libSBML Perl API  libSBML 5.17.2 Perl API
FbcReactionPlugin Class Reference
Inheritance diagram for FbcReactionPlugin:
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Detailed Description

{fbc}

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 FbcReactionPluginclone () const
 Creates and returns a deep copy of this FbcReactionPlugin object. More...
 
GeneProductAssociationcreateGeneProductAssociation ()
 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 ListgetAllElements (ElementFilter *filter=NULL)
 Returns a List of all child SBase objects, including those nested to an arbitrary depth. More...
 
virtual SBasegetElementByMetaId (const std::string &metaid)
 Return the first child object found with a given meta identifier. More...
 
virtual SBasegetElementBySId (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 GeneProductAssociationgetGeneProductAssociation () const
 Returns the GeneProductAssociation from this FbcReactionPlugin object. More...
 
GeneProductAssociationgetGeneProductAssociation ()
 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...
 
SBasegetParentSBMLObject ()
 Returns the parent object to which this plugin object is connected. More...
 
const SBasegetParentSBMLObject () 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...
 
SBMLDocumentgetSBMLDocument ()
 Returns the SBMLDocument object containing this object instance. More...
 
const SBMLDocumentgetSBMLDocument () 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
 
FbcReactionPluginoperator= (const FbcReactionPlugin &rhs)
 Assignment operator for FbcReactionPlugin. 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
urithe URI of the SBML Level 3 package implemented by this libSBML package extension.
prefixthe XML namespace prefix being used for the package.
fbcnsthe namespaces object for the package.

◆ FbcReactionPlugin() [2/2]

FbcReactionPlugin::FbcReactionPlugin ( const FbcReactionPlugin orig)

Copy constructor for FbcReactionPlugin.

Parameters
origthe FbcReactionPlugin instance to copy.

◆ ~FbcReactionPlugin()

FbcReactionPlugin::~FbcReactionPlugin ( )
virtual

Destructor for FbcReactionPlugin.

Member Function Documentation

◆ 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 SBasePlugin.

◆ createGeneProductAssociation()

GeneProductAssociation * FbcReactionPlugin::createGeneProductAssociation ( )

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

Returns
the newly created GeneProductAssociation object.

◆ 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 SBasePlugin.

◆ getElementByMetaId()

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
metaidstring, 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.

◆ getElementBySId()

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.

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
idstring 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.

◆ 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]

const GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation ( ) const

Returns the GeneProductAssociation from this FbcReactionPlugin object.

Returns
the GeneProductAssociation from object in this FbcReactionPlugin object.

◆ getGeneProductAssociation() [2/2]

GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation ( )

Returns the GeneProductAssociation from this FbcReactionPlugin object.

Returns
the GeneProductAssociation from object in this FbcReactionPlugin object.

◆ 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()

◆ getLowerFluxBound()

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

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

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

◆ 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.

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.

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.

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.

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

◆ renameMetaIdRefs()

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

◆ renameSIdRefs()

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

Reimplemented from SBasePlugin.

◆ renameUnitSIdRefs()

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

◆ 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
urithe URI to assign to this object.

◆ setGeneProductAssociation()

int FbcReactionPlugin::setGeneProductAssociation ( const GeneProductAssociation geneProductAssociation)

Sets the GeneProductAssociation element in this FbcReactionPlugin object.

Parameters
geneProductAssociationthe geneProductAssociation to be set.

◆ setLowerFluxBound()

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

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

Parameters
lowerFluxBoundthe value of the "lowerFluxBound" attribute to be set.

◆ setUpperFluxBound()

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

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

Parameters
upperFluxBoundthe value of the "upperFluxBound" attribute to be set.

◆ unsetGeneProductAssociation()

int FbcReactionPlugin::unsetGeneProductAssociation ( )
virtual

Unsets the the "geneProduct" element of this FbcReactionPlugin.

◆ unsetLowerFluxBound()

int FbcReactionPlugin::unsetLowerFluxBound ( )
virtual

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

◆ unsetUpperFluxBound()

int FbcReactionPlugin::unsetUpperFluxBound ( )
virtual

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