org.sbml.jsbml.ext.groups

Class GroupsModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.groups.GroupsModelPlugin

All Implemented Interfaces:

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

public class GroupsModelPlugin
extends AbstractSBasePlugin

Since:

1.0

Version:

$Rev: 834 $

Author:

Nicolas Rodriguez, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected ListOf<Group>	listOfGroups
private static long	serialVersionUID Generated serial version identifier.

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
GroupsModelPlugin(GroupsModelPlugin groupModelPlugin)
GroupsModelPlugin(Model model)

Method Summary

Methods

Modifier and Type	Method and Description
void	addGroup(Group group)
GroupsModelPlugin	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
Group	createGroup() Creates a new instance of Group and add it to this GroupsModelPlugin.
Group	createGroup(java.lang.String id) Creates a new instance of Group and add it to this GroupsModelPlugin.
Group	createGroup(java.lang.String id, java.lang.String... memberIds) Creates a new instance of Group and add it to this GroupsModelPlugin.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
Group	getGroup(int i)
SBase	getGroup(java.lang.String sbmlID) Gets the Group that has the given id.
int	getGroupCount() Returns the number of Groups of this GroupsModelPlugin.
ListOf<Group>	getListOfGroups()
int	getNumGroups() Returns the number of Groups of this GroupsModelPlugin.
java.lang.String	getPackageName() Returns the package name of this plugin object.
SBMLDocument	getParent()
SBMLDocument	getParentSBMLObject() Returns the parent SBase object to which this plugin object connected.
java.lang.String	getPrefix() Returns the prefix of the package extension of this plugin object.
java.lang.String	getURI() Gets the URI to which this element belongs to.
private void	initDefaults()
boolean	isSetListOfGroups()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Reads and sets the attribute if it is know from this SBasePlugin.
void	setListOfGroups(ListOf<Group> listOfGroups)
java.lang.String	toString()
boolean	unsetListOfGroups() Removes the listOfGroups from this Model and notifies all registered instances of TreeNodeChangeListener.
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.AbstractSBasePlugin

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getExtendedSBase, 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, 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 identifier.

See Also:

Constant Field Values

listOfGroups

protected ListOf<Group> listOfGroups

Constructor Detail

GroupsModelPlugin

public GroupsModelPlugin(Model model)

Parameters:

model -

GroupsModelPlugin

public GroupsModelPlugin(GroupsModelPlugin groupModelPlugin)

Parameters:

groupModelPlugin -

Method Detail

getElementNamespace

public java.lang.String getElementNamespace()

Description copied from interface: SBasePlugin

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

Returns:

the URI of the package extension of this plugin object.

getPackageName

public java.lang.String getPackageName()

Description copied from interface: SBasePlugin

Returns the package name of this plugin object.

Returns:

the package name of this plugin object.

getPrefix

public java.lang.String getPrefix()

Description copied from interface: SBasePlugin

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

Returns:

the prefix of the package extension of this plugin object.

getURI

public java.lang.String getURI()

Description copied from interface: SBasePlugin

Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/' Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found it will return the result of getElementNamespace

Returns:

the URI for this element

getParent

public SBMLDocument getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBMLDocument getParentSBMLObject()

Description copied from interface: SBasePlugin

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

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

Returns:

the parent SBase object to which this plugin object connected.

initDefaults

private void initDefaults()

addGroup

public void addGroup(Group group)

Parameters:

group -

getGroup

public Group getGroup(int i)

Parameters:

i -

Returns:

getListOfGroups

public ListOf<Group> getListOfGroups()

Returns:

getGroupCount

public int getGroupCount()

Returns the number of Groups of this GroupsModelPlugin.

Returns:

the number of Groups of this GroupsModelPlugin.

getNumGroups

public int getNumGroups()

Returns the number of Groups of this GroupsModelPlugin.

Returns:

the number of Groups of this GroupsModelPlugin.

isSetListOfGroups

public boolean isSetListOfGroups()

Returns:

setListOfGroups

public void setListOfGroups(ListOf<Group> listOfGroups)

Parameters:

listOfGroups -

unsetListOfGroups

public boolean unsetListOfGroups()

Removes the listOfGroups from this Model and notifies all registered instances of TreeNodeChangeListener.

Returns:

true if calling this method lead to a change in this data structure.

clone

public GroupsModelPlugin 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.

toString

public java.lang.String toString()

Overrides:

toString in class AbstractTreeNode

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBasePlugin

Reads and sets the attribute if it is know from this SBasePlugin.

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

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 AbstractSBasePlugin

Returns:

a Map containing the XML attributes of this object.

getChildAt

public SBase getChildAt(int childIndex)

getChildCount

public int getChildCount()

getAllowsChildren

public boolean getAllowsChildren()

createGroup

public Group createGroup()

Creates a new instance of Group and add it to this GroupsModelPlugin.

Returns:

the new Group instance.

createGroup

public Group createGroup(java.lang.String id)

Creates a new instance of Group and add it to this GroupsModelPlugin.

Parameters:

id - the id to be set to the new Group.

Returns:

the new Group instance.

createGroup

public Group createGroup(java.lang.String id,
                java.lang.String... memberIds)

Creates a new instance of Group and add it to this GroupsModelPlugin. For each id in the memberIds array, a new Member instance is created and added to the Group as well.

Parameters:

id - the id to be set to the new Group.

memberIds - the ids to be set to the new Member instances.

Returns:

the new Group instance.

getGroup

public SBase getGroup(java.lang.String sbmlID)

Gets the Group that has the given id.

Parameters:

sbmlID -

Returns:

the Group that has the given id or null if no Group is found that matches sbmlID.