libSBML C API
libSBML 5.8.0 C API
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Representation of a plug-in object of SBML's package extension.
Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase* createObject (XMLInputStream& stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase* parentObject, XMLInputStream& stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object instead of the SBase::readAnnotation(XMLInputStream& stream) and/or SBase::readNotes(XMLInputStream& stream) functions.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (const XMLAttributes& attributes, const ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream& stream) const
writing attributes :
virtual void writeAttributes (XMLOutputStream& stream) const
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream& stream) const
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements() const
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes() const
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument* d)
virtual void connectToParent(SBase *sbase)
virtual void enablePackageInternal(const std::string& pkgURI, const std::string& pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()