org.sbml.jsbml.ext.distrib

Class DistribSBasePlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.distrib.DistribSBasePlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class DistribSBasePlugin
extends AbstractSBasePlugin

Since:

1.1

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

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

elementNamespace, extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
DistribSBasePlugin() Creates a new DistribSBasePlugin instance.
DistribSBasePlugin(DistribSBasePlugin obj) Creates a new DistribSBasePlugin instance, cloned from the input parameter.
DistribSBasePlugin(SBase sbase) Creates a new DistribSBasePlugin instance.

Method Summary

Modifier and Type	Method and Description
boolean	addUncertainty(Uncertainty uncertainty) Adds a new Uncertainty to the listOfUncertainties.
AbstractSBasePlugin	clone()
Uncertainty	createUncertainty() Creates a new Uncertainty element and adds it to the listOfUncertainties list.
Uncertainty	createUncertainty(String id) Creates a new Uncertainty element and adds it to the listOfUncertainties list.
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<Uncertainty>	getListOfUncertainties() Returns the listOfUncertainties.
int	getNumUncertainties() Returns the number of Uncertaintys in this DistribSBasePlugin.
String	getPackageName()
String	getPrefix()
Uncertainty	getUncertainty(int i) Gets an element from the listOfUncertainties at the given index.
Uncertainty	getUncertainty(String uncertaintyId) Gets an element from the listOfUncertainties, with the given id.
int	getUncertaintyCount() Returns the number of Uncertaintys in this DistribSBasePlugin.
String	getURI()
boolean	isSetListOfUncertainties() Returns true if listOfUncertainties contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
Uncertainty	removeUncertainty(int i) Removes an element from the listOfUncertainties at the given index.
Uncertainty	removeUncertainty(String uncertaintyId) Removes an element from the listOfUncertainties.
boolean	removeUncertainty(Uncertainty uncertainty) Removes an element from the listOfUncertainties.
void	setListOfUncertainties(ListOf<Uncertainty> listOfUncertainties) Sets the given ListOf<Uncertainty>.
boolean	unsetListOfUncertainties() Returns true if listOfUncertainties contains at least one element, otherwise false.

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

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getParentSBMLObject, getSBMLDocument, getVersion, hashCode, isSetExtendedSBase, isSetPackageVersion, removeFromParent, setExtendedSBase, setNamespace, setPackageVersion, writeXMLAttributes

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, isCloningInProgress, isInvalidSBMLAllowed, 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.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, getParent, isLeaf

Constructor Detail

DistribSBasePlugin

public DistribSBasePlugin()

Creates a new DistribSBasePlugin instance.

DistribSBasePlugin

public DistribSBasePlugin(SBase sbase)

Creates a new DistribSBasePlugin instance.

Parameters:

sbase - the SBase to be extended.

DistribSBasePlugin

public DistribSBasePlugin(DistribSBasePlugin obj)

Creates a new DistribSBasePlugin instance, cloned from the input parameter.

Parameters:

obj - the DistribSBasePlugin to clone

Method Detail

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getChildCount

public int getChildCount()

getChildAt

public TreeNode getChildAt(int index)

getAllowsChildren

public boolean getAllowsChildren()

clone

public AbstractSBasePlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

readAttribute

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

isSetListOfUncertainties

public boolean isSetListOfUncertainties()

Returns true if listOfUncertainties contains at least one element.

Returns:

true if listOfUncertainties contains at least one element, otherwise false.

getListOfUncertainties

public ListOf<Uncertainty> getListOfUncertainties()

Returns the listOfUncertainties. Creates it if it does not already exist.

Returns:

the listOfUncertainties.

setListOfUncertainties

public void setListOfUncertainties(ListOf<Uncertainty> listOfUncertainties)

Sets the given ListOf<Uncertainty>. If listOfUncertainties was defined before and contains some elements, they are all unset.

Parameters:

listOfUncertainties - the list to set

unsetListOfUncertainties

public boolean unsetListOfUncertainties()

Returns true if listOfUncertainties contains at least one element, otherwise false.

Returns:

true if listOfUncertainties contains at least one element, otherwise false.

addUncertainty

public boolean addUncertainty(Uncertainty uncertainty)

Adds a new Uncertainty to the listOfUncertainties.

The listOfUncertainties is initialized if necessary.

Parameters:

uncertainty - the element to add to the list

Returns:

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

See Also:

Collection.add(Object)

removeUncertainty

public boolean removeUncertainty(Uncertainty uncertainty)

Removes an element from the listOfUncertainties.

Parameters:

uncertainty - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeUncertainty

public Uncertainty removeUncertainty(String uncertaintyId)

Removes an element from the listOfUncertainties.

Parameters:

uncertaintyId - the id of the element to be removed from the list.

Returns:

the removed element, if it was successfully found and removed or null.

removeUncertainty

public Uncertainty removeUncertainty(int i)

Removes an element from the listOfUncertainties at the given index.

Parameters:

i - the index where to remove the Uncertainty.

Returns:

the specified element if it was successfully found and removed.

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfUncertainties)).

createUncertainty

public Uncertainty createUncertainty()

Creates a new Uncertainty element and adds it to the listOfUncertainties list.

Returns:

the newly created element, i.e., the last item in the listOfUncertainties

createUncertainty

public Uncertainty createUncertainty(String id)

Creates a new Uncertainty element and adds it to the listOfUncertainties list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created Uncertainty element, which is the last element in the listOfUncertainties.

getUncertainty

public Uncertainty getUncertainty(int i)

Gets an element from the listOfUncertainties at the given index.

Parameters:

i - the index of the Uncertainty element to get.

Returns:

an element from the listOfUncertainties at the given index.

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

getUncertainty

public Uncertainty getUncertainty(String uncertaintyId)

Gets an element from the listOfUncertainties, with the given id.

Parameters:

uncertaintyId - the id of the Uncertainty element to get.

Returns:

an element from the listOfUncertainties with the given id or null.

getUncertaintyCount

public int getUncertaintyCount()

Returns the number of Uncertaintys in this DistribSBasePlugin.

Returns:

the number of Uncertaintys in this DistribSBasePlugin.

getNumUncertainties

public int getNumUncertainties()

Returns the number of Uncertaintys in this DistribSBasePlugin.

Returns:

the number of Uncertaintys in this DistribSBasePlugin.

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

same as getUncertaintyCount()