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:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

Direct Known Subclasses:

CompModelPlugin, CompSBMLDocumentPlugin

public class CompSBasePlugin
extends AbstractSBasePlugin

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

Author:

Nicolas Rodriguez

See Also:

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

Method Summary

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	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<ReplacedElement>	getListOfReplacedElements() Returns the listOfReplacedElements
int	getNumReplacedElements() Returns the number of ReplacedElement of this CompSBasePlugin.
String	getPackageName()
SBase	getParent()
SBase	getParentSBMLObject()
String	getPrefix()
ReplacedBy	getReplacedBy() Returns the value of replacedBy
ReplacedElement	getReplacedElement(int index) Returns the n-th ReplacedElement object in this CompSBasePlugin.
ReplacedElement	getReplacedElement(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.
String	getURI()
int	hashCode()
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(String attributeName, String prefix, String value)
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.
boolean	unsetListOfReplacedElements() Returns true, if listOfReplacedElements contained at least one element, otherwise false
boolean	unsetReplacedBy() Unsets the variable replacedBy
Map<String,String>	writeXMLAttributes()

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

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

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, 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, isLeaf

Constructor Detail

CompSBasePlugin

public CompSBasePlugin()

Creates an CompSBasePlugin instance

CompSBasePlugin

public CompSBasePlugin(SBase extendedSBase)

Creates a CompSBasePlugin instance with a level and version.

Parameters:

extendedSBase - the core SBase that is extended.

CompSBasePlugin

public CompSBasePlugin(CompSBasePlugin obj)

Clone constructor

Parameters:

obj - the instance to clone

Method Detail

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getParent

public SBase getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBase getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

clone

public CompSBasePlugin clone()

clones this class

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

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

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.

Parameters:

replacedBy - the value of replacedBy

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:

index - an index

Returns:

the ReplacedElement with the given index if it exists.

Throws:

IndexOutOfBoundsException - if the index is out of range: (index < 0 || index >= size())

getReplacedElement

public ReplacedElement getReplacedElement(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.

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

use getReplacedElementCount()

setListOfReplacedElements

public void setListOfReplacedElements(ListOf<ReplacedElement> listOfReplacedElements)

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

Parameters:

listOfReplacedElements - the list of ReplacedElements.

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 - the element to be added to the list

Returns:

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

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:

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.

readAttribute

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

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

getAllowsChildren

public boolean getAllowsChildren()

getChildCount

public int getChildCount()

getChildAt

public TreeNode getChildAt(int index)