libSBML Perl API
libSBML 5.17.2 Perl API
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{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.
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) |
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... | |
FbcReactionPlugin::FbcReactionPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
FbcPkgNamespaces * | fbcns | ||
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Creates a new FbcReactionPlugin object using the given parameters.
"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/"
.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.
orig | the FbcReactionPlugin instance to copy. |
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virtual |
Destructor for FbcReactionPlugin.
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virtual |
Creates and 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.
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virtual |
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Reimplemented from SBasePlugin.
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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.
metaid | string, the metaid of the object to find. |
metaid
. Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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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.
id | string representing the identifier of the object to find. |
id
. Reimplemented in QualModelPlugin, GroupsModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
const GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation | ( | ) | const |
Returns the GeneProductAssociation from this FbcReactionPlugin object.
GeneProductAssociation * FbcReactionPlugin::getGeneProductAssociation | ( | ) |
Returns the GeneProductAssociation from this FbcReactionPlugin object.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
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virtual |
Returns the value of the "lowerFluxBound" attribute of this FbcReactionPlugin.
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inherited |
Returns the short-form name of the package to which this plugin object belongs.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the parent object to which this plugin object is connected.
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inherited |
Returns the XML namespace prefix of the package to which this plugin object belongs.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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inherited |
Returns the SBMLDocument object containing this object instance.
This method allows the caller to obtain the SBMLDocument for the current object.
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virtual |
Returns the value of the "upperFluxBound" attribute of this FbcReactionPlugin.
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inherited |
Returns the XML namespace URI for the package to which this object belongs.
"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().
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inherited |
Returns the Version within the SBML Level of the package extension of this plugin object.
bool FbcReactionPlugin::isSetGeneProductAssociation | ( | ) | const |
Predicate returning true
if this FbcReactionPlugin's "GeneProductAssociation" element has been set.
true
if the "GeneProductAssociation" element has been set, otherwise false
is returned.
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virtual |
Predicate returning true
if this FbcReactionPlugin's "lowerFluxBound" attribute is set.
true
if this FbcReactionPlugin's "lowerFluxBound" attribute has been set, otherwise false
is returned.
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virtual |
Predicate returning true
if this FbcReactionPlugin's "upperFluxBound" attribute is set.
true
if this FbcReactionPlugin's "upperFluxBound" attribute has been set, otherwise false
is returned.
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virtualinherited |
FbcReactionPlugin & FbcReactionPlugin::operator= | ( | const FbcReactionPlugin & | rhs | ) |
Assignment operator for FbcReactionPlugin.
rhs | the object whose values are used as the basis of the assignment. |
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virtualinherited |
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virtual |
Reimplemented from SBasePlugin.
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virtualinherited |
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inherited |
Sets the XML namespace to which this object belongs.
"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/"
.uri | the URI to assign to this object. |
int FbcReactionPlugin::setGeneProductAssociation | ( | const GeneProductAssociation * | geneProductAssociation | ) |
Sets the GeneProductAssociation element in this FbcReactionPlugin object.
geneProductAssociation | the geneProductAssociation to be set. |
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virtual |
Sets the value of the "lowerFluxBound" attribute of this FbcReactionPlugin.
lowerFluxBound | the value of the "lowerFluxBound" attribute to be set. |
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virtual |
Sets the value of the "upperFluxBound" attribute of this FbcReactionPlugin.
upperFluxBound | the value of the "upperFluxBound" attribute to be set. |
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Unsets the the "geneProduct" element of this FbcReactionPlugin.
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virtual |
Unsets the value of the "lowerFluxBound" attribute of this FbcReactionPlugin.
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Unsets the value of the "upperFluxBound" attribute of this FbcReactionPlugin.