Inheritance diagram for libsbmlcs.FbcReactionPlugin:

Detailed Description

fbc Extension of Reaction by the “fbc” package.

The FbcReactionPlugin class inherits from the SBasePlugin class, and codifies the extentions to the Reaction class defined in the Flux Balance Constraints package (“fbc”). This extention allows the modeler to define (in Version 2 of the “fbc” package) an upper and lower flux bound, with the 'upperFluxBound' and 'lowerFluxBound' attributes, as well as a way to reference any GeneProduct associated with this Reaction, through the GeneProductAssociation child.

Note: In Version 1 of “fbc”, the FluxBound element is used instead of the 'upperFluxBound' and 'lowerFluxBound' attributes. There is no equivalent of the GeneProductAssociation, which was added in Version 2.

Public Member Functions
new SBasePlugin	clone ()
	Creates and returns a deep copy of this FbcReactionPlugin object. More...

GeneProductAssociation	createGeneProductAssociation ()
	Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object. More...

override void	Dispose ()

	FbcReactionPlugin (string uri, string prefix, FbcPkgNamespaces fbcns)
	Creates a new FbcReactionPlugin object using the given parameters. More...

	FbcReactionPlugin (FbcReactionPlugin orig)
	Copy constructor for FbcReactionPlugin. More...

long	getColumn ()

new SBase	getElementByMetaId (string metaid)
	Return the first child object found with a given meta identifier. More...

new SBase	getElementBySId (string id)
	Return the first child object found with a given identifier. More...

string	getElementNamespace ()
	Returns the namespace URI of the package to which this plugin object belongs. More...

GeneProductAssociation	getGeneProductAssociation ()
	Returns the GeneProductAssociation from this FbcReactionPlugin object. More...

long	getLevel ()
	Returns the SBML Level of the package extension of this plugin object. More...

long	getLine ()

SBaseList	getListOfAllElements (ElementFilter filter)

SBaseList	getListOfAllElements ()

new string	getLowerFluxBound ()
	Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...

string	getPackageName ()
	Returns the short-form name of the package to which this plugin object belongs. More...

long	getPackageVersion ()
	Returns the package version of the package extension of this plugin object. More...

SBase	getParentSBMLObject ()
	Returns the parent object to which this plugin object is connected. More...

string	getPrefix ()
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...

SBMLDocument	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...

SBMLExtension	getSBMLExtension ()

new string	getUpperFluxBound ()
	Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...

string	getURI ()
	Returns the XML namespace URI for the package to which this object belongs. More...

long	getVersion ()
	Returns the Version within the SBML Level of the package extension of this plugin object. More...

bool	isSetGeneProductAssociation ()
	Predicate returning `true` if this FbcReactionPlugin's 'GeneProductAssociation' element has been set. More...

new bool	isSetLowerFluxBound ()
	Predicate returning `true` if this FbcReactionPlugin's 'lowerFluxBound' attribute is set. More...

new bool	isSetUpperFluxBound ()
	Predicate returning `true` if this FbcReactionPlugin's 'upperFluxBound' attribute is set. More...

new bool	isValidTypeForList (SBase item)

new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

int	setElementNamespace (string uri)
	Sets the XML namespace to which this object belongs. More...

int	setGeneProductAssociation (GeneProductAssociation geneProductAssociation)
	Sets the GeneProductAssociation element in this FbcReactionPlugin object. More...

new int	setLowerFluxBound (string lowerFluxBound)
	Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...

new int	setUpperFluxBound (string upperFluxBound)
	Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...

new int	unsetGeneProductAssociation ()
	Unsets the the 'geneProduct' element of this FbcReactionPlugin. More...

new int	unsetLowerFluxBound ()
	Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin. More...

new int	unsetUpperFluxBound ()
	Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation

libsbmlcs.FbcReactionPlugin.FbcReactionPlugin	(	string	uri,
		string	prefix,
		FbcPkgNamespaces	fbcns
	)

Creates a new FbcReactionPlugin object using the given parameters.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters

uri	the URI of the SBML Level 3 package implemented by this libSBML package extension.
prefix	the XML namespace prefix being used for the package.
fbcns	the namespaces object for the package.

libsbmlcs.FbcReactionPlugin.FbcReactionPlugin ( FbcReactionPlugin orig )

Copy constructor for FbcReactionPlugin.

Parameters

orig	the FbcReactionPlugin instance to copy.

Member Function Documentation

new SBasePlugin libsbmlcs.FbcReactionPlugin.clone ( )

Creates and returns a deep copy of this FbcReactionPlugin object.

Returns: a (deep) copy of this FbcReactionPlugin object.

GeneProductAssociation libsbmlcs.FbcReactionPlugin.createGeneProductAssociation ( )

Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the newly created GeneProductAssociation object.

override void libsbmlcs.FbcReactionPlugin.Dispose ( )

virtual

Reimplemented from libsbmlcs.SBasePlugin.

long libsbmlcs.SBasePlugin.getColumn ( )

inherited

new SBase libsbmlcs.SBasePlugin.getElementByMetaId ( string metaid )

inherited

Return the first child object found with a given meta identifier.

This method searches all the subobjects under this one, compares their meta identifiers to metaid, and returns the first one that machines.

Parameters

metaid string, the metaid of the object to find.

Returns: pointer to the first object found with the given metaid.

new SBase libsbmlcs.SBasePlugin.getElementBySId ( string id )

inherited

Return the first child object found with a given identifier.

This method searches all the subobjects under this one, compares their identifiers to id, and returns the first one that machines.

Normally, SId type identifier values are unique across a model in SBML. However, in some circumstances they may not be, such as if a model is invalid because of multiple objects having the same identifier.

Parameters

id	string representing the identifier of the object to find.

Returns: pointer to the first object with the given id.

string libsbmlcs.SBasePlugin.getElementNamespace ( )

inherited

Returns the namespace URI of the package to which this plugin object belongs.

Returns: the XML namespace URI of the SBML Level 3 package implemented by this libSBML package extension.

GeneProductAssociation libsbmlcs.FbcReactionPlugin.getGeneProductAssociation ( )

Returns the GeneProductAssociation from this FbcReactionPlugin object.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: the GeneProductAssociation from object in this FbcReactionPlugin object.

long libsbmlcs.SBasePlugin.getLevel ( )

inherited

Returns the SBML Level of the package extension of this plugin object.

Returns: the SBML Level.

See also: getVersion()

long libsbmlcs.SBasePlugin.getLine ( )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( ElementFilter filter )

inherited

SBaseList libsbmlcs.SBasePlugin.getListOfAllElements ( )

inherited

new string libsbmlcs.FbcReactionPlugin.getLowerFluxBound ( )

Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin as a string.

string libsbmlcs.SBasePlugin.getPackageName ( )

inherited

Returns the short-form name of the package to which this plugin object belongs.

Returns: the short-form package name (or nickname) of the SBML package implemented by this package extension.

long libsbmlcs.SBasePlugin.getPackageVersion ( )

inherited

Returns the package version of the package extension of this plugin object.

Returns: the package version of the package extension of this plugin object.

See also: getLevel(); getVersion()

SBase libsbmlcs.SBasePlugin.getParentSBMLObject ( )

inherited

Returns the parent object to which this plugin object is connected.

Returns: the parent object of this object.

string libsbmlcs.SBasePlugin.getPrefix ( )

inherited

Returns the XML namespace prefix of the package to which this plugin object belongs.

Returns: the XML namespace prefix of the SBML Level 3 package implemented by this libSBML package extension.

SBMLDocument libsbmlcs.SBasePlugin.getSBMLDocument ( )

inherited

Returns the SBMLDocument object containing this object instance.

LibSBML uses the class SBMLDocument as a top-level container for storing SBML content and data associated with it (such as warnings and error messages). An SBML model in libSBML is contained inside an SBMLDocument object. SBMLDocument corresponds roughly to the class SBML defined in the SBML Level 3 and Level 2 specifications, but it does not have a direct correspondence in SBML Level 1. (But, it is created by libSBML no matter whether the model is Level 1, Level 2 or Level 3.)

This method allows the caller to obtain the SBMLDocument for the current object.

Returns: the parent SBMLDocument object of this plugin object.

See also: getParentSBMLObject()

SBMLExtension libsbmlcs.SBasePlugin.getSBMLExtension ( )

inherited

new string libsbmlcs.FbcReactionPlugin.getUpperFluxBound ( )

Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: the value of the 'upperFluxBound' attribute of this FbcReactionPlugin as a string.

string libsbmlcs.SBasePlugin.getURI ( )

inherited

Returns the XML namespace URI for the package to which this object belongs.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.

This method first looks into the SBMLNamespaces object possessed by the parent SBMLDocument object of the current object. If this cannot be found, this method returns the result of getElementNamespace().

Returns: a string, the URI of the XML namespace to which this object belongs.

See also: getPackageName(); getElementNamespace(); getSBMLDocument()

long libsbmlcs.SBasePlugin.getVersion ( )

inherited

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns: the SBML Version.

See also: getLevel()

bool libsbmlcs.FbcReactionPlugin.isSetGeneProductAssociation ( )

Predicate returning true if this FbcReactionPlugin's 'GeneProductAssociation' element has been set.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Returns: true if the 'GeneProductAssociation' element has been set, otherwise false is returned.

new bool libsbmlcs.FbcReactionPlugin.isSetLowerFluxBound ( )

Predicate returning true if this FbcReactionPlugin's 'lowerFluxBound' attribute is set.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: true if this FbcReactionPlugin's 'lowerFluxBound' attribute has been set, otherwise false is returned.

new bool libsbmlcs.FbcReactionPlugin.isSetUpperFluxBound ( )

Predicate returning true if this FbcReactionPlugin's 'upperFluxBound' attribute is set.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns: true if this FbcReactionPlugin's 'upperFluxBound' attribute has been set, otherwise false is returned.

new bool libsbmlcs.SBasePlugin.isValidTypeForList ( SBase item )

inherited

new void libsbmlcs.SBasePlugin.renameMetaIdRefs	(	string	oldid,
		string	newid
	)

inherited

Replaces all uses of a given meta identifier attribute value with another value.

In SBML, object 'meta' identifiers are of the XML data type ID; the SBML object attribute itself is typically named metaid. All attributes that hold values referring to values of type ID are of the XML data type IDREF. They are also sometimes informally referred to as 'metaid refs', in analogy to the SBML-defined type SIdRef.

This method works by looking at all meta-identifier attribute values, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

new void libsbmlcs.FbcReactionPlugin.renameSIdRefs	(	string	oldid,
		string	newid
	)

Replaces all uses of a given SIdRef type attribute value with another value.

In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRef in Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

new void libsbmlcs.SBasePlugin.renameUnitSIdRefs	(	string	oldid,
		string	newid
	)

inherited

Replaces all uses of a given UnitSIdRef type attribute value with another value.

In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values; in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.

This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.

Parameters

oldid	the old identifier.
newid	the new identifier.

int libsbmlcs.SBasePlugin.setElementNamespace ( string uri )

inherited

Sets the XML namespace to which this object belongs.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.

Parameters

uri	the URI to assign to this object.

Returns

integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:

LIBSBML_OPERATION_SUCCESS

See also: getElementNamespace()

int libsbmlcs.FbcReactionPlugin.setGeneProductAssociation ( GeneProductAssociation geneProductAssociation )

Sets the GeneProductAssociation element in this FbcReactionPlugin object.

Note: GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.

Parameters

geneProductAssociation the geneProductAssociation to be set.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

new int libsbmlcs.FbcReactionPlugin.setLowerFluxBound ( string lowerFluxBound )

Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Parameters

lowerFluxBound the value of the 'lowerFluxBound' attribute to be set.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

new int libsbmlcs.FbcReactionPlugin.setUpperFluxBound ( string upperFluxBound )

Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Parameters

upperFluxBound the value of the 'upperFluxBound' attribute to be set.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

new int libsbmlcs.FbcReactionPlugin.unsetGeneProductAssociation ( )

Unsets the the 'geneProduct' element of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

new int libsbmlcs.FbcReactionPlugin.unsetLowerFluxBound ( )

Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

new int libsbmlcs.FbcReactionPlugin.unsetUpperFluxBound ( )

Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.

Note: The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

Returns

integer value indicating success/failure of the function. The possible values returned by this function are:

Member Data Documentation

bool libsbmlcs.SBasePlugin.swigCMemOwn

protectedinherited

Detailed Description

Public Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation