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

{core}

Base class for extending SBML objects in packages.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

The SBasePlugin class is libSBML's base class for extensions of core SBML component objects. SBasePlugin defines basic virtual methods for reading/writing/checking additional attributes and/or subobjects; these methods should be overridden by subclasses to implement the necessary features of an extended SBML object.

Public Member Functions

virtual SBasePluginclone () const
 Creates and returns a deep copy of this SBasePlugin object. More...
 
virtual ListgetAllElements (ElementFilter *filter=NULL)
 Returns all child objects of this object. 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...
 
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...
 
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...
 
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 isValidTypeForList (SBase *item) const
 
SBasePluginoperator= (const SBasePlugin &orig)
 Assignment operator for SBasePlugin. 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...
 
virtual ~SBasePlugin ()
 Destroy this SBasePlugin object. More...
 

Constructor & Destructor Documentation

◆ ~SBasePlugin()

SBasePlugin::~SBasePlugin ( )
virtual

Destroy this SBasePlugin object.

Member Function Documentation

◆ clone()

◆ getAllElements()

List * SBasePlugin::getAllElements ( ElementFilter filter = NULL)
virtual

Returns all child objects of this object.

This returns a List object containing all child SBase objects of this one, at any nesting depth. Optionally, callers can supply a filter that will establish the search criteria for matching objects.

Parameters
filtera pointer to an ElementFilter, which causes the function to return only elements that match a particular set of constraints. If NULL (the default), the function will return all child objects.
Returns
a List of pointers to all children objects.

Reimplemented in GroupsModelPlugin, FbcModelPlugin, MultiCompartmentPlugin, MultiSpeciesPlugin, LayoutModelPlugin, MultiSimpleSpeciesReferencePlugin, RenderListOfLayoutsPlugin, FbcReactionPlugin, CompModelPlugin, CompSBasePlugin, CompSBMLDocumentPlugin, RenderLayoutPlugin, MultiSpeciesReferencePlugin, MultiModelPlugin, and QualModelPlugin.

◆ getElementByMetaId()

SBase * SBasePlugin::getElementByMetaId ( const std::string &  metaid)
virtual

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)
virtual

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

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.

◆ getLevel()

unsigned int SBasePlugin::getLevel ( ) const

Returns the SBML Level of the package extension of this plugin object.

Returns
the SBML Level.
See also
getVersion()

◆ getPackageName()

const std::string & SBasePlugin::getPackageName ( ) const

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

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 ( )

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

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

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 ( )

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

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()

◆ getURI()

std::string SBasePlugin::getURI ( ) const

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

Returns the Version within the SBML Level of the package extension of this plugin object.

Returns
the SBML Version.
See also
getLevel()

◆ isValidTypeForList()

virtual bool SBasePlugin::isValidTypeForList ( SBase item) const
virtual

◆ operator=()

SBasePlugin & SBasePlugin::operator= ( const SBasePlugin orig)

Assignment operator for SBasePlugin.

Parameters
origthe object whose values are used as the basis of the assignment.

◆ renameMetaIdRefs()

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

◆ renameSIdRefs()

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

Reimplemented in FbcReactionPlugin.

◆ renameUnitSIdRefs()

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

◆ setElementNamespace()

int SBasePlugin::setElementNamespace ( const std::string &  uri)

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.