org.sbml.jsbml.ext.comp

Class CompSBasePlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.comp.CompSBasePlugin

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SBasePlugin, TreeNodeWithChangeSupport

Direct Known Subclasses:

CompModelPlugin, CompSBMLDocumentPlugin

public class CompSBasePlugin
extends AbstractSBasePlugin

The CompSBasePlugin class extends the SBase class by adding an optional ListOfReplacedElements child and a single optional ReplacedBy child.

The CompSBasePlugin class codifies the extensions to the SBase class defined in the 'Hierarchical Model Composition' package (comp). These extensions allows the modeler to define one or more Submodel elements which the parent SBase object replaces, and/or a single Submodel element which replaces the parent SBase object.
This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a Submodel element to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a Submodel element which is to replace the containing SBase object.

If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.

Since:

1.0

Version:

$Rev: 1776 $

Author:

Nicolas Rodriguez

See Also:

ReplacedElement, ReplacedBy, Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
(package private) ListOf<ReplacedElement>	listOfReplacedElements
(package private) ReplacedBy	replacedBy
private static long	serialVersionUID Generated serial version identifier.

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

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addReplacedElement(ReplacedElement replacedElement) Adds a new element to listOfReplacedElements.
CompSBasePlugin	clone() clones this class
ReplacedBy	createReplacedBy() Creates a new ReplacedBy element and sets it in this CompSBasePlugin.
ReplacedElement	createReplacedElement() Creates a new ReplacedElement element and adds it to the ListOfReplacedElements list.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
ListOf<ReplacedElement>	getListOfReplacedElements() Returns the listOfReplacedElements
int	getNumReplacedElements() Returns the number of ReplacedElement of this CompSBasePlugin.
java.lang.String	getPackageName() Returns the package name of this plugin object.
SBase	getParent()
SBase	getParentSBMLObject() Returns the parent SBase object to which this plugin object connected.
java.lang.String	getPrefix() Returns the prefix of the package extension of this plugin object.
ReplacedBy	getReplacedBy() Returns the value of replacedBy
ReplacedElement	getReplacedElement(int index) Returns the n-th ReplacedElement object in this CompSBasePlugin.
ReplacedElement	getReplacedElement(java.lang.String id) Returns a ReplacedElement element that has the given 'id' within this CompSBasePlugin or null if no such element can be found.
int	getReplacedElementCount() Returns the number of ReplacedElement objects in this CompSBasePlugin.
java.lang.String	getURI() Gets the URI to which this element belongs to.
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetListOfReplacedElements() Returns true, if listOfReplacedElements contains at least one element, otherwise false
boolean	isSetReplacedBy() Returns whether replacedBy is set
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.
void	removeReplacedElement(int i) Removes the ith element from the ListOfReplacedElements.
boolean	removeReplacedElement(ReplacedElement replacedElement) Removes an element from listOfReplacedElements.
void	setListOfReplacedElements(ListOf<ReplacedElement> listOfReplacedElements) Sets the listOfReplacedElements.
void	setReplacedBy(ReplacedBy replacedBy) Sets the value of the optional replacedBy element.
java.lang.String	toString()
boolean	unsetListOfReplacedElements() Returns true, if listOfReplacedElements contained at least one element, otherwise false
boolean	unsetReplacedBy() Unsets the variable replacedBy
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

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

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

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

listOfReplacedElements

ListOf<ReplacedElement> listOfReplacedElements

replacedBy

ReplacedBy replacedBy

Constructor Detail

CompSBasePlugin

public CompSBasePlugin()

Creates an CompSBasePlugin instance

CompSBasePlugin

public CompSBasePlugin(SBase extendedSBase)

Creates a CompSBasePlugin instance with a level and version.

Parameters:

level -

version -

CompSBasePlugin

public CompSBasePlugin(CompSBasePlugin obj)

Clone constructor

Method Detail

getElementNamespace

public java.lang.String getElementNamespace()

Description copied from interface: SBasePlugin

Returns the XML namespace (URI) of the package extension of this plugin object.

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.

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.

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

Returns:

the URI for this element

getParent

public SBase getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBase getParentSBMLObject()

Description copied from interface: SBasePlugin

Returns the parent SBase object to which this plugin object connected.

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

Returns:

the parent SBase object to which this plugin object connected.

clone

public CompSBasePlugin 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.

getReplacedBy

public ReplacedBy getReplacedBy()

Returns the value of replacedBy

Returns:

the value of replacedBy

isSetReplacedBy

public boolean isSetReplacedBy()

Returns whether replacedBy is set

Returns:

whether replacedBy is set

setReplacedBy

public void setReplacedBy(ReplacedBy replacedBy)

Sets the value of the optional replacedBy element.

createReplacedBy

public ReplacedBy createReplacedBy()

Creates a new ReplacedBy element and sets it in this CompSBasePlugin.

Returns:

a new ReplacedBy element.

unsetReplacedBy

public boolean unsetReplacedBy()

Unsets the variable replacedBy

Returns:

true, if replacedBy was set before, otherwise false

isSetListOfReplacedElements

public boolean isSetListOfReplacedElements()

Returns true, if listOfReplacedElements contains at least one element, otherwise false

Returns:

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

getReplacedElement

public ReplacedElement getReplacedElement(int index)

Returns the n-th ReplacedElement object in this CompSBasePlugin.

Parameters:

n - an index

Returns:

the ReplacedElement with the given index if it exists.

Throws:

java.lang.IndexOutOfBoundsException

getReplacedElement

public ReplacedElement getReplacedElement(java.lang.String id)

Returns a ReplacedElement element that has the given 'id' within this CompSBasePlugin or null if no such element can be found.

Parameters:

id - an id indicating a ReplacedElement element of the CompSBasePlugin.

Returns:

a ReplacedElement element of the CompSBasePlugin that has the given 'id' as id or null if no element with this 'id' can be found.

getReplacedElementCount

public int getReplacedElementCount()

Returns the number of ReplacedElement objects in this CompSBasePlugin.

Returns:

the number of ReplacedElement objects in this CompSBasePlugin.

getListOfReplacedElements

public ListOf<ReplacedElement> getListOfReplacedElements()

Returns the listOfReplacedElements

Returns:

the listOfReplacedElements

getNumReplacedElements

public int getNumReplacedElements()

Returns the number of ReplacedElement of this CompSBasePlugin.

Returns:

the number of ReplacedElement of this CompSBasePlugin.

setListOfReplacedElements

public void setListOfReplacedElements(ListOf<ReplacedElement> listOfReplacedElements)

Sets the listOfReplacedElements. If there was already some elements defined on listOfReplacedElements, the will be unset beforehand. If present it must contain at least one ReplacedElement object.

Parameters:

listOfReplacedElements -

unsetListOfReplacedElements

public boolean unsetListOfReplacedElements()

Returns true, if listOfReplacedElements contained at least one element, otherwise false

Returns:

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

addReplacedElement

public boolean addReplacedElement(ReplacedElement replacedElement)

Adds a new element to listOfReplacedElements.

listOfReplacedElements is initialized if necessary.

Parameters:

replacedElement -

Returns:

true (as specified by Collection.add)

removeReplacedElement

public boolean removeReplacedElement(ReplacedElement replacedElement)

Removes an element from listOfReplacedElements.

Parameters:

replacedElement - the element to be removed from the list

Returns:

true if this list contained the specified element

See Also:

List.remove(Object)

removeReplacedElement

public void removeReplacedElement(int i)

Removes the ith element from the ListOfReplacedElements.

Parameters:

i - the index of the element to be removed

Throws:

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

createReplacedElement

public ReplacedElement createReplacedElement()

Creates a new ReplacedElement element and adds it to the ListOfReplacedElements list.

Returns:

a new ReplacedElement element.

toString

public java.lang.String toString()

Overrides:

toString in class AbstractTreeNode

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.

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.

getAllowsChildren

public boolean getAllowsChildren()

getChildCount

public int getChildCount()

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)