org.sbml.libsbml

Class LayoutExtension

java.lang.Object

org.sbml.libsbml.SBMLExtension

org.sbml.libsbml.LayoutExtension

public class LayoutExtension
extends SBMLExtension

layout The core module of the 'layout' package extension.

Constructor Summary

Constructors

Constructor and Description
LayoutExtension() Constructor
LayoutExtension(LayoutExtension arg0) Copy constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	addL2Namespaces(XMLNamespaces xmlns) adds all L2 Extension namespaces to the namespace list.
LayoutExtension	cloneObject() Creates and returns a deep copy of this LayoutExtension object.
void	delete() Explicitly deletes the underlying native object.
SBase	DowncastSBase(long cPtr, boolean owner) SBMLExtension derived classes must override this method
SBasePlugin	DowncastSBasePlugin(long cPtr, boolean owner) SBMLExtension derived classes must override this method
void	enableL2NamespaceForDocument(SBMLDocument doc) Adds the L2 Namespace to the document and enables the extension.
static long	getDefaultLevel() Returns the default SBML Level this extension.
static long	getDefaultPackageVersion() Returns the default SBML version this extension.
static long	getDefaultVersion() Returns the default SBML Version this extension.
long	getLevel(java.lang.String uri) Returns the SBML Level for the given URI of this package.
java.lang.String	getName() Returns the name of this package ('layout')
static java.lang.String	getPackageName() Returns the package name of this extension.
long	getPackageVersion(java.lang.String uri) Returns the package version for the given URI of this package.
SBMLNamespaces	getSBMLExtensionNamespaces(java.lang.String uri) Returns an LayoutPkgNamespaces object.
java.lang.String	getStringFromTypeCode(int typeCode) Takes a type code of the &ldquolayout&rdquo package and returns a string describing the code.
java.lang.String	getURI(long sbmlLevel, long sbmlVersion, long pkgVersion) Returns the namespace URI corresponding to the combination of the given SBML Level, Version, and package version.
long	getVersion(java.lang.String uri) Returns the SBML Version for the given URI of this package.
static java.lang.String	getXmlnsL2()
static java.lang.String	getXmlnsL3V1V1() Returns URI of supported versions of this package.
static java.lang.String	getXmlnsXSI()
boolean	isInUse(SBMLDocument doc) Determines whether this extension is being used by the given SBMLDocument
void	removeL2Namespaces(XMLNamespaces xmlns) Removes the L2 Namespace from a document.

Methods inherited from class org.sbml.libsbml.SBMLExtension

getCategory, getErrorIdOffset, getMessage, getNumOfSBasePlugins, getNumOfSupportedPackageURI, getSeverity, getShortMessage, getSupportedPackageURI, isEnabled, isSupported, setEnabled

Methods inherited from class java.lang.Object

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

Constructor Detail

LayoutExtension

public LayoutExtension()

Constructor

LayoutExtension

public LayoutExtension(LayoutExtension arg0)

Copy constructor.

Method Detail

addL2Namespaces

public void addL2Namespaces(XMLNamespaces xmlns)

adds all L2 Extension namespaces to the namespace list.

This method should be overridden by all extensions that want to serialize to an L2 annotation.

Overrides:

addL2Namespaces in class SBMLExtension

cloneObject

public LayoutExtension cloneObject()

Creates and returns a deep copy of this LayoutExtension object.

Overrides:

cloneObject in class SBMLExtension

Returns:

a (deep) copy of this LayoutExtension object

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 LayoutExtension.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 LayoutExtension.delete() themselves.

Overrides:

delete in class SBMLExtension

DowncastSBase

public SBase DowncastSBase(long cPtr,
                  boolean owner)

SBMLExtension derived classes must override this method

Overrides:

DowncastSBase in class SBMLExtension

Returns:

the most specific Java object possible for the given SBase

DowncastSBasePlugin

public SBasePlugin DowncastSBasePlugin(long cPtr,
                              boolean owner)

Description copied from class: SBMLExtension

SBMLExtension derived classes must override this method

Overrides:

DowncastSBasePlugin in class SBMLExtension

enableL2NamespaceForDocument

public void enableL2NamespaceForDocument(SBMLDocument doc)

Adds the L2 Namespace to the document and enables the extension.

If the extension supports serialization to SBML L2 Annotations, this method should be overrridden, so it will be activated.

Overrides:

enableL2NamespaceForDocument in class SBMLExtension

getDefaultLevel

public static long getDefaultLevel()

Returns the default SBML Level this extension.

getDefaultPackageVersion

public static long getDefaultPackageVersion()

Returns the default SBML version this extension.

getDefaultVersion

public static long getDefaultVersion()

Returns the default SBML Version this extension.

getLevel

public long getLevel(java.lang.String uri)

Returns the SBML Level for the given URI of this package.

Overrides:

getLevel in class SBMLExtension

Parameters:

uri - the string of URI that represents one of versions of the &ldquolayout&rdquo package

Returns:

the SBML Level with the given URI of this package, or 0 if the given URI is invalid.

getName

public java.lang.String getName()

Returns the name of this package ('layout')

Overrides:

getName in class SBMLExtension

Returns:

the name of this package ('layout')

getPackageName

public static java.lang.String getPackageName()

Returns the package name of this extension.

getPackageVersion

public long getPackageVersion(java.lang.String uri)

Returns the package version for the given URI of this package.

Overrides:

getPackageVersion in class SBMLExtension

Parameters:

uri - the string of URI that represents one of versions of the &ldquolayout&rdquo package

Returns:

the package version with the given URI of this package, or 0 if the given URI is invalid.

getSBMLExtensionNamespaces

public SBMLNamespaces getSBMLExtensionNamespaces(java.lang.String uri)

Returns an LayoutPkgNamespaces object.

Overrides:

getSBMLExtensionNamespaces in class SBMLExtension

Parameters:

uri - the string of URI that represents one of versions of the &ldquolayout&rdquo package

Returns:

an LayoutPkgNamespace object corresponding to the given uri, or null if the URI is not defined in the Layout package.

getStringFromTypeCode

public java.lang.String getStringFromTypeCode(int typeCode)

Takes a type code of the &ldquolayout&rdquo package and returns a string describing the code.

Overrides:

getStringFromTypeCode in class SBMLExtension

getURI

public java.lang.String getURI(long sbmlLevel,
                      long sbmlVersion,
                      long pkgVersion)

Returns the namespace URI corresponding to the combination of the given SBML Level, Version, and package version.

Overrides:

getURI in class SBMLExtension

Parameters:

sbmlLevel - the level of SBML

sbmlVersion - the version of SBML

pkgVersion - the version of package

Returns:

a string of the package URI, or an empty string if no corresponding URI exists.

getVersion

public long getVersion(java.lang.String uri)

Returns the SBML Version for the given URI of this package.

Overrides:

getVersion in class SBMLExtension

Parameters:

uri - the string of URI that represents one of versions of the &ldquolayout&rdquo package

Returns:

the SBML version with the given URI of this package, or 0 if the given URI is invalid.

getXmlnsL2

public static java.lang.String getXmlnsL2()

getXmlnsL3V1V1

public static java.lang.String getXmlnsL3V1V1()

Returns URI of supported versions of this package.

getXmlnsXSI

public static java.lang.String getXmlnsXSI()

isInUse

public boolean isInUse(SBMLDocument doc)

Determines whether this extension is being used by the given SBMLDocument

The implementation returns true if the model object contains one or more layouts.

Overrides:

isInUse in class SBMLExtension

Parameters:

doc - the sbml document to test.

Returns:

a boolean indicating whether the extension is actually being used byy the document.

removeL2Namespaces

public void removeL2Namespaces(XMLNamespaces xmlns)

Removes the L2 Namespace from a document.

This method should be overridden by all extensions that want to serialize to an L2 annotation.

Overrides:

removeL2Namespaces in class SBMLExtension