libSBML Perl API
libSBML 5.12.0 Perl API
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{fbc}
fbc Extension of Species.The Flux Balance Constraints package extends the SBML Level 3 Version 1 Core Species class with the addition of two attributes: 'charge' and 'chemicalFormula'.
Public Member Functions | |
virtual FbcSpeciesPlugin * | clone () const |
Creates and returns a deep copy of this FbcSpeciesPlugin object. More... | |
FbcSpeciesPlugin (const std::string &uri, const std::string &prefix, FbcPkgNamespaces *fbcns) | |
Creates a new FbcSpeciesPlugin. More... | |
FbcSpeciesPlugin (const FbcSpeciesPlugin &orig) | |
Copy constructor for FbcSpeciesPlugin. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
doxygenLibsbmlInternal More... | |
virtual int | getCharge () const |
Returns the value of the "charge" attribute of this FbcSpeciesPlugin. More... | |
virtual const std::string & | getChemicalFormula () const |
Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. 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... | |
unsigned int | getLevel () const |
Returns the SBML Level of the package extension of this plugin object. 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... | |
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... | |
virtual bool | hasRequiredElements () const |
doxygenLibsbmlInternal More... | |
virtual bool | isSetCharge () const |
Predicate returning true or false depending on whether this FbcSpeciesPlugin's "charge" attribute has been set. More... | |
virtual bool | isSetChemicalFormula () const |
Predicate returning true or false depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set. More... | |
virtual bool | isValidTypeForList (SBase *item) const |
FbcSpeciesPlugin & | operator= (const FbcSpeciesPlugin &rhs) |
Assignment operator for FbcSpeciesPlugin. 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) |
virtual int | setCharge (int charge) |
Sets the value of the "charge" attribute of this FbcSpeciesPlugin. More... | |
virtual int | setChemicalFormula (const std::string &chemicalFormula) |
Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More... | |
int | setElementNamespace (const std::string &uri) |
Sets the XML namespace to which this object belongs. More... | |
virtual int | unsetCharge () |
Unsets the value of the "charge" attribute of this FbcSpeciesPlugin. More... | |
virtual int | unsetChemicalFormula () |
Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin. More... | |
virtual | ~FbcSpeciesPlugin () |
Destructor for FbcSpeciesPlugin. More... | |
FbcSpeciesPlugin::FbcSpeciesPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
FbcPkgNamespaces * | fbcns | ||
) |
Creates a new FbcSpeciesPlugin.
FbcSpeciesPlugin::FbcSpeciesPlugin | ( | const FbcSpeciesPlugin & | orig | ) |
Copy constructor for FbcSpeciesPlugin.
orig; | the FbcSpeciesPlugin instance to copy. |
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Destructor for FbcSpeciesPlugin.
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virtual |
Creates and returns a deep copy of this FbcSpeciesPlugin object.
Reimplemented from SBasePlugin.
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virtual |
doxygenLibsbmlInternal
doxygenLibsbmlInternal doxygenLibsbmlInternal Returns a List of all child SBase objects, including those nested to an arbitrary depth.
doxygenLibsbmlInternal doxygenLibsbmlInternal
Reimplemented from SBasePlugin.
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virtual |
Returns the value of the "charge" attribute of this FbcSpeciesPlugin.
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virtual |
Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
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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 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 CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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inherited |
Returns the namespace URI of the package to which this plugin object belongs.
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inherited |
Returns the SBML Level of the package extension of this plugin object.
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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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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.
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virtual |
doxygenLibsbmlInternal
doxygenLibsbmlInternal Checks if this plugin object has all the required elements.
Subclasses must override this method if they have their specific elements.
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virtual |
Predicate returning true
or false
depending on whether this FbcSpeciesPlugin's "charge" attribute has been set.
true
if this FbcSpeciesPlugin's "charge" attribute has been set, otherwise false
is returned.
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Predicate returning true
or false
depending on whether this FbcSpeciesPlugin's "chemicalFormula" attribute has been set.
true
if this FbcSpeciesPlugin's "chemicalFormula" attribute has been set, otherwise false
is returned.
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virtualinherited |
FbcSpeciesPlugin & FbcSpeciesPlugin::operator= | ( | const FbcSpeciesPlugin & | rhs | ) |
Assignment operator for FbcSpeciesPlugin.
rhs; | the object whose values are used as the basis of the assignment |
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virtualinherited |
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virtualinherited |
Reimplemented in FbcReactionPlugin.
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virtualinherited |
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Sets the value of the "charge" attribute of this FbcSpeciesPlugin.
charge; | int value of the "charge" attribute to be set |
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Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
chemicalFormula; | const std::string& value of the "chemicalFormula" attribute to be set |
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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. |
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Unsets the value of the "charge" attribute of this FbcSpeciesPlugin.
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Unsets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.