libSBML Perl API
libSBML 5.10.0 Perl API
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{fbc} Implementation of the 'fbc' package extention to the Species construct.
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) | |
Constructor. More... | |
FbcSpeciesPlugin (const FbcSpeciesPlugin &orig) | |
Copy constructor. More... | |
virtual List * | getAllElements (ElementFilter *filter=NULL) |
Returns a List of all child SBase objects, including those nested to an arbitrary depth. 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) |
Returns the first child element it can find with the given metaid , or NULL if no such object is found. More... | |
virtual SBase * | getElementBySId (const std::string &id) |
Returns the first child element found 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 XML namespace (URI) of the package extension of this plugin object. 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 package name of this plugin object. More... | |
unsigned int | getPackageVersion () const |
Returns the package version of the package extension of this plugin object. More... | |
SBase * | getParentSBMLObject () |
Returns the parent SBase object to which this plugin object connected. More... | |
const SBase * | getParentSBMLObject () const |
Returns the parent SBase object to which this plugin object connected. More... | |
const std::string & | getPrefix () const |
Returns the prefix of the package extension of this plugin object. More... | |
SBMLDocument * | getSBMLDocument () |
Returns the parent SBMLDocument of this plugin object. More... | |
const SBMLDocument * | getSBMLDocument () const |
Returns the parent SBMLDocument of this plugin object. More... | |
std::string | getURI () const |
Gets the URI to which this element belongs to. More... | |
unsigned int | getVersion () const |
Returns the SBML version of the package extension of this plugin object. More... | |
virtual bool | isSetCharge () const |
Predicate returning true or false depending on whether this FbcSpeciesPlugin "charge" attribute has been set. More... | |
virtual bool | isSetChemicalFormula () const |
Predicate returning true or false depending on whether this FbcSpeciesPlugin "chemicalFormula" attribute has been set. More... | |
FbcSpeciesPlugin & | operator= (const FbcSpeciesPlugin &orig) |
Assignment operator for FbcSpeciesPlugin . More... | |
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 element belongs to. 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 () |
Destroy this object. More... | |
FbcSpeciesPlugin::FbcSpeciesPlugin | ( | const std::string & | uri, |
const std::string & | prefix, | ||
FbcPkgNamespaces * | fbcns | ||
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Constructor.
FbcSpeciesPlugin::FbcSpeciesPlugin | ( | const FbcSpeciesPlugin & | orig | ) |
Copy constructor.
Creates a copy of this FbcSpeciesPlugin object.
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virtual |
Destroy this object.
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virtual |
Creates and returns a deep copy of this FbcSpeciesPlugin object.
Implements SBasePlugin.
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virtualinherited |
Returns a List of all child SBase objects, including those nested to an arbitrary depth.
Reimplemented in LayoutModelPlugin, FbcModelPlugin, CompModelPlugin, CompSBasePlugin, CompSBMLDocumentPlugin, and QualModelPlugin.
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Returns the value of the "charge" attribute of this FbcSpeciesPlugin.
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Returns the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
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virtualinherited |
Returns the first child element it can find with the given metaid
, or NULL
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
. Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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virtualinherited |
Returns the first child element found that has the given id
in the model-wide SId namespace, or NULL
if no such object is found.
id | string representing the id of objects to find |
id
. Reimplemented in FbcModelPlugin, CompModelPlugin, CompSBasePlugin, and CompSBMLDocumentPlugin.
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inherited |
Returns the XML namespace (URI) of the package extension of this plugin object.
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inherited |
Returns the SBML level of the package extension of this plugin object.
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inherited |
Returns the package name of this plugin object.
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inherited |
Returns the package version of the package extension of this plugin object.
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inherited |
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inherited |
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inherited |
Returns the prefix of the package extension of this plugin object.
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inherited |
Returns the parent SBMLDocument of this plugin object.
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inherited |
Returns the parent SBMLDocument of this plugin object.
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inherited |
Gets the URI to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI "http://www.sbml.org/sbml/level3/version1/layout/version1/"
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
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inherited |
Returns the SBML version of the package extension of this plugin object.
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virtual |
Predicate returning true
or false
depending on whether this FbcSpeciesPlugin "charge" attribute has been set.
true
if this FbcSpeciesPlugin "charge" attribute has been set, otherwise false
is returned.
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virtual |
Predicate returning true
or false
depending on whether this FbcSpeciesPlugin "chemicalFormula" attribute has been set.
true
if this FbcSpeciesPlugin "chemicalFormula" attribute has been set, otherwise false
is returned. FbcSpeciesPlugin & FbcSpeciesPlugin::operator= | ( | const FbcSpeciesPlugin & | orig | ) |
Assignment operator for FbcSpeciesPlugin .
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Sets the value of the "charge" attribute of this FbcSpeciesPlugin.
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Sets the value of the "chemicalFormula" attribute of this FbcSpeciesPlugin.
The format of chemicalFormula must consist only of atomic names (as in the Periodic Table) or user defined compounds either of which take the form of a single capital letter followed by zero or more lowercase letters. Where there is more than a single atom present, this is indicated with an integer. With regards to order (and enhance inter-operability) it is recommended to use the Hill system order. (However, no error-checking is performed by this routine.)
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inherited |
Sets the XML namespace to which this element belongs to.
For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/core"; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to "http://www.sbml.org/sbml/level3/version1/layout/version1/"
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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.