org.sbml.jsbml.ext

Class AbstractSBasePlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public abstract class AbstractSBasePlugin
extends AbstractTreeNode
implements SBasePlugin

Since:

1.0

Version:

$Rev$

Author:

Andreas Dräger, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	elementNamespace
protected SBase	extendedSBase
private static org.apache.log4j.Logger	logger
protected int	packageVersion
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
AbstractSBasePlugin()
AbstractSBasePlugin(SBase extendedSBase)
AbstractSBasePlugin(SBasePlugin plugin) This method will need to be further tested

Method Summary

Modifier and Type	Method and Description
abstract SBasePlugin	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
boolean	equals(java.lang.Object object)
void	fireNodeAddedEvent() All TreeNodeChangeListener instances linked to this TreeNode are informed about the adding of this Object to an owning parent Object.
void	fireNodeRemovedEvent() All TreeNodeChangeListener instances linked to this TreeNode are informed about the deletion of this TreeNode from a parent Object.
void	firePropertyChange(java.lang.String propertyName, java.lang.Object oldValue, java.lang.Object newValue) All TreeNodeChangeListeners are informed about the change in this TreeNodeWithChangeSupport.
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
SBase	getExtendedSBase() Returns the SBase object that is extended by this plug-in.
int	getLevel() Returns the SBML level of this plugin object.
int	getPackageVersion() Returns the package version of the package extension of this plugin object.
SBase	getParentSBMLObject() Returns the parent SBase object to which this plugin object connected.
SBMLDocument	getSBMLDocument() Returns the parent SBMLDocument of this plugin object.
int	getVersion() Returns the SBML version of this plugin object.
int	hashCode()
boolean	isSetExtendedSBase() Check whether an extended SBase has been set.
boolean	isSetPackageVersion() Returns true if a package version is set, false otherwise.
boolean	removeFromParent() This method is designed to be overridden for non-independent child nodes
void	setExtendedSBase(SBase extendedSBase) Sets the extended SBase.
void	setNamespace(java.lang.String namespace) Sets the XML namespace to which this SBasePlugin belong.
void	setPackageVersion(int packageVersion) Sets the package version.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a Map containing the XML attributes of this object.

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.ext.SBasePlugin

getPackageName, getPrefix, getURI, readAttribute

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

extendedSBase

protected SBase extendedSBase

packageVersion

protected int packageVersion

elementNamespace

protected java.lang.String elementNamespace

Constructor Detail

AbstractSBasePlugin

public AbstractSBasePlugin()

AbstractSBasePlugin

public AbstractSBasePlugin(SBase extendedSBase)

Parameters:

extendedSBase -

AbstractSBasePlugin

public AbstractSBasePlugin(SBasePlugin plugin)

This method will need to be further tested

Parameters:

plugin -

Method Detail

clone

public abstract SBasePlugin clone()

Description copied from interface: SBasePlugin

Creates a new instance of SBasePlugin from this SBasePlugin.

Specified by:

clone in interface SBasePlugin

Specified by:

clone in class AbstractTreeNode

Returns:

a new instance of SBasePlugin from this SBasePlugin.

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBasePlugin

Overrides:

equals in class AbstractTreeNode

fireNodeAddedEvent

public void fireNodeAddedEvent()

Description copied from interface: TreeNodeWithChangeSupport

All TreeNodeChangeListener instances linked to this TreeNode are informed about the adding of this Object to an owning parent Object.

Specified by:

fireNodeAddedEvent in interface TreeNodeWithChangeSupport

Overrides:

fireNodeAddedEvent in class AbstractTreeNode

fireNodeRemovedEvent

public void fireNodeRemovedEvent()

Description copied from interface: TreeNodeWithChangeSupport

All TreeNodeChangeListener instances linked to this TreeNode are informed about the deletion of this TreeNode from a parent Object.

Specified by:

fireNodeRemovedEvent in interface TreeNodeWithChangeSupport

Overrides:

fireNodeRemovedEvent in class AbstractTreeNode

firePropertyChange

public void firePropertyChange(java.lang.String propertyName,
                               java.lang.Object oldValue,
                               java.lang.Object newValue)

Description copied from interface: TreeNodeWithChangeSupport

All TreeNodeChangeListeners are informed about the change in this TreeNodeWithChangeSupport.

Specified by:

firePropertyChange in interface TreeNodeWithChangeSupport

Overrides:

firePropertyChange in class AbstractTreeNode

Parameters:

propertyName - Tells the TreeNodeChangeListener the name of the property whose value has been changed.

oldValue - This is the value before the change.

newValue - This gives the new value that is now the new value for the given property..

getElementNamespace

public java.lang.String getElementNamespace()

Description copied from interface: SBasePlugin

Returns the XML namespace (URI) of the package extension of this plugin object.

Specified by:

getElementNamespace in interface SBasePlugin

Returns:

the URI of the package extension of this plugin object.

See Also:

SBasePlugin.getURI()

getExtendedSBase

public SBase getExtendedSBase()

Description copied from interface: SBasePlugin

Returns the SBase object that is extended by this plug-in.

Specified by:

getExtendedSBase in interface SBasePlugin

Returns:

the SBase object that is extended by this plug-in.

getLevel

public int getLevel()

Description copied from interface: SBasePlugin

Returns the SBML level of this plugin object.

Specified by:

getLevel in interface SBasePlugin

Returns:

the SBML level of this plugin object.

See Also:

SBase.getLevel()

getPackageVersion

public int getPackageVersion()

Description copied from interface: SBasePlugin

Returns the package version of the package extension of this plugin object.

Specified by:

getPackageVersion in interface SBasePlugin

Returns:

the package version of the package extension of this plugin object.

getParentSBMLObject

public SBase getParentSBMLObject()

Description copied from interface: SBasePlugin

Returns the parent SBase object to which this plugin object connected.

Specified by:

getParentSBMLObject in interface SBasePlugin

Returns:

the parent SBase object to which this plugin object connected.

getSBMLDocument

public SBMLDocument getSBMLDocument()

Description copied from interface: SBasePlugin

Returns the parent SBMLDocument of this plugin object.

Specified by:

getSBMLDocument in interface SBasePlugin

Returns:

the parent SBMLDocument object of this plugin object.

getVersion

public int getVersion()

Description copied from interface: SBasePlugin

Returns the SBML version of this plugin object.

Specified by:

getVersion in interface SBasePlugin

Returns:

the SBML version of this plugin object.

See Also:

SBase.getVersion()

hashCode

public int hashCode()

Specified by:

hashCode in interface SBasePlugin

Overrides:

hashCode in class AbstractTreeNode

isSetExtendedSBase

public boolean isSetExtendedSBase()

Description copied from interface: SBasePlugin

Check whether an extended SBase has been set.

Specified by:

isSetExtendedSBase in interface SBasePlugin

Returns:

true if an extended SBase has been set.

isSetPackageVersion

public boolean isSetPackageVersion()

Description copied from interface: SBasePlugin

Returns true if a package version is set, false otherwise.

Specified by:

isSetPackageVersion in interface SBasePlugin

Returns:

true if a package version is set, false otherwise.

removeFromParent

public boolean removeFromParent()

Description copied from class: AbstractTreeNode

This method is designed to be overridden for non-independent child nodes

Specified by:

removeFromParent in interface TreeNodeWithChangeSupport

Overrides:

removeFromParent in class AbstractTreeNode

Returns:

false if this element is a root node, true otherwise.

See Also:

TreeNodeWithChangeSupport.removeFromParent()

setNamespace

public void setNamespace(java.lang.String namespace)

Sets the XML namespace to which this SBasePlugin belong.

This an internal method that should not be used outside of the main jsbml code (core + packages). One class should always belong to the same namespace, although the namespaces can have different level and version (and package version). You have to know what you are doing when using this method.

Parameters:

namespace - the XML namespace to which this SBasePlugin belong.

setExtendedSBase

public void setExtendedSBase(SBase extendedSBase)

Sets the extended SBase.

This method should not be called in general but it is necessary to use it after cloning an SBasePlugin to be able to set properly the new parent/extended SBase.

Parameters:

extendedSBase -

setPackageVersion

public void setPackageVersion(int packageVersion)

Description copied from interface: SBasePlugin

Sets the package version.

Specified by:

setPackageVersion in interface SBasePlugin

Parameters:

packageVersion - the packageVersion to set

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBasePlugin

Returns a Map containing the XML attributes of this object.

Specified by:

writeXMLAttributes in interface SBasePlugin

Returns:

a Map containing the XML attributes of this object.