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:

Serializable, Cloneable, 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

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

Modifier and Type	Method and Description
void	addGroup(Group group)
GroupsModelPlugin	clone()
Group	createGroup() Creates a new instance of Group and add it to this GroupsModelPlugin.
Group	createGroup(String id) Creates a new instance of Group and add it to this GroupsModelPlugin.
Group	createGroup(String id, String... memberIds) Creates a new instance of Group and add it to this GroupsModelPlugin.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
String	getElementNamespace()
Group	getGroup(int i)
SBase	getGroup(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.
String	getPackageName()
SBMLDocument	getParent()
SBMLDocument	getParentSBMLObject()
String	getPrefix()
String	getURI()
boolean	isSetListOfGroups()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setListOfGroups(ListOf<Group> listOfGroups)
String	toString()
boolean	unsetListOfGroups() Removes the listOfGroups from this Model and notifies all registered instances of TreeNodeChangeListener.
Map<String,String>	writeXMLAttributes()

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

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 String getElementNamespace()

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getParent

public SBMLDocument getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBMLDocument getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

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.

Note: this method is kept here as it exist in libSBML.

same as getGroupCount()

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()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

toString

public String toString()

Overrides:

toString in class AbstractTreeNode

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

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(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(String id,
                         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(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.