Inheritance diagram for 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
virtual FbcReactionPlugin *	clone () const
	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...

	FbcReactionPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
	Creates a new FbcReactionPlugin object using the given parameters. More...

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

virtual List *	getAllElements (ElementFilter *filter=NULL)
	Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...

virtual SBase *	getElementByMetaId (const std::string &metaid)
	Return the first child object found with a given meta identifier. More...

virtual SBase *	getElementBySId (const std::string &id)
	Return the first child object found with a given identifier. More...

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

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

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

unsigned int	getLevel () const
	Returns the SBML Level of the package extension of this plugin object. More...

virtual const std::string &	getLowerFluxBound () const
	Returns the value of the "lowerFluxBound" attribute of this FbcReactionPlugin. More...

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

unsigned int	getPackageVersion () const
	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...

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

const std::string &	getPrefix () const
	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...

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

virtual const std::string &	getUpperFluxBound () const
	Returns the value of the "upperFluxBound" attribute of this FbcReactionPlugin. More...

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

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

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

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

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

virtual bool	isValidTypeForList (SBase *item) const

FbcReactionPlugin &	operator= (const FbcReactionPlugin &rhs)
	Assignment operator for FbcReactionPlugin. More...

virtual void	renameMetaIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...

virtual void	renameSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `SIdRef` type attribute value with another value. More...

virtual void	renameUnitSIdRefs (const std::string &oldid, const std::string &newid)
	Replaces all uses of a given `UnitSIdRef` type attribute value with another value. More...

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

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

virtual int	setLowerFluxBound (const std::string &lowerFluxBound)
	Sets the value of the "lowerFluxBound" attribute of this FbcReactionPlugin. More...

virtual int	setUpperFluxBound (const std::string &upperFluxBound)
	Sets the value of the "upperFluxBound" attribute of this FbcReactionPlugin. More...

virtual int	unsetGeneProductAssociation ()
	Unsets the the "geneProduct" element of this FbcReactionPlugin. More...

virtual int	unsetLowerFluxBound ()
	Unsets the value of the "lowerFluxBound" attribute of this FbcReactionPlugin. More...

virtual int	unsetUpperFluxBound ()
	Unsets the value of the "upperFluxBound" attribute of this FbcReactionPlugin. More...

virtual	~FbcReactionPlugin ()
	Destructor for FbcReactionPlugin. More...

Constructor & Destructor Documentation

FbcReactionPlugin::FbcReactionPlugin	(	const std::string &	uri,
		const std::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.

FbcReactionPlugin::FbcReactionPlugin ( const FbcReactionPlugin & orig )

Copy constructor for FbcReactionPlugin.

Parameters

orig	the FbcReactionPlugin instance to copy.

FbcReactionPlugin::~FbcReactionPlugin ( )

virtual

Destructor for FbcReactionPlugin.

Member Function Documentation

FbcReactionPlugin * FbcReactionPlugin::clone ( ) const

virtual

Creates and returns a deep copy of this FbcReactionPlugin object.

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

Reimplemented from SBasePlugin.

GeneProductAssociation * 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.

List * FbcReactionPlugin::getAllElements ( ElementFilter * filter = NULL )

virtual

Returns a List of all child SBase objects, including those nested to an arbitrary depth.

Returns: a List of pointers to all child objects.

Reimplemented from SBasePlugin.

SBase * SBasePlugin::getElementByMetaId ( const std::string & metaid )

virtualinherited

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.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

SBase * SBasePlugin::getElementBySId ( const std::string & id )

virtualinherited

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. It uses SBasePlugin::getAllElements(ElementFilter* filter) to get the list of identifiers, so the order in which identifiers are searched is the order in which they appear in the results returned by that method.

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.

Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.

const std::string & SBasePlugin::getElementNamespace ( ) const

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.

const GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation ( ) const

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.

GeneProductAssociation * 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.

unsigned int SBasePlugin::getLevel ( ) const

inherited

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

Returns: the SBML Level.

See also: getVersion()

const std::string & FbcReactionPlugin::getLowerFluxBound ( ) const

virtual

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.

const std::string & SBasePlugin::getPackageName ( ) const

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.

unsigned int SBasePlugin::getPackageVersion ( ) const

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 * SBasePlugin::getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

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

Returns: the parent object of this object.

const std::string & SBasePlugin::getPrefix ( ) const

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 * 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()

const SBMLDocument * SBasePlugin::getSBMLDocument ( ) const

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()

const std::string & FbcReactionPlugin::getUpperFluxBound ( ) const

virtual

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.

std::string SBasePlugin::getURI ( ) const

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()

unsigned int SBasePlugin::getVersion ( ) const

inherited

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

Returns: the SBML Version.

See also: getLevel()

bool FbcReactionPlugin::isSetGeneProductAssociation ( ) const

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.

bool FbcReactionPlugin::isSetLowerFluxBound ( ) const

virtual

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.

bool FbcReactionPlugin::isSetUpperFluxBound ( ) const

virtual

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.

virtual bool SBasePlugin::isValidTypeForList ( SBase * item ) const

virtualinherited

FbcReactionPlugin & FbcReactionPlugin::operator= ( const FbcReactionPlugin & rhs )

Assignment operator for FbcReactionPlugin.

Parameters

rhs	the object whose values are used as the basis of the assignment.

virtual void SBasePlugin::renameMetaIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

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.

virtual void FbcReactionPlugin::renameSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtual

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.

Reimplemented from SBasePlugin.

virtual void SBasePlugin::renameUnitSIdRefs	(	const std::string &	oldid,
		const std::string &	newid
	)

virtualinherited

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 SBasePlugin::setElementNamespace ( const std::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. The value is drawn from the enumeration OperationReturnValues_t. 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()

Examples:: convertLayout.cpp.

int FbcReactionPlugin::setGeneProductAssociation ( const 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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

LIBSBML_OPERATION_SUCCESS

int FbcReactionPlugin::setLowerFluxBound ( const std::string & lowerFluxBound )

virtual

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcReactionPlugin::setUpperFluxBound ( const std::string & upperFluxBound )

virtual

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcReactionPlugin::unsetGeneProductAssociation ( )

virtual

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcReactionPlugin::unsetLowerFluxBound ( )

virtual

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

int FbcReactionPlugin::unsetUpperFluxBound ( )

virtual

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 value is drawn from the enumeration OperationReturnValues_t. The possible values returned by this function are:

Detailed Description

Public Member Functions

Constructor & Destructor Documentation

Member Function Documentation