org.sbml.jsbml.ext.arrays

Class ArraysSBasePlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, IdManager, TreeNodeWithChangeSupport

public class ArraysSBasePlugin
extends AbstractSBasePlugin
implements IdManager

The ArraysSBasePlugin class extends the SBase class by adding an optional ListOfDimensions child and a single optional Index child.

The ArraysSBasePlugin class codifies the extensions to the SBase class defined in the 'Arrays' package. These extensions allows the modeler to define one or more Dimension elements to indicate the parent SBase object is arrayed. In addition, these extensions allows the definition of one or more Index elements to reference the parent SBase that has one or more array dimensions.

Since:

1.0

Version:

$Rev$

Author:

Leandro Watanabe

See Also:

Dimension, Index, Serialized Form

Last modified:

May 9, 2014

Field Summary

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
ArraysSBasePlugin() Creates an ArraysSBasePlugin instance
ArraysSBasePlugin(ArraysSBasePlugin obj) Clone constructor
ArraysSBasePlugin(SBase extendedSBase) Creates an ArraysSBasePlugin with a level and a version.

Method Summary

Modifier and Type	Method and Description
boolean	accept(SBase sbase)
boolean	addDimension(Dimension field) Adds a new Dimension to the listOfDimensions.
boolean	addIndex(Index field) Adds a new Index to the listOfIndices.
ArraysSBasePlugin	clone()
Dimension	createDimension() Creates a new Dimension element and adds it to the ListOfDimensions list.
Dimension	createDimension(String id) Creates a new Dimension element and adds it to the ListOfDimensions list.
Index	createIndex() Creates a new Index element and adds it to the listOfIndices list.
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int childIndex)
int	getChildCount()
Dimension	getDimension(int i) Gets an element from the listOfDimensions at the given index.
Dimension	getDimension(String fieldId) Gets an element from the listOfDimensions, with the given id.
Dimension	getDimensionByArrayDimension(int i) Gets an element from the listOfDimensions at the given arrayDimension.
int	getDimensionCount() Returns the number of Dimensions in this ArraysSBasePlugin.
String	getElementNamespace()
Index	getIndex(int i) Gets an element from the listOfIndices at the given index.
Index	getIndex(int dim, String attribute) Gets an element from the listOfIndices based on array dimension and referenced attribute.
int	getIndexCount() Returns the number of Indexs in this ArraysSBasePlugin.
ListOf<Dimension>	getListOfDimensions() Returns the listOfDimensions.
ListOf<Index>	getListOfIndices() Returns the listOfIndices.
int	getNumDimensions() Returns the number of Dimensions in this ArraysSBasePlugin.
int	getNumIndices() Returns the number of Indexs in this ArraysSBasePlugin.
String	getPackageName()
String	getPrefix()
String	getURI()
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetListOfDimensions() Returns true, if listOfDimensions contains at least one element.
boolean	isSetListOfIndices() Returns true, if listOfIndices contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	register(SBase sbase)
boolean	removeDimension(Dimension field) Removes an element from the listOfDimensions.
Dimension	removeDimension(int i) Removes an element from the listOfDimensions at the given index.
Dimension	removeDimension(String fieldId) Removes an element from the listOfDimensions.
Dimension	removeDimensionByArrayDimension(int arrayDim) Removes an element from the listOfDimensions by array dimension.
boolean	removeIndex(Index field) Removes an element from the listOfIndices.
Index	removeIndex(int i) Removes an element from the listOfIndices at the given index.
boolean	removeIndexByArrayDimension(int arrayDim) Removes an element from the listOfIndices based on array dimension.
void	setListOfDimensions(ListOf<Dimension> listOfDimensions) Sets the given ListOf<Dimension>.
void	setListOfIndices(ListOf<Index> listOfIndices) Sets the given ListOf<Index>.
boolean	unregister(SBase sbase)
boolean	unsetListOfDimensions() Returns true, if listOfDimensions contain at least one element, otherwise false.
boolean	unsetListOfIndices() Returns true, if listOfIndices contain at least one element, otherwise false.
Map<String,String>	writeXMLAttributes()

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

fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getExtendedSBase, getLevel, getPackageVersion, getParentSBMLObject, getSBMLDocument, getVersion, isSetExtendedSBase, removeFromParent, setExtendedSBase

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

ArraysSBasePlugin

public ArraysSBasePlugin()

Creates an ArraysSBasePlugin instance

ArraysSBasePlugin

public ArraysSBasePlugin(SBase extendedSBase)

Creates an ArraysSBasePlugin with a level and a version.

Parameters:

extendedSBase -

ArraysSBasePlugin

public ArraysSBasePlugin(ArraysSBasePlugin obj)

Clone constructor

Method Detail

clone

public ArraysSBasePlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isSetListOfIndices

public boolean isSetListOfIndices()

Returns true, if listOfIndices contains at least one element.

Returns:

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

getListOfIndices

public ListOf<Index> getListOfIndices()

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

Returns:

the listOfIndices.

setListOfIndices

public void setListOfIndices(ListOf<Index> listOfIndices)

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

Parameters:

listOfIndices -

unsetListOfIndices

public boolean unsetListOfIndices()

Returns true, if listOfIndices contain at least one element, otherwise false.

Returns:

true, if listOfIndices contain at least one element, otherwise false.

addIndex

public boolean addIndex(Index field)

Adds a new Index to the listOfIndices.

The listOfIndices is initialized if necessary.

Parameters:

field - the element to add to the list

Returns:

true (as specified by Collection#add)

removeIndex

public boolean removeIndex(Index field)

Removes an element from the listOfIndices.

Parameters:

field - 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)

removeIndexByArrayDimension

public boolean removeIndexByArrayDimension(int arrayDim)

Removes an element from the listOfIndices based on array dimension.

Parameters:

arrayDim - the element with given array dimension to be removed from the list.

Returns:

true if the list contained the specified element with given array dimension and it was removed.

See Also:

List#remove(Object)

removeIndex

public Index removeIndex(int i)

Removes an element from the listOfIndices at the given index.

Parameters:

i - the index where to remove the Index.

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 (index < 0 || index > list.size).

createIndex

public Index createIndex()

Creates a new Index element and adds it to the listOfIndices list.

getIndex

public Index getIndex(int i)

Gets an element from the listOfIndices at the given index.

Parameters:

i - the index of the Index element to get.

Returns:

an element from the listOfIndices 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).

getIndex

public Index getIndex(int dim,
                      String attribute)

Gets an element from the listOfIndices based on array dimension and referenced attribute.

Parameters:

dim - the index of the Index element to get.

attribute -

Returns:

an element from the listOfIndices at the given index.

getIndexCount

public int getIndexCount()

Returns the number of Indexs in this ArraysSBasePlugin.

Returns:

the number of Indexs in this ArraysSBasePlugin.

getNumIndices

public int getNumIndices()

Returns the number of Indexs in this ArraysSBasePlugin.

Returns:

the number of Indexs in this ArraysSBasePlugin.

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

same as getIndexCount()

isSetListOfDimensions

public boolean isSetListOfDimensions()

Returns true, if listOfDimensions contains at least one element.

Returns:

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

getListOfDimensions

public ListOf<Dimension> getListOfDimensions()

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

Returns:

the listOfDimensions.

setListOfDimensions

public void setListOfDimensions(ListOf<Dimension> listOfDimensions)

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

Parameters:

listOfDimensions -

unsetListOfDimensions

public boolean unsetListOfDimensions()

Returns true, if listOfDimensions contain at least one element, otherwise false.

Returns:

true, if listOfDimensions contain at least one element, otherwise false.

addDimension

public boolean addDimension(Dimension field)

Adds a new Dimension to the listOfDimensions.

The listOfDimensions is initialized if necessary.

Parameters:

field - the element to add to the list

Returns:

true (as specified by Collection#add)

removeDimension

public boolean removeDimension(Dimension field)

Removes an element from the listOfDimensions.

Parameters:

field - 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)

removeDimension

public Dimension removeDimension(String fieldId)

Removes an element from the listOfDimensions.

Parameters:

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

Returns:

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

removeDimensionByArrayDimension

public Dimension removeDimensionByArrayDimension(int arrayDim)

Removes an element from the listOfDimensions by array dimension.

Parameters:

arrayDim - the array dimension of the element to be removed from the list.

Returns:

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

removeDimension

public Dimension removeDimension(int i)

Removes an element from the listOfDimensions at the given index.

Parameters:

i - the index where to remove the Dimension.

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 (index < 0 || index > list.size).

createDimension

public Dimension createDimension()

Creates a new Dimension element and adds it to the ListOfDimensions list.

createDimension

public Dimension createDimension(String id)

Creates a new Dimension element and adds it to the ListOfDimensions list.

Returns:

a new Dimension element.

getDimension

public Dimension getDimension(int i)

Gets an element from the listOfDimensions at the given index.

Parameters:

i - the dimension of the Dimension element to get.

Returns:

an element from the listOfDimensions at the given index.

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > 2).

getDimensionByArrayDimension

public Dimension getDimensionByArrayDimension(int i)

Gets an element from the listOfDimensions at the given arrayDimension.

Parameters:

i - the dimension of the Dimension element to get.

Returns:

an element from the listOfDimensions at the given index or null.

getDimension

public Dimension getDimension(String fieldId)

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

Parameters:

fieldId - the id of the Dimension element to get.

Returns:

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

getDimensionCount

public int getDimensionCount()

Returns the number of Dimensions in this ArraysSBasePlugin.

Returns:

the number of Dimensions in this ArraysSBasePlugin.

getNumDimensions

public int getNumDimensions()

Returns the number of Dimensions in this ArraysSBasePlugin.

Returns:

the number of Dimensions in this ArraysSBasePlugin.

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

same as getDimensionCount()

getElementNamespace

public String getElementNamespace()

Specified by:

getElementNamespace in interface SBasePlugin

getPackageName

public String getPackageName()

Specified by:

getPackageName in interface SBasePlugin

getPrefix

public String getPrefix()

Specified by:

getPrefix in interface SBasePlugin

getURI

public String getURI()

Specified by:

getURI in interface SBasePlugin

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

getChildAt

public TreeNode getChildAt(int childIndex)

Specified by:

getChildAt in interface TreeNode

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

readAttribute

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

Specified by:

readAttribute in interface SBasePlugin

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

accept

public boolean accept(SBase sbase)

Specified by:

accept in interface IdManager

register

public boolean register(SBase sbase)

Specified by:

register in interface IdManager

unregister

public boolean unregister(SBase sbase)

Specified by:

unregister in interface IdManager

hashCode

public int hashCode()

Specified by:

hashCode in interface SBasePlugin

Overrides:

hashCode in class AbstractSBasePlugin

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBasePlugin

Overrides:

equals in class AbstractSBasePlugin