libSBML Perl API  libSBML 5.19.7 Perl API
FbcReactionPlugin Class Reference
Inheritance diagram for FbcReactionPlugin:
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Detailed Description

@sbmlpackage{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

int addKeyValuePair (const KeyValuePair *kvp)
 Adds a copy of the given KeyValuePair to this FbcSBasePlugin. More...
 
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...
 
KeyValuePaircreateKeyValuePair ()
 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 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)
 Returns the first child element that has the given metaid, or NULL if no such object is found. More...
 
virtual SBasegetElementBySId (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...
 
GeneProductAssociationgetGeneProductAssociation ()
 Returns the GeneProductAssociation from this FbcReactionPlugin object. More...
 
const GeneProductAssociationgetGeneProductAssociation () const
 Returns the GeneProductAssociation from this FbcReactionPlugin object. More...
 
KeyValuePairgetKeyValuePair (const std::string &sid)
 Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...
 
const KeyValuePairgetKeyValuePair (const std::string &sid) const
 Get a KeyValuePair from the FbcSBasePlugin based on its identifier. More...
 
KeyValuePairgetKeyValuePair (unsigned int n)
 Get a KeyValuePair from the FbcSBasePlugin. More...
 
const KeyValuePairgetKeyValuePair (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...
 
ListOfKeyValuePairsgetListOfKeyValuePairs ()
 Returns the ListOfKeyValuePairs from this FbcSBasePlugin. More...
 
const ListOfKeyValuePairsgetListOfKeyValuePairs () 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...
 
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...
 
KeyValuePairremoveKeyValuePair (const std::string &sid)
 Removes the KeyValuePair from this FbcSBasePlugin based on its identifier and returns a pointer to it. More...
 
KeyValuePairremoveKeyValuePair (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
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

◆ addKeyValuePair()

int FbcSBasePlugin::addKeyValuePair ( const KeyValuePair kvp)
inherited

Adds a copy of the given KeyValuePair to this FbcSBasePlugin.

Parameters
kvpthe KeyValuePair object to add.

◆ 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.

Returns
the newly created GeneProductAssociation object.

◆ createKeyValuePair()

◆ 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
metaida 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
ida 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.

Returns
the GeneProductAssociation from object in this FbcReactionPlugin object.

◆ getGeneProductAssociation() [2/2]

const GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation ( ) const

Returns the GeneProductAssociation from this FbcReactionPlugin object.

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
sida 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.
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
sida 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.
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

◆ getKeyValuePair() [4/4]

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

◆ 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]

◆ getListOfKeyValuePairs() [2/2]

◆ 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.

◆ getNumKeyValuePairs()

◆ 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.

◆ 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
sida 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.
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
nan unsigned int representing the index of the KeyValuePair to remove.
Returns
a pointer to the nth KeyValuePair in this FbcSBasePlugin.
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

◆ 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.