org.sbml.libsbml

Class MultiSBMLDocumentPlugin

java.lang.Object

org.sbml.libsbml.SBasePlugin

org.sbml.libsbml.SBMLDocumentPlugin

org.sbml.libsbml.MultiSBMLDocumentPlugin

public class MultiSBMLDocumentPlugin
extends SBMLDocumentPlugin

multi Extension of SBMLDocument for the 'multi' package.

The MultiSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Multistate and Multicomponent Species ('multi') package. This extension defines a required flag named 'required', which indicates whether 'multi' constructs can be used to change the core mathematical interpretation of the Model defined in the SBML input. Since 'multi' constructs can, this attribute must be set to the value 'true'.

Constructor Summary

Constructors

Constructor and Description
MultiSBMLDocumentPlugin(MultiSBMLDocumentPlugin orig) Copy constructor for MultiSBMLDocumentPlugin.
MultiSBMLDocumentPlugin(java.lang.String uri, java.lang.String prefix, MultiPkgNamespaces multins) Creates a new MultiSBMLDocumentPlugin object.

Method Summary

Modifier and Type	Method and Description
SBasePlugin	cloneObject() Creates and returns a deep copy of this MultiSBMLDocumentPlugin object.
void	delete() Explicitly deletes the underlying native object.

Methods inherited from class org.sbml.libsbml.SBMLDocumentPlugin

getRequired, isSetRequired, setRequired, unsetRequired

Methods inherited from class org.sbml.libsbml.SBasePlugin

getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultiSBMLDocumentPlugin

public MultiSBMLDocumentPlugin(java.lang.String uri,
                               java.lang.String prefix,
                               MultiPkgNamespaces multins)

Creates a new MultiSBMLDocumentPlugin object.

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/'.

The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.

Parameters:

uri - the URI of the SBML Level 3 package implemented by this libSBML package extension.

prefix - the XML namespace prefix being used for the package.

multins - the namespaces object for the package.

MultiSBMLDocumentPlugin

public MultiSBMLDocumentPlugin(MultiSBMLDocumentPlugin orig)

Copy constructor for MultiSBMLDocumentPlugin.

Parameters:

orig - the MultiSBMLDocumentPlugin instance to copy.

Method Detail

delete

public void delete()

Explicitly deletes the underlying native object.

In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the MultiSBMLDocumentPlugin.delete() method on the libSBML object.

This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke MultiSBMLDocumentPlugin.delete() themselves.

Overrides:

delete in class SBMLDocumentPlugin

cloneObject

public SBasePlugin cloneObject()

Creates and returns a deep copy of this MultiSBMLDocumentPlugin object.

Overrides:

cloneObject in class SBMLDocumentPlugin

Returns:

a (deep) copy of this MultiSBMLDocumentPlugin object.