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, org.sbml.jsbml.ext.SBasePlugin, org.sbml.jsbml.util.TreeNodeWithChangeSupport

public class GroupsModelPlugin
extends org.sbml.jsbml.ext.AbstractSBasePlugin

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.sbml.jsbml.ListOf<Group>	listOfGroups

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

elementNamespace, extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
GroupsModelPlugin(GroupsModelPlugin groupModelPlugin) Creates a new GroupsModelPlugin instance cloned from the given parameter.
GroupsModelPlugin(org.sbml.jsbml.Model model) Creates a new GroupsModelPlugin instance

Method Summary

Modifier and Type	Method and Description
boolean	addGroup(Group group) Adds a new element to the listOfGroups.
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()
org.sbml.jsbml.SBase	getChildAt(int childIndex)
int	getChildCount()
Group	getGroup(int i) Returns the n-th Group object in this GroupsModelPlugin.
org.sbml.jsbml.SBase	getGroup(String sbmlID) Gets the Group that has the given id.
int	getGroupCount() Returns the number of Groups of this GroupsModelPlugin.
org.sbml.jsbml.ListOf<Group>	getListOfGroups() Returns the listOfGroups.
int	getNumGroups() Returns the number of Groups of this GroupsModelPlugin.
String	getPackageName()
org.sbml.jsbml.SBMLDocument	getParent()
org.sbml.jsbml.SBMLDocument	getParentSBMLObject()
String	getPrefix()
String	getURI()
boolean	isSetListOfGroups()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setListOfGroups(org.sbml.jsbml.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, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase, isSetPackageVersion, removeFromParent, setExtendedSBase, setNamespace, setPackageVersion

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 org.sbml.jsbml.ListOf<Group> listOfGroups

Constructor Detail

GroupsModelPlugin

public GroupsModelPlugin(GroupsModelPlugin groupModelPlugin)

Creates a new GroupsModelPlugin instance cloned from the given parameter.

Parameters:

groupModelPlugin -

GroupsModelPlugin

public GroupsModelPlugin(org.sbml.jsbml.Model model)

Creates a new GroupsModelPlugin instance

Parameters:

model -

Method Detail

addGroup

public boolean addGroup(Group group)

Adds a new element to the listOfGroups.

listOfGroups is initialized if necessary.

Parameters:

group -

Returns:

true (as specified by Collection.add(E))

clone

public GroupsModelPlugin clone()

Specified by:

clone in interface org.sbml.jsbml.ext.SBasePlugin

Overrides:

clone in class org.sbml.jsbml.ext.AbstractSBasePlugin

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.

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public org.sbml.jsbml.SBase getChildAt(int childIndex)

getChildCount

public int getChildCount()

getGroup

public Group getGroup(int i)

Returns the n-th Group object in this GroupsModelPlugin.

Parameters:

i - an index

Returns:

the Group with the given index if it exists.

Throws:

IndexOutOfBoundsException

getGroup

public org.sbml.jsbml.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.

getGroupCount

public int getGroupCount()

Returns the number of Groups of this GroupsModelPlugin.

Returns:

the number of Groups of this GroupsModelPlugin.

getListOfGroups

public org.sbml.jsbml.ListOf<Group> getListOfGroups()

Returns the listOfGroups. If the ListOf is not defined, creates an empty one.

Returns:

the listOfGroups

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()

getPackageName

public String getPackageName()

getParent

public org.sbml.jsbml.SBMLDocument getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class org.sbml.jsbml.AbstractTreeNode

getParentSBMLObject

public org.sbml.jsbml.SBMLDocument getParentSBMLObject()

Specified by:

getParentSBMLObject in interface org.sbml.jsbml.ext.SBasePlugin

Overrides:

getParentSBMLObject in class org.sbml.jsbml.ext.AbstractSBasePlugin

getPrefix

public String getPrefix()

getURI

public String getURI()

isSetListOfGroups

public boolean isSetListOfGroups()

Returns:

readAttribute

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

setListOfGroups

public void setListOfGroups(org.sbml.jsbml.ListOf<Group> listOfGroups)

Parameters:

listOfGroups -

toString

public String toString()

Overrides:

toString in class org.sbml.jsbml.AbstractTreeNode

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.

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface org.sbml.jsbml.ext.SBasePlugin

Overrides:

writeXMLAttributes in class org.sbml.jsbml.ext.AbstractSBasePlugin