org.sbml.jsbml.ext.spatial

Class SpatialModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.spatial.AbstractSpatialSBasePlugin

org.sbml.jsbml.ext.spatial.SpatialModelPlugin

All Implemented Interfaces:

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

public class SpatialModelPlugin
extends AbstractSpatialSBasePlugin
implements IdManager

Since:

1.0

Version:

$Rev: 1980 $

Author:

Alex Thomas

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private Geometry	geometry
private static org.apache.log4j.Logger	logger A logger for this class.
private static long	serialVersionUID Generated serial version ID
private java.util.HashMap<java.lang.String,SpatialNamedSBase>	spatialIdMap

Fields inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
SpatialModelPlugin()
SpatialModelPlugin(Model model)
SpatialModelPlugin(SpatialModelPlugin spatialModelPlugin)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	accept(SBase sbase) Returns true if this IdManager can register or unregister the given SBase.
SpatialModelPlugin	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
Geometry	createGeometry() Creates a new Geometry, adds it to this object and returns a pointer to it.
boolean	getAllowsChildren()
Geometry	getChildAt(int index)
int	getChildCount()
Model	getExtendedSBase() Returns the SBase object that is extended by this plug-in.
Geometry	getGeometry() Returns the value of geometry
boolean	isSetGeometry() Returns whether geometry is set
boolean	register(SBase sbase) Registers the given SBase element and all of it's children in this IdManager.
void	setGeometry(Geometry geometry) Sets the value of geometry
boolean	unregister(SBase sbase) Unregisters the given SBase element and all of it's children in this IdManager.
boolean	unsetGeometry() Unsets the variable geometry
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.ext.spatial.AbstractSpatialSBasePlugin

getElementNamespace, getModel, getPackageName, getParent, getParentSBMLObject, getPrefix, getURI, readAttribute

Methods inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase, removeFromParent, setExtendedSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, 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.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, getIndex, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version ID

See Also:

Constant Field Values

geometry

private Geometry geometry

spatialIdMap

private java.util.HashMap<java.lang.String,SpatialNamedSBase> spatialIdMap

logger

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

A logger for this class.

Constructor Detail

SpatialModelPlugin

public SpatialModelPlugin()

SpatialModelPlugin

public SpatialModelPlugin(Model model)

Parameters:

model -

SpatialModelPlugin

public SpatialModelPlugin(SpatialModelPlugin spatialModelPlugin)

Parameters:

spatialModelPlugin -

Method Detail

getGeometry

public Geometry getGeometry()

Returns the value of geometry

Returns:

the value of geometry

createGeometry

public Geometry createGeometry()

Creates a new Geometry, adds it to this object and returns a pointer to it.

Returns:

a new Geometry object.

isSetGeometry

public boolean isSetGeometry()

Returns whether geometry is set

Returns:

whether geometry is set

setGeometry

public void setGeometry(Geometry geometry)

Sets the value of geometry

unsetGeometry

public boolean unsetGeometry()

Unsets the variable geometry

Returns:

true, if geometry was set before, otherwise false

getExtendedSBase

public Model getExtendedSBase()

Description copied from interface: SBasePlugin

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

Specified by:

getExtendedSBase in interface SBasePlugin

Overrides:

getExtendedSBase in class AbstractSBasePlugin

Returns:

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

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

Overrides:

writeXMLAttributes in class AbstractSpatialSBasePlugin

Returns:

a Map containing the XML attributes of this object.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

getChildAt

public Geometry getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

clone

public SpatialModelPlugin 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 AbstractSBasePlugin

Returns:

a new instance of SBasePlugin from this SBasePlugin.

accept

public boolean accept(SBase sbase)

Description copied from interface: IdManager

Returns true if this IdManager can register or unregister the given SBase.

Specified by:

accept in interface IdManager

Returns:

true if this IdManager can register or unregister the given SBase.

register

public boolean register(SBase sbase)

Description copied from interface: IdManager

Registers the given SBase element and all of it's children in this IdManager.

Specified by:

register in interface IdManager

Returns:

true if this operation was successfully performed, false otherwise.

unregister

public boolean unregister(SBase sbase)

Description copied from interface: IdManager

Unregisters the given SBase element and all of it's children in this IdManager.

Specified by:

unregister in interface IdManager

Returns:

true if this operation was successfully performed, false otherwise.