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
int	addKeyValuePair (const KeyValuePair *kvp)
	Adds a copy of the given KeyValuePair to this FbcSBasePlugin. More...

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...

KeyValuePair *	createKeyValuePair ()
	Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created. More...

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

	FbcReactionPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns)
	Creates a new FbcReactionPlugin object using the given parameters. 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)
	Returns the first child element that has the given `metaid`, or `NULL` if no such object is found. More...

virtual SBase *	getElementBySId (const std::string &id)
	Returns the first child element that has the given `id` in the model-wide SId namespace, or `NULL` if no such object is found. More...

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

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

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

KeyValuePair *	getKeyValuePair (const std::string &sid)
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

const KeyValuePair *	getKeyValuePair (const std::string &sid) const
	Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...

KeyValuePair *	getKeyValuePair (unsigned int n)
	Get a KeyValuePair from the FbcSBasePlugin. More...

const KeyValuePair *	getKeyValuePair (unsigned int n) const
	Get a KeyValuePair from the FbcSBasePlugin. More...

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

ListOfKeyValuePairs *	getListOfKeyValuePairs ()
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

const ListOfKeyValuePairs *	getListOfKeyValuePairs () const
	Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...

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

unsigned int	getNumKeyValuePairs () const
	Get the number of KeyValuePair objects in this FbcSBasePlugin. 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...

KeyValuePair *	removeKeyValuePair (const std::string &sid)
	Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it. More...

KeyValuePair *	removeKeyValuePair (unsigned int n)
	Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it. More...

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

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

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

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() [1/2]

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() [2/2]

FbcReactionPlugin::FbcReactionPlugin ( const FbcReactionPlugin & orig )

Copy constructor for FbcReactionPlugin.

Parameters

orig	the FbcReactionPlugin instance to copy.

◆ ~FbcReactionPlugin()

FbcReactionPlugin::~FbcReactionPlugin ( )

virtual

Destructor for FbcReactionPlugin.

Member Function Documentation

◆ addKeyValuePair()

int FbcSBasePlugin::addKeyValuePair ( const KeyValuePair * kvp )

inherited

Adds a copy of the given KeyValuePair to this FbcSBasePlugin.

Parameters

kvp	the KeyValuePair object to add.

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: This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

See also: createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ clone()

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 FbcSBasePlugin.

◆ createGeneProductAssociation()

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.

◆ createKeyValuePair()

KeyValuePair * FbcSBasePlugin::createKeyValuePair ( )

inherited

Creates a new KeyValuePair object, adds it to this FbcSBasePlugin object and returns the KeyValuePair object created.

Returns: a new KeyValuePair object instance.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getAllElements()

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 FbcSBasePlugin.

◆ getElementByMetaId()

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

virtualinherited

Returns the first child element that has the given metaid, or NULL if no such object is found.

Parameters

metaid a string representing the metaid attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given metaid. If no such object is found this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementBySId()

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

virtualinherited

Returns the first child element that has the given id in the model-wide SId namespace, or NULL if no such object is found.

Parameters

id	a string representing the id attribute of the object to retrieve.

Returns: a pointer to the SBase element with the given id. If no such object is found, this method returns NULL.

Reimplemented from SBasePlugin.

Reimplemented in FbcModelPlugin.

◆ getElementNamespace()

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.

◆ getGeneProductAssociation() [1/2]

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.

◆ getGeneProductAssociation() [2/2]

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.

◆ getKeyValuePair() [1/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid )

inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [2/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( const std::string & sid ) const

inherited

Get a KeyValuePair from the FbcSBasePlugin based on its identifier.

Parameters

sid	a string representing the identifier of the KeyValuePair to retrieve.

Returns: the KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin with the given sid or NULL if no such KeyValuePair exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [3/4]

KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n )

inherited

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getKeyValuePair() [4/4]

const KeyValuePair * FbcSBasePlugin::getKeyValuePair ( unsigned int n ) const

inherited

Get a KeyValuePair from the FbcSBasePlugin.

Parameters

n	an unsigned int representing the index of the KeyValuePair to retrieve.

Returns: the nth KeyValuePair in the ListOfKeyValuePairs within this FbcSBasePlugin or NULL if no such object exists.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getLevel()

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()

◆ getListOfKeyValuePairs() [1/2]

ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( )

inherited

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getListOfKeyValuePairs() [2/2]

const ListOfKeyValuePairs * FbcSBasePlugin::getListOfKeyValuePairs ( ) const

inherited

Returns the ListOfKeyValuePairs from this FbcSBasePlugin.

Returns: the ListOfKeyValuePairs from this FbcSBasePlugin.

Note: The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getLowerFluxBound()

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.

◆ getNumKeyValuePairs()

unsigned int FbcSBasePlugin::getNumKeyValuePairs ( ) const

inherited

Get the number of KeyValuePair objects in this FbcSBasePlugin.

Returns: the number of KeyValuePair objects in this FbcSBasePlugin.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); removeKeyValuePair(const std::string& sid); removeKeyValuePair(unsigned int n)

◆ getPackageName()

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.

◆ getPackageVersion()

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()

◆ getParentSBMLObject() [1/2]

SBase * SBasePlugin::getParentSBMLObject ( )

inherited

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

Returns: the parent object of this object.

◆ getParentSBMLObject() [2/2]

const SBase * SBasePlugin::getParentSBMLObject ( ) const

inherited

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

Returns: the parent object of this object.

◆ getPrefix()

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.

◆ getSBMLDocument() [1/2]

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()

◆ getSBMLDocument() [2/2]

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()

◆ getUpperFluxBound()

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.

◆ getURI()

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()

◆ getVersion()

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()

◆ isSetGeneProductAssociation()

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.

◆ isSetLowerFluxBound()

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.

◆ isSetUpperFluxBound()

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.

◆ isValidTypeForList()

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

virtualinherited

◆ operator=()

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

Assignment operator for FbcReactionPlugin.

Parameters

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

◆ removeKeyValuePair() [1/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( const std::string & sid )

inherited

Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it.

Parameters

sid	a string representing the identifier of the KeyValuePair to remove.

Returns: the KeyValuePair in this FbcSBasePlugin based on the identifier or NULL if no such KeyValuePair exists.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(unsigned int n)

◆ removeKeyValuePair() [2/2]

KeyValuePair * FbcSBasePlugin::removeKeyValuePair ( unsigned int n )

inherited

Removes the nth KeyValuePair from this FbcSBasePlugin and returns a pointer to it.

Parameters

n	an unsigned int representing the index of the KeyValuePair to remove.

Returns: a pointer to the nth KeyValuePair in this FbcSBasePlugin.

Warning: The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the "disownedItem" in the ListOf::appendAndOwn() or ListOf::insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

See also: addKeyValuePair(const KeyValuePair* object); createKeyValuePair(); getKeyValuePair(const std::string& sid); getKeyValuePair(unsigned int n); getNumKeyValuePairs(); removeKeyValuePair(const std::string& sid)

◆ renameMetaIdRefs()

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.

◆ renameSIdRefs()

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.

◆ renameUnitSIdRefs()

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.

◆ setElementNamespace()

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.

◆ setGeneProductAssociation()

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

◆ setLowerFluxBound()

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:

◆ setUpperFluxBound()

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:

◆ unsetGeneProductAssociation()

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:

◆ unsetLowerFluxBound()

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:

◆ unsetUpperFluxBound()

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

◆ FbcReactionPlugin() [1/2]

◆ FbcReactionPlugin() [2/2]

◆ ~FbcReactionPlugin()

Member Function Documentation

◆ addKeyValuePair()

◆ clone()

◆ createGeneProductAssociation()

◆ createKeyValuePair()

◆ getAllElements()

◆ getElementByMetaId()

◆ getElementBySId()

◆ getElementNamespace()

◆ getGeneProductAssociation() [1/2]

◆ getGeneProductAssociation() [2/2]

◆ getKeyValuePair() [1/4]

◆ getKeyValuePair() [2/4]

◆ getKeyValuePair() [3/4]

◆ getKeyValuePair() [4/4]

◆ getLevel()

◆ getListOfKeyValuePairs() [1/2]

◆ getListOfKeyValuePairs() [2/2]

◆ getLowerFluxBound()

◆ getNumKeyValuePairs()

◆ getPackageName()

◆ getPackageVersion()

◆ getParentSBMLObject() [1/2]

◆ getParentSBMLObject() [2/2]

◆ getPrefix()

◆ getSBMLDocument() [1/2]

◆ getSBMLDocument() [2/2]

◆ getUpperFluxBound()

◆ getURI()

◆ getVersion()

◆ isSetGeneProductAssociation()

◆ isSetLowerFluxBound()

◆ isSetUpperFluxBound()

◆ isValidTypeForList()

◆ operator=()

◆ removeKeyValuePair() [1/2]

◆ removeKeyValuePair() [2/2]

◆ renameMetaIdRefs()

◆ renameSIdRefs()

◆ renameUnitSIdRefs()

◆ setElementNamespace()

◆ setGeneProductAssociation()

◆ setLowerFluxBound()

◆ setUpperFluxBound()

◆ unsetGeneProductAssociation()

◆ unsetLowerFluxBound()

◆ unsetUpperFluxBound()