org.sbml.jsbml.ext.req

Class ReqSBasePlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.req.ReqSBasePlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, org.sbml.jsbml.ext.SBasePlugin, org.sbml.jsbml.util.TreeNodeWithChangeSupport

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

Represents the extended SBase as define in the req package.

The Required Elements package is an exceedingly small package that allows model writers to declare specifically which components of the model have had their mathematics changed, by which package or annotation, and whether interpretation of those components in the absence of any package information results in a workable model. It accomplishes this by defining a class that can be added as an optional child of any SBML element with mathematical meaning.

To define that an SBase can have some optional ChangedMath children.

Since:

1.0

Version:

$Rev$

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, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
ReqSBasePlugin() Creates an ReqSBasePlugin instance
ReqSBasePlugin(ReqSBasePlugin obj) Clone constructor
ReqSBasePlugin(org.sbml.jsbml.SBase sbase) Creates a ReqSBasePlugin instance associated with the given SBase.

Method Summary

Modifier and Type	Method and Description
boolean	addChangedMath(ChangedMath changedMath) Adds a new ChangedMath to the listOfChangedMaths.
ReqSBasePlugin	clone() clones this class
ChangedMath	createChangedMath() Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
ChangedMath	createChangedMath(String id) Creates a new ChangedMath element and adds it to the ListOfMathChangeds list
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
org.sbml.jsbml.ListOf<ChangedMath>	getListOfChangedMaths() Returns the listOfChangedMaths.
String	getPackageName()
String	getPrefix()
String	getURI()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetListOfChangedMaths() Returns true, if listOfChangedMaths contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeChangedMath(ChangedMath changedMath) Removes an element from the listOfChangedMaths.
void	removeChangedMath(int i) Removes an element from the listOfChangedMaths at the given index.
void	removeChangedMath(String id) Removes an element from the listOfChangedMaths with the given id.
void	setListOfChangedMaths(org.sbml.jsbml.ListOf<ChangedMath> listOfChangedMaths) Sets the given ListOf<ChangedMath>.
boolean	unsetListOfChangedMaths() Removes all of the elements from this list of ChangedMaths.

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, 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, getParent, isLeaf

Constructor Detail

ReqSBasePlugin

public ReqSBasePlugin()

Creates an ReqSBasePlugin instance

ReqSBasePlugin

public ReqSBasePlugin(org.sbml.jsbml.SBase sbase)

Creates a ReqSBasePlugin instance associated with the given SBase.

Parameters:

sbase -

ReqSBasePlugin

public ReqSBasePlugin(ReqSBasePlugin obj)

Clone constructor

Parameters:

obj -

Method Detail

clone

public ReqSBasePlugin clone()

clones this class

Specified by:

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

Overrides:

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

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

readAttribute

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

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getAllowsChildren

public boolean getAllowsChildren()

isSetListOfChangedMaths

public boolean isSetListOfChangedMaths()

Returns true, if listOfChangedMaths contains at least one element.

Returns:

true, if listOfChangedMaths contains at least one element, otherwise false

getListOfChangedMaths

public org.sbml.jsbml.ListOf<ChangedMath> getListOfChangedMaths()

Returns the listOfChangedMaths. Creates it if it is not already existing.

Returns:

the listOfChangedMaths

setListOfChangedMaths

public void setListOfChangedMaths(org.sbml.jsbml.ListOf<ChangedMath> listOfChangedMaths)

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

Parameters:

listOfChangedMaths -

unsetListOfChangedMaths

public boolean unsetListOfChangedMaths()

Removes all of the elements from this list of ChangedMaths.

Returns:

true, if listOfChangedMaths contained at least one element, otherwise false

addChangedMath

public boolean addChangedMath(ChangedMath changedMath)

Adds a new ChangedMath to the listOfChangedMaths.

The listOfChangedMaths is initialized if necessary.

Parameters:

changedMath - the element to add to the list

Returns:

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

removeChangedMath

public boolean removeChangedMath(ChangedMath changedMath)

Removes an element from the listOfChangedMaths.

Parameters:

changedMath - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeChangedMath

public void removeChangedMath(int i)

Removes an element from the listOfChangedMaths at the given index.

Parameters:

i - - the index where to remove the ChangedMath

Throws:

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

removeChangedMath

public void removeChangedMath(String id)

Removes an element from the listOfChangedMaths with the given id.

Parameters:

id - - the id of the ChangedMath to be removed

createChangedMath

public ChangedMath createChangedMath()

Creates a new ChangedMath element and adds it to the ListOfMathChangeds list

Returns:

createChangedMath

public ChangedMath createChangedMath(String id)

Creates a new ChangedMath element and adds it to the ListOfMathChangeds list

Parameters:

id -

Returns:

a new ChangedMath element

getChildCount

public int getChildCount()

getChildAt

public TreeNode getChildAt(int index)