluxBound_t *fb)
	Takes an FluxBound_t structure and returns its identifier. More...

const char *	FluxBound_getName (FluxBound_t *fb)
	Takes a FluxBound_t structure and returns its name. More...

const char *	FluxBound_getOperation (FluxBound_t *fb)
	Takes a FluxBound_t structure and returns its operation. More...

const char *	FluxBound_getReaction (FluxBound_t *fb)
	Takes a FluxBound_t structure and returns its reaction. More...

double	FluxBound_getValue (FluxBound_t *fb)
	Takes a FluxBound_t structure and returns its value. More...

int	FluxBound_isSetId (FluxBound_t *fb)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBound_t structure's identifier is set. More...

int	FluxBound_isSetName (FluxBound_t *fb)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBound_t structure's name is set. More...

int	FluxBound_isSetOperation (FluxBound_t *fb)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBound_t structure's operation is set. More...

int	FluxBound_isSetReaction (FluxBound_t *fb)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBound_t structure's reaction is set. More...

int	FluxBound_isSetValue (FluxBound_t *fb)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBound_t structure's value is set. More...

int	FluxBound_setId (FluxBound_t fb, const char sid)
	Assigns the identifier of an FluxBound_t structure. More...

int	FluxBound_setName (FluxBound_t fb, const char name)
	Sets the name of the given FluxBound_t to a copy of `name`. More...

int	FluxBound_setOperation (FluxBound_t fb, const char operation)
	Sets the operation of the given FluxBound_t to a copy of `operation`. More...

int	FluxBound_setReaction (FluxBound_t fb, const char reaction)
	Sets the reaction of the given FluxBound_t to a copy of `reaction`. More...

int	FluxBound_setValue (FluxBound_t *fb, double value)
	Sets the "value" attribute of the given FluxBound_t structure. More...

int	FluxBound_unsetId (FluxBound_t *fb)
	Unsets the "id" attribute of the given FluxBound_t structure. More...

int	FluxBound_unsetName (FluxBound_t *fb)
	Unsets the "name" attribute of the given FluxBound_t structure. More...

int	FluxBound_unsetOperation (FluxBound_t *fb)
	Unsets the "operation" attribute of the given FluxBound_t structure. More...

int	FluxBound_unsetReaction (FluxBound_t *fb)
	Unsets the "reaction" attribute of the given FluxBound_t structure. More...

int	FluxBound_unsetValue (FluxBound_t *fb)
	Unsets the "value" attribute of the given FluxBound_t structure. More...

FluxBoundOperation_t	FluxBoundOperation_fromString (const char *s)
	Returns the FluxBoundOperation_t enumeration corresponding to the given string, or FLUXBOUND_OPERATION_UNKNOWN if there is no such match. More...

int	FluxBoundOperation_isValidFluxBoundOperation (FluxBoundOperation_t type)
	Predicate returning `1` (true) or `0` (false) depending on whether the given FluxBoundOperation_t is valid. More...

int	FluxBoundOperation_isValidFluxBoundOperationString (const char *s)
	Predicate returning `1` (true) or `0` (false) depending on whether the given string is a valid FluxBoundOperation_t. More...

const char *	FluxBoundOperation_toString (FluxBoundOperation_t type)
	Returns the string version of the provided FluxBoundOperation_t enumeration. More...

Member Function Documentation

FluxBound_t * FluxBound_create	(	unsigned int	level,
		unsigned int	version,
		unsigned int	pkgVersion
	)

Creates a new FluxBound_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 FluxBound_t.
version	an unsigned int, the SBML Version to assign to this FluxBound_t.
pkgVersion	an unsigned int, the SBML 'fbc' package Version to assign to this FluxBound_t.

Returns: a pointer to the newly created FluxBound_t structure.

const char * FluxBound_getId ( FluxBound_t * fb )

Takes an FluxBound_t structure and returns its identifier.

Parameters

fb	the FluxBound_t structure whose identifier is sought.

Returns: the identifier of the given FluxBound_t, as a pointer to a string.

const char * FluxBound_getName ( FluxBound_t * fb )

Takes a FluxBound_t structure and returns its name.

Parameters

fb	the FluxBound_t whose name is sought.

Returns: the name of the given FluxBound_t, as a pointer to a string.

const char * FluxBound_getOperation ( FluxBound_t * fb )

Takes a FluxBound_t structure and returns its operation.

Parameters

fb	the FluxBound_t whose operation is sought.

Returns: the operation of the given FluxBound_t, as a pointer to a string.

const char * FluxBound_getReaction ( FluxBound_t * fb )

Takes a FluxBound_t structure and returns its reaction.

Parameters

fb	the FluxBound_t whose reaction is sought.

Returns: the reaction of the given FluxBound_t, as a pointer to a string.

double FluxBound_getValue ( FluxBound_t * fb )

Takes a FluxBound_t structure and returns its value.

Parameters

fb	the FluxBound_t whose value is sought.

Returns: the value attribute of the given FluxBound_t, as a double.

int FluxBound_isSetId ( FluxBound_t * fb )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBound_t structure's identifier is set.

Parameters

fb	the FluxBound_t structure to query.

Returns: 1 (true) if the "id" attribute of the given FluxBound_t structure is set, 0 (false) otherwise.

int FluxBound_isSetName ( FluxBound_t * fb )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBound_t structure's name is set.

Parameters

fb	the FluxBound_t structure to query.

Returns: 1 (true) if the "name" attribute of the given FluxBound_t structure is set, 0 (false) otherwise.

int FluxBound_isSetOperation ( FluxBound_t * fb )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBound_t structure's operation is set.

Parameters

fb	the FluxBound_t structure to query.

Returns: 1 (true) if the "operation" attribute of the given FluxBound_t structure is set, 0 (false) otherwise.

int FluxBound_isSetReaction ( FluxBound_t * fb )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBound_t structure's reaction is set.

Parameters

fb	the FluxBound_t structure to query.

Returns: 1 (true) if the "reaction" attribute of the given FluxBound_t structure is set, 0 (false) otherwise.

int FluxBound_isSetValue ( FluxBound_t * fb )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBound_t structure's value is set.

Parameters

fb	the FluxBound_t structure to query.

Returns: 1 (true) if the "value" attribute of the given FluxBound_t structure is set, 0 (false) otherwise.

int FluxBound_setId	(	FluxBound_t *	fb,
		const char *	sid
	)

Assigns the identifier of an FluxBound_t structure.

This makes a copy of the string passed in the parameter sid.

Parameters

fb	the FluxBound_t structure to set.
sid	the string to use as the identifier.

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 an sid of NULL is equivalent to unsetting the "id" attribute.

int FluxBound_setName	(	FluxBound_t *	fb,
		const char *	name
	)

Sets the name of the given FluxBound_t to a copy of name.

Parameters

fb	the FluxBound_t structure to set.
name	the name to assign to the given FluxBound_t's "name" attribute.

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 the name set to NULL is equivalent to unsetting the "name" attribute.

int FluxBound_setOperation	(	FluxBound_t *	fb,
		const char *	operation
	)

Sets the operation of the given FluxBound_t to a copy of operation.

Parameters

fb	the FluxBound_t structure to set.
operation	the operation to assign to the given FluxBound_t's "operation" attribute.

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 the name set to NULL is equivalent to unsetting the "operation" attribute.

int FluxBound_setReaction	(	FluxBound_t *	fb,
		const char *	reaction
	)

Sets the reaction of the given FluxBound_t to a copy of reaction.

Parameters

fb	the FluxBound_t structure to set.
reaction	the reaction to assign to the given FluxBound_t's "reaction" attribute.

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 the name set to NULL is equivalent to unsetting the "reaction" attribute.

int FluxBound_setValue	(	FluxBound_t *	fb,
		double	value
	)

Sets the "value" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure.
value	the value of value to assign to the "value" attribute.

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 FluxBound_unsetId ( FluxBound_t * fb )

Unsets the "id" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure to unset.

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 FluxBound_unsetName ( FluxBound_t * fb )

Unsets the "name" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure to unset.

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 FluxBound_unsetOperation ( FluxBound_t * fb )

Unsets the "operation" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure to unset.

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 FluxBound_unsetReaction ( FluxBound_t * fb )

Unsets the "reaction" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure to unset.

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 FluxBound_unsetValue ( FluxBound_t * fb )

Unsets the "value" attribute of the given FluxBound_t structure.

Parameters

fb	the FluxBound_t structure to unset.

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:

FluxBoundOperation_t FluxBoundOperation_fromString ( const char * s )

Returns the FluxBoundOperation_t enumeration corresponding to the given string, or FLUXBOUND_OPERATION_UNKNOWN if there is no such match.

The matching is case-sensitive: "lessEqual" will return FLUXBOUND_OPERATION_LESS_EQUAL, but "lessequal" will return FLUXBOUND_OPERATION_UNKNOWN.

Parameters

s	the string to convert to a FluxBoundOperation_t.

Returns: The corresponding FluxBoundOperation_t, or FLUXBOUND_OPERATION_UNKNOWN if no match found.

Note: In an earlier version of this specification, "less" and "greater" were options that were dropped in the final version of the specification. Accordingly, "less" is always converted to "lessEqual", and "greater" is always converted to "greaterEqual".

int FluxBoundOperation_isValidFluxBoundOperation ( FluxBoundOperation_t type )

Predicate returning 1 (true) or 0 (false) depending on whether the given FluxBoundOperation_t is valid.

Parameters

type	the FluxBoundOperation_t enumeration to query.

Returns: 1 (true) if the FluxBoundOperation_t is FLUXBOUND_OPERATION_LESS_EQUAL, FLUXBOUND_OPERATION_GREATER_EQUAL, FLUXBOUND_OPERATION_LESS, FLUXBOUND_OPERATION_GREATER, or FLUXBOUND_OPERATION_EQUAL; 0 (false) otherwise (including FLUXBOUND_OPERATION_UNKNOWN).

Note: In an earlier version of this specification, "less" and "greater" were options that were dropped in the final version of the specification. Accordingly, "less" is always converted to "lessEqual", and "greater" is always converted to "greaterEqual".

int FluxBoundOperation_isValidFluxBoundOperationString ( const char * s )

Predicate returning 1 (true) or 0 (false) depending on whether the given string is a valid FluxBoundOperation_t.

The matching is case-sensitive: "lessEqual" will return 1 (true), but "lessequal" will return 0 (false).

Parameters

s	the string to query.

Returns: 1 (true) if the string is "lessEqual", "greaterEqual", "less", "greater", or "equal"; 0 (false) otherwise.

Note: In an earlier version of this specification, "less" and "greater" were options that were dropped in the final version of the specification. Accordingly, "less" is always converted to "lessEqual", and "greater" is always converted to "greaterEqual".

const char * FluxBoundOperation_toString ( FluxBoundOperation_t type )

Returns the string version of the provided FluxBoundOperation_t enumeration.

Parameters

type	the FluxBoundOperation_t enumeration to convert.

Returns: A string corresponding to the given effect: "lessEqual", "greaterEqual", "equal", or NULL if the value is FLUXBOUND_OPERATION_UNKNOWN or another invalid enumeration value.

Note: In an earlier version of this specification, "less" and "greater" were options that were dropped in the final version of the specification. Accordingly, "less" is always converted to "lessEqual", and "greater" is always converted to "greaterEqual".

Detailed Description

Attributes on FluxBound_t

Public Member Functions

Member Function Documentation