org.sbml.jsbml.ext.multi

Class MultiCompartmentPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.multi.MultiCompartmentPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class MultiCompartmentPlugin
extends AbstractSBasePlugin

Since:

1.0

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

Constructor Summary

Constructors

Constructor and Description
MultiCompartmentPlugin() Creates an MultiCompartmentPlugin instance.
MultiCompartmentPlugin(Compartment compartment) Creates a MultiCompartmentPlugin instance associated with the given Compartment.
MultiCompartmentPlugin(MultiCompartmentPlugin obj) Clone constructor.

Method Summary

Modifier and Type	Method and Description
boolean	addCompartmentReference(CompartmentReference compartmentReference) Adds a new CompartmentReference to the listOfCompartmentReferences.
MultiCompartmentPlugin	clone()
CompartmentReference	createCompartmentReference() Creates a new CompartmentReference element and adds it to the listOfCompartmentReferences list.
CompartmentReference	createCompartmentReference(String id) Creates a new CompartmentReference element and adds it to the listOfCompartmentReferences list.
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
CompartmentReference	getCompartmentReference(int i) Gets an element from the listOfCompartmentReferences at the given index.
CompartmentReference	getCompartmentReference(String compartmentReferenceId) Gets an element from the listOfCompartmentReferences, with the given id.
int	getCompartmentReferenceCount() Returns the number of CompartmentReferences in this MultiCompartmentPlugin.
String	getCompartmentType() Returns the value of compartmentType.
boolean	getIsType() Returns the value of isType.
ListOf<CompartmentReference>	getListOfCompartmentReferences() Returns the listOfCompartmentReferences.
int	getNumCompartmentReferences() Returns the number of CompartmentReferences in this MultiCompartmentPlugin.
String	getPackageName()
Compartment	getParent()
Compartment	getParentSBMLObject()
String	getPrefix()
String	getURI()
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetCompartmentType() Returns whether compartmentType is set.
boolean	isSetIsType() Returns whether isType is set.
boolean	isSetListOfCompartmentReferences() Returns true if listOfCompartmentReferences contains at least one element.
boolean	isType() Returns the value of isType, return false if isType is not defined.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeCompartmentReference(CompartmentReference compartmentReference) Removes an element from the listOfCompartmentReferences.
CompartmentReference	removeCompartmentReference(int i) Removes an element from the listOfCompartmentReferences at the given index.
CompartmentReference	removeCompartmentReference(String compartmentReferenceId) Removes an element from the listOfCompartmentReferences.
void	setCompartmentType(String compartmentType) Sets the value of compartmentType
void	setIsType(boolean isType) Sets the value of isType
void	setListOfCompartmentReferences(ListOf<CompartmentReference> listOfCompartmentReferences) Sets the given ListOf<CompartmentReference>.
boolean	unsetCompartmentType() Unsets the variable compartmentType.
boolean	unsetIsType() Unsets the variable isType.
boolean	unsetListOfCompartmentReferences() Returns true if listOfCompartmentReferences contains at least one element, otherwise false.
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

MultiCompartmentPlugin

public MultiCompartmentPlugin()

Creates an MultiCompartmentPlugin instance.

MultiCompartmentPlugin

public MultiCompartmentPlugin(Compartment compartment)

Creates a MultiCompartmentPlugin instance associated with the given Compartment.

Parameters:

compartment - the compartment to extend.

MultiCompartmentPlugin

public MultiCompartmentPlugin(MultiCompartmentPlugin obj)

Clone constructor.

Parameters:

obj - the MultiCompartmentPlugin to clone

Method Detail

clone

public MultiCompartmentPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getParent

public Compartment getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public Compartment getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

isSetListOfCompartmentReferences

public boolean isSetListOfCompartmentReferences()

Returns true if listOfCompartmentReferences contains at least one element.

Returns:

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

getListOfCompartmentReferences

public ListOf<CompartmentReference> getListOfCompartmentReferences()

Returns the listOfCompartmentReferences. Creates it if it does not already exist.

Returns:

the listOfCompartmentReferences.

setListOfCompartmentReferences

public void setListOfCompartmentReferences(ListOf<CompartmentReference> listOfCompartmentReferences)

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

Parameters:

listOfCompartmentReferences - the list of CompartmentReferences to set

unsetListOfCompartmentReferences

public boolean unsetListOfCompartmentReferences()

Returns true if listOfCompartmentReferences contains at least one element, otherwise false.

Returns:

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

addCompartmentReference

public boolean addCompartmentReference(CompartmentReference compartmentReference)

Adds a new CompartmentReference to the listOfCompartmentReferences.

The listOfCompartmentReferences is initialized if necessary.

Parameters:

compartmentReference - the element to add to the list

Returns:

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

See Also:

Collection.add(Object)

removeCompartmentReference

public boolean removeCompartmentReference(CompartmentReference compartmentReference)

Removes an element from the listOfCompartmentReferences.

Parameters:

compartmentReference - 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)

removeCompartmentReference

public CompartmentReference removeCompartmentReference(String compartmentReferenceId)

Removes an element from the listOfCompartmentReferences.

Parameters:

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

Returns:

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

removeCompartmentReference

public CompartmentReference removeCompartmentReference(int i)

Removes an element from the listOfCompartmentReferences at the given index.

Parameters:

i - the index where to remove the CompartmentReference.

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 ((i < 0) || (i > listOfCompartmentReferences)).

createCompartmentReference

public CompartmentReference createCompartmentReference()

Creates a new CompartmentReference element and adds it to the listOfCompartmentReferences list.

Returns:

the newly created element, i.e., the last item in the listOfCompartmentReferences

createCompartmentReference

public CompartmentReference createCompartmentReference(String id)

Creates a new CompartmentReference element and adds it to the listOfCompartmentReferences list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created CompartmentReference element, which is the last element in the listOfCompartmentReferences.

getCompartmentReference

public CompartmentReference getCompartmentReference(int i)

Gets an element from the listOfCompartmentReferences at the given index.

Parameters:

i - the index of the CompartmentReference element to get.

Returns:

an element from the listOfCompartmentReferences 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).

getCompartmentReference

public CompartmentReference getCompartmentReference(String compartmentReferenceId)

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

Parameters:

compartmentReferenceId - the id of the CompartmentReference element to get.

Returns:

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

getCompartmentReferenceCount

public int getCompartmentReferenceCount()

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

Returns:

the number of CompartmentReferences in this MultiCompartmentPlugin.

getNumCompartmentReferences

public int getNumCompartmentReferences()

Returns the number of CompartmentReferences in this MultiCompartmentPlugin.

Returns:

the number of CompartmentReferences in this MultiCompartmentPlugin.

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

same as getCompartmentReferenceCount()

getCompartmentType

public String getCompartmentType()

Returns the value of compartmentType.

Returns:

the value of compartmentType.

isSetCompartmentType

public boolean isSetCompartmentType()

Returns whether compartmentType is set.

Returns:

whether compartmentType is set.

setCompartmentType

public void setCompartmentType(String compartmentType)

Sets the value of compartmentType

Parameters:

compartmentType - the value of compartmentType to be set.

unsetCompartmentType

public boolean unsetCompartmentType()

Unsets the variable compartmentType.

Returns:

true if compartmentType was set before, otherwise false.

getIsType

public boolean getIsType()

Returns the value of isType.

Returns:

the value of isType.

isType

public boolean isType()

Returns the value of isType, return false if isType is not defined.

Returns:

the value of isType, return false if isType is not defined.

isSetIsType

public boolean isSetIsType()

Returns whether isType is set.

Returns:

whether isType is set.

setIsType

public void setIsType(boolean isType)

Sets the value of isType

Parameters:

isType - the value of isType to be set.

unsetIsType

public boolean unsetIsType()

Unsets the variable isType.

Returns:

true if isType was set before, otherwise false.

getAllowsChildren

public boolean getAllowsChildren()

getChildCount

public int getChildCount()

getChildAt

public TreeNode getChildAt(int index)

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

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

readAttribute

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