libsbmlcs.SBMLDocumentPlugin Class Reference

Inheritance diagram for libsbmlcs.SBMLDocumentPlugin:

Detailed Description

{core}

Base class for extending SBMLDocument 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 SBMLDocumentPlugin class is a specialization of SBasePlugin designed specifically for extending SBMLDocument. All package extensions must extend SBMLDocument to implement support for SBML Level 3 packages; these extensions can be subclasses of this class or from a derived class of this class.

Basic principles of SBML package extensions in libSBML

SBML Level 3's package structure permits modular extensions to the core SBML format. In libSBML, support for SBML Level 3 packages is provided through optional package extensions that can be plugged into libSBML at the time it is built/compiled. Users of libSBML can thus choose which extensions are enabled in their software applications.

LibSBML defines a number of classes that developers of package extensions can use to implement support for an SBML Level 3 package. These classes make it easier to extend libSBML objects with new attributes and/or subobjects as needed by a particular Level 3 package. Three overall categories of classes make up libSBML's facilities for implementing package extensions. There are (1) classes that serve as base classes meant to be subclassed, (2) template classes meant to be instantiated rather than subclassed, and (3) support classes that provide utility features. A given package implementation for libSBML will take the form of code using these and other libSBML classes, placed in a subdirectory of src/sbml/packages/.

The basic libSBML distribution includes a number of package extensions implementing support for officially-endorsed SBML Level 3 packages; among these are Flux Balance Constraints ('fbc'), Hierarchical Model Composition ('comp'), Layout ('layout'), and Qualitative Models ('qual'). They can serve as working examples for developers working to implement other packages.

Extensions in libSBML can currently only be implemented in C++ or C; there is no mechanism to implement them first in languages such as Java or Python. However, once implemented in C++ or C, language interfaces can be generated semi-automatically using the framework in place in libSBML. (The approach is based on using SWIG and facilities in libSBML's build system.)

Public Member Functions
new SBasePlugin	clone ()
	Creates and returns a deep copy of this SBMLDocumentPlugin object. More...
override void	Dispose ()
long	getColumn ()
new SBase	getElementByMetaId (string metaid)
	Return the first child object found with a given meta identifier. More...
new SBase	getElementBySId (string id)
	Return the first child object found with a given identifier. More...
string	getElementNamespace ()
	Returns the namespace URI of the package to which this plugin object belongs. More...
long	getLevel ()
	Returns the SBML Level of the package extension of this plugin object. More...
long	getLine ()
SBaseList	getListOfAllElements (ElementFilter filter)
SBaseList	getListOfAllElements ()
string	getPackageName ()
	Returns the short-form name of the package to which this plugin object belongs. More...
long	getPackageVersion ()
	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...
string	getPrefix ()
	Returns the XML namespace prefix of the package to which this plugin object belongs. More...
new bool	getRequired ()
	Returns the value of the 'required' attribute. More...
SBMLDocument	getSBMLDocument ()
	Returns the SBMLDocument object containing this object instance. More...
SBMLExtension	getSBMLExtension ()
string	getURI ()
	Returns the XML namespace URI for the package to which this object belongs. More...
long	getVersion ()
	Returns the Version within the SBML Level of the package extension of this plugin object. More...
new bool	isSetRequired ()
	Returns the value of the 'required' attribute. More...
new bool	isValidTypeForList (SBase item)
new void	renameMetaIdRefs (string oldid, string newid)
	Replaces all uses of a given meta identifier attribute value with another value. More...
new void	renameSIdRefs (string oldid, string newid)
	Replaces all uses of a given SIdRef type attribute value with another value. More...
new void	renameUnitSIdRefs (string oldid, string newid)
	Replaces all uses of a given UnitSIdRef type attribute value with another value. More...
	SBMLDocumentPlugin (string uri, string prefix, SBMLNamespaces sbmlns)
	Creates a new SBMLDocumentPlugin object using the given parameters. More...
	SBMLDocumentPlugin (SBMLDocumentPlugin orig)
	Copy constructor. More...
int	setElementNamespace (string uri)
	Sets the XML namespace to which this object belongs. More...
new int	setRequired (bool value)
	Sets the SBML 'required' attribute value. More...
new int	unsetRequired ()
	Unsets the value of the 'required' attribute of this SBMLDocumentPlugin. More...

Protected Attributes
bool	swigCMemOwn

Constructor & Destructor Documentation