ArraysSBasePlugin

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.ext.AbstractSBasePlugin
  - - org.sbml.jsbml.ext.arrays.ArraysSBasePlugin

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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: 1960 $

Author:

Leandro Watanabe

See Also:
Dimension, Index, Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`private ListOf<Dimension>`	`listOfDimensions`
`private ListOf<Index>`	`listOfIndices`
`private static org.apache.log4j.Logger`	`logger` A `Logger` for this class.
`(package private) java.util.Map<java.lang.String,Dimension>`	`mapOfDimensions` Maps between the `Dimension` identifiers and themselves.
`private static long`	`serialVersionUID`

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

Methods
Modifier and Type	Method and Description
`boolean`	`accept(SBase sbase)` Returns true if this `IdManager` can register or unregister the given `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()` clones this class
`Dimension`	`createDimension()` Creates a new Dimension element and adds it to the ListOfDimensions list.
`Dimension`	`createDimension(java.lang.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(java.lang.Object obj)`
`boolean`	`getAllowsChildren()`
`javax.swing.tree.TreeNode`	`getChildAt(int childIndex)`
`int`	`getChildCount()`
`Dimension`	`getDimension(int i)` Gets an element from the listOfDimensions at the given index.
`Dimension`	`getDimension(java.lang.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 `Dimension`s in this `ArraysSBasePlugin`.
`java.lang.String`	`getElementNamespace()` Returns the XML namespace (URI) of the package extension of this plugin object.
`Index`	`getIndex(int i)` Gets an element from the listOfIndices at the given index.
`Index`	`getIndex(int dim, java.lang.String attribute)` Gets an element from the listOfIndices based on array dimension and referenced attribute.
`int`	`getIndexCount()` Returns the number of `Index`s in this `ArraysSBasePlugin`.
`ListOf<Dimension>`	`getListOfDimensions()` Returns the listOfDimensions.
`ListOf<Index>`	`getListOfIndices()` Returns the listOfIndices.
`int`	`getNumDimensions()` Returns the number of `Dimension`s in this `ArraysSBasePlugin`.
`int`	`getNumIndices()` Returns the number of `Index`s in this `ArraysSBasePlugin`.
`java.lang.String`	`getPackageName()` Returns the package name of this plugin object.
`java.lang.String`	`getPrefix()` Returns the prefix of the package extension of this plugin object.
`java.lang.String`	`getURI()` Gets the URI to which this element belongs to.
`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(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Reads and sets the attribute if it is know from this `SBasePlugin`.
`boolean`	`register(SBase sbase)` Registers the given `SBase` element and all of it's children in this `IdManager`.
`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(java.lang.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)` Unregisters the given `SBase` element and all of it's children in this `IdManager`.
`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`.
`java.util.Map<java.lang.String,java.lang.String>`	`writeXMLAttributes()` Returns a `Map` containing the XML attributes of this object.

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 java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface javax.swing.tree.TreeNode
children, getIndex, getParent, isLeaf

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    See Also:
    Constant Field Values
  - logger
```
private static final transient org.apache.log4j.Logger logger
```
    A Logger for this class.
  - mapOfDimensions
```
java.util.Map<java.lang.String,Dimension> mapOfDimensions
```
    Maps between the Dimension identifiers and themselves.
  - listOfIndices
```
private ListOf<Index> listOfIndices
```
  - listOfDimensions
```
private ListOf<Dimension> listOfDimensions
```
- 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()
```
    clones this class
    
    Specified by:
    
    clone in interface SBasePlugin
    
    Specified by:
    
    clone in class AbstractSBasePlugin
    
    Returns:
    a new instance of SBasePlugin from this SBasePlugin.
  - 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:
    field - 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:
    
    java.lang.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:
    
    java.lang.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,
             java.lang.String attribute)
```
    Gets an element from the listOfIndices based on array dimension and referenced attribute.
    
    Parameters:
    i - the index of the Index element to get.
    
    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.
  - 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(java.lang.String fieldId)
```
    Removes an element from the listOfDimensions.
    
    Parameters:
    id - 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:
    
    java.lang.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(java.lang.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:
    
    java.lang.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(java.lang.String fieldId)
```
    Gets an element from the listOfDimensions, with the given id.
    
    Parameters:
    id - 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.
  - getElementNamespace
```
public java.lang.String getElementNamespace()
```
    Description copied from interface: SBasePlugin
    
    Returns the XML namespace (URI) of the package extension of this plugin object.
    
    Specified by:
    
    getElementNamespace in interface SBasePlugin
    
    Returns:
    the URI of the package extension of this plugin object.
  - getPackageName
```
public java.lang.String getPackageName()
```
    Description copied from interface: SBasePlugin
    
    Returns the package name of this plugin object.
    
    Specified by:
    
    getPackageName in interface SBasePlugin
    
    Returns:
    the package name of this plugin object.
  - getPrefix
```
public java.lang.String getPrefix()
```
    Description copied from interface: SBasePlugin
    
    Returns the prefix of the package extension of this plugin object.
    
    Specified by:
    
    getPrefix in interface SBasePlugin
    
    Returns:
    the prefix of the package extension of this plugin object.
  - getURI
```
public java.lang.String getURI()
```
    Description copied from interface: SBasePlugin
    
    Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/' Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. If not found it will return the result of getElementNamespace
    
    Specified by:
    
    getURI in interface SBasePlugin
    
    Returns:
    the URI for this element
  - getAllowsChildren
```
public boolean getAllowsChildren()
```
    Specified by:
    
    getAllowsChildren in interface javax.swing.tree.TreeNode
  - getChildAt
```
public javax.swing.tree.TreeNode getChildAt(int childIndex)
```
    Specified by:
    
    getChildAt in interface javax.swing.tree.TreeNode
  - getChildCount
```
public int getChildCount()
```
    Specified by:
    
    getChildCount in interface javax.swing.tree.TreeNode
  - readAttribute
```
public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)
```
    Description copied from interface: SBasePlugin
    
    Reads and sets the attribute if it is know from this SBasePlugin.
    
    Specified by:
    
    readAttribute in interface SBasePlugin
    
    Parameters:
    attributeName - localName of the XML attribute
    prefix - prefix of the XML attribute
    value - value of the XML attribute
    
    Returns:
    true if the attribute has been successfully read.
  - writeXMLAttributes
```
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
```
    Description copied from interface: SBasePlugin
    
    Returns a Map containing the XML attributes of this object.
    
    Specified by:
    
    writeXMLAttributes in interface SBasePlugin
    
    Overrides:
    
    writeXMLAttributes in class AbstractSBasePlugin
    
    Returns:
    a Map containing the XML attributes of this object.
  - accept
```
public boolean accept(SBase sbase)
```
    Description copied from interface: IdManager
    
    Returns true if this IdManager can register or unregister the given SBase.
    
    Specified by:
    
    accept in interface IdManager
    
    Returns:
    true if this IdManager can register or unregister the given SBase.
  - register
```
public boolean register(SBase sbase)
```
    Description copied from interface: IdManager
    
    Registers the given SBase element and all of it's children in this IdManager.
    
    Specified by:
    
    register in interface IdManager
    
    Returns:
    true if this operation was successfully performed, false otherwise.
  - unregister
```
public boolean unregister(SBase sbase)
```
    Description copied from interface: IdManager
    
    Unregisters the given SBase element and all of it's children in this IdManager.
    
    Specified by:
    
    unregister in interface IdManager
    
    Returns:
    true if this operation was successfully performed, false otherwise.
  - hashCode
```
public int hashCode()
```
    Specified by:
    
    hashCode in interface SBasePlugin
    
    Overrides:
    
    hashCode in class AbstractSBasePlugin
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Specified by:
    
    equals in interface SBasePlugin
    
    Overrides:
    
    equals in class AbstractSBasePlugin

Class ArraysSBasePlugin

Field Summary

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

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

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

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

Methods inherited from interface javax.swing.tree.TreeNode

Field Detail

serialVersionUID

logger

mapOfDimensions

listOfIndices

listOfDimensions

Constructor Detail

ArraysSBasePlugin

ArraysSBasePlugin

ArraysSBasePlugin

Method Detail

clone

initDefaults

isSetListOfIndices

getListOfIndices

setListOfIndices

unsetListOfIndices

addIndex

removeIndex

removeIndexByArrayDimension

removeIndex

createIndex

getIndex

getIndex

getIndexCount

getNumIndices

isSetListOfDimensions

getListOfDimensions

setListOfDimensions

unsetListOfDimensions

addDimension

removeDimension

removeDimension

removeDimensionByArrayDimension

removeDimension

createDimension

createDimension

getDimension

getDimensionByArrayDimension

getDimension

getDimensionCount

getNumDimensions

getElementNamespace

getPackageName

getPrefix

getURI

getAllowsChildren

getChildAt

getChildCount

readAttribute

writeXMLAttributes

accept

register

unregister

hashCode

equals