org.sbml.jsbml.ext.comp

Class CompModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.comp.CompSBasePlugin

org.sbml.jsbml.ext.comp.CompModelPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, IdManager, TreeNodeWithChangeSupport

public class CompModelPlugin
extends CompSBasePlugin
implements IdManager

Adds two lists, one for holding Submodels and the other for holding Ports.

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
CompModelPlugin(CompModelPlugin obj) Creates a new CompModelPlugin instance that is a copy of the current CompModelPlugin.
CompModelPlugin(Model model) Creates a new CompModelPlugin instance, associated with the given Model

Method Summary

Modifier and Type	Method and Description
boolean	accept(SBase sbase)
boolean	addPort(Port port) Adds a new Port to the listOfPorts.
boolean	addSubmodel(Submodel submodel) Adds a new Submodel to the listOfSubmodels.
CompModelPlugin	clone() clones this class
Port	createPort() Creates a new Port element and adds it to the ListOfPorts list
Port	createPort(String id) Creates a new Port element and adds it to the ListOfPorts list
Submodel	createSubmodel() Creates a new Submodel element and adds it to the ListOfSubmodels list
Submodel	createSubmodel(String id) Creates a new Submodel element and adds it to the ListOfSubmodels list
boolean	equals(Object obj)
Port	findPort(String id) Returns a Port element that has the given 'id' within this Model or null if no such element can be found.
boolean	getAllowsChildren()
TreeNode	getChildAt(int childIndex)
int	getChildCount()
ListOf<Port>	getListOfPorts() Returns the listOfPorts.
ListOf<Submodel>	getListOfSubmodels() Returns the listOfSubmodels.
int	getNumPorts() Returns the number of Port of this CompModelPlugin.
int	getNumSubmodels() Returns the number of Submodel of this CompModelPlugin.
Port	getPort(int index) Returns the n-th Port object in this CompModelPlugin.
Port	getPort(String id) Returns a Port element that has the given 'id' within this CompModelPlugin or null if no such element can be found.
int	getPortCount() Returns the number of Port objects in this CompModelPlugin.
Submodel	getSubmodel(int index) Returns the n-th Submodel object in this CompModelPlugin.
Submodel	getSubmodel(String id) Returns a Submodel element that has the given 'id' within this CompModelPlugin or null if no such element can be found.
int	getSubmodelCount() Returns the number of Submodel objects in this CompModelPlugin.
int	hashCode()
boolean	isSetListOfPorts() Returns true, if listOfPorts contains at least one element.
boolean	isSetListOfSubmodels() Returns true, if listOfSubmodels contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	register(SBase sbase)
void	removePort(int i) Removes an element from the listOfPorts at the given index.
boolean	removePort(Port port) Removes an element from the listOfPorts.
void	removeSubmodel(int i) Removes an element from the listOfSubmodels at the given index.
boolean	removeSubmodel(String id) Removes an element from the listOfSubmodels.
boolean	removeSubmodel(Submodel submodel) Removes an element from the listOfSubmodels.
void	setListOfPorts(ListOf<Port> listOfPorts) Sets the optional ListOf<Port>.
void	setListOfSubmodels(ListOf<Submodel> listOfSubmodels) Sets the optional ListOf<Submodel>.
boolean	unregister(SBase sbase)
boolean	unsetListOfPorts() Returns true, if listOfPorts contain at least one element, otherwise false
boolean	unsetListOfSubmodels() Returns true, if listOfSubmodels contain at least one element, otherwise false
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.comp.CompSBasePlugin

addReplacedElement, createReplacedBy, createReplacedElement, getListOfReplacedElements, getNumReplacedElements, getPackageName, getParent, getParentSBMLObject, getPrefix, getReplacedBy, getReplacedElement, getReplacedElement, getReplacedElementCount, getURI, initDefaults, isSetListOfReplacedElements, isSetReplacedBy, removeReplacedElement, removeReplacedElement, setListOfReplacedElements, setReplacedBy, unsetListOfReplacedElements, unsetReplacedBy

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

CompModelPlugin

public CompModelPlugin(CompModelPlugin obj)

Creates a new CompModelPlugin instance that is a copy of the current CompModelPlugin.

Parameters:

obj - the CompModelPlugin to clone.

CompModelPlugin

public CompModelPlugin(Model model)

Creates a new CompModelPlugin instance, associated with the given Model

Parameters:

model - the extended core Model

Method Detail

addPort

public boolean addPort(Port port)

Adds a new Port to the listOfPorts.

The listOfPorts is initialized if necessary.

Parameters:

port - the element to add to the list

Returns:

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

addSubmodel

public boolean addSubmodel(Submodel submodel)

Adds a new Submodel to the listOfSubmodels.

The listOfSubmodels is initialized if necessary.

Parameters:

submodel - the element to add to the list

Returns:

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

clone

public CompModelPlugin clone()

Description copied from class: CompSBasePlugin

clones this class

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class CompSBasePlugin

hashCode

public int hashCode()

Specified by:

hashCode in interface SBasePlugin

Overrides:

hashCode in class CompSBasePlugin

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBasePlugin

Overrides:

equals in class CompSBasePlugin

createPort

public Port createPort()

Creates a new Port element and adds it to the ListOfPorts list

Returns:

a new Port instance.

createPort

public Port createPort(String id)

Creates a new Port element and adds it to the ListOfPorts list

Parameters:

id - the id

Returns:

a new Port element

createSubmodel

public Submodel createSubmodel()

Creates a new Submodel element and adds it to the ListOfSubmodels list

Returns:

a new Submodel element

createSubmodel

public Submodel createSubmodel(String id)

Creates a new Submodel element and adds it to the ListOfSubmodels list

Parameters:

id - the id

Returns:

a new Submodel element

findPort

public Port findPort(String id)

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

Parameters:

id - an id indicating a Port element of the Model.

Returns:

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

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class CompSBasePlugin

getChildAt

public TreeNode getChildAt(int childIndex)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class CompSBasePlugin

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class CompSBasePlugin

getListOfPorts

public ListOf<Port> getListOfPorts()

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

Returns:

the listOfPorts

getListOfSubmodels

public ListOf<Submodel> getListOfSubmodels()

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

Returns:

the listOfSubmodels

getNumPorts

public int getNumPorts()

Returns the number of Port of this CompModelPlugin.

Returns:

the number of Port of this CompModelPlugin.

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

use getPortCount()

getNumSubmodels

public int getNumSubmodels()

Returns the number of Submodel of this CompModelPlugin.

Returns:

the number of Submodel of this CompModelPlugin.

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

use getSubmodelCount()

getPort

public Port getPort(int index)

Returns the n-th Port object in this CompModelPlugin.

Parameters:

index - an index

Returns:

the Port with the given index if it exists.

Throws:

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

getPort

public Port getPort(String id)

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

Parameters:

id - an id indicating a Port element of the CompModelPlugin.

Returns:

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

getPortCount

public int getPortCount()

Returns the number of Port objects in this CompModelPlugin.

Returns:

the number of Port objects in this CompModelPlugin.

getSubmodel

public Submodel getSubmodel(int index)

Returns the n-th Submodel object in this CompModelPlugin.

Parameters:

index - an index

Returns:

the Submodel with the given index if it exists.

Throws:

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

getSubmodel

public Submodel getSubmodel(String id)

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

Parameters:

id - an id indicating a Submodel element of the CompModelPlugin.

Returns:

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

getSubmodelCount

public int getSubmodelCount()

Returns the number of Submodel objects in this CompModelPlugin.

Returns:

the number of Submodel objects in this CompModelPlugin.

isSetListOfPorts

public boolean isSetListOfPorts()

Returns true, if listOfPorts contains at least one element.

Returns:

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

isSetListOfSubmodels

public boolean isSetListOfSubmodels()

Returns true, if listOfSubmodels contains at least one element.

Returns:

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

readAttribute

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

Specified by:

readAttribute in interface SBasePlugin

Overrides:

readAttribute in class CompSBasePlugin

removePort

public void removePort(int i)

Removes an element from the listOfPorts at the given index.

Parameters:

i - the index where to remove the Port

Throws:

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

removePort

public boolean removePort(Port port)

Removes an element from the listOfPorts.

Parameters:

port - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeSubmodel

public void removeSubmodel(int i)

Removes an element from the listOfSubmodels at the given index.

Parameters:

i - the index where to remove the Submodel

Throws:

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

removeSubmodel

public boolean removeSubmodel(String id)

Removes an element from the listOfSubmodels.

Parameters:

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

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeSubmodel

public boolean removeSubmodel(Submodel submodel)

Removes an element from the listOfSubmodels.

Parameters:

submodel - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

setListOfPorts

public void setListOfPorts(ListOf<Port> listOfPorts)

Sets the optional ListOf<Port>. If listOfPorts was defined before and contains some elements, they are all unset.

Parameters:

listOfPorts - the list of Ports.

setListOfSubmodels

public void setListOfSubmodels(ListOf<Submodel> listOfSubmodels)

Sets the optional ListOf<Submodel>. If listOfSubmodels was defined before and contains some elements, they are all unset.

Parameters:

listOfSubmodels - the list of Submodels.

unsetListOfPorts

public boolean unsetListOfPorts()

Returns true, if listOfPorts contain at least one element, otherwise false

Returns:

true, if listOfPorts contain at least one element, otherwise false

unsetListOfSubmodels

public boolean unsetListOfSubmodels()

Returns true, if listOfSubmodels contain at least one element, otherwise false

Returns:

true, if listOfSubmodels contain at least one element, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class CompSBasePlugin

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