org.sbml.jsbml.ext.comp

Class CompSBMLDocumentPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.comp.CompSBasePlugin

org.sbml.jsbml.ext.comp.CompSBMLDocumentPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class CompSBMLDocumentPlugin
extends CompSBasePlugin

Allows SBML documents to contain more than one model.

The top level of an SBMLDocument is a container whose structure is defined by the object class SBML in the SBML Level 3 Version 1 Core specification. In Level 3 Core, this container can contain only one object of class Model. The Hierarchical Model Composition package allows SBML documents to contain more than one model.

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
CompSBMLDocumentPlugin(CompSBMLDocumentPlugin compSBMLDocumentPlugin) Creates a new CompSBMLDocumentPlugin instance.
CompSBMLDocumentPlugin(SBMLDocument doc) Creates a new CompSBMLDocumentPlugin instance.

Method Summary

Modifier and Type	Method and Description
boolean	addExternalModelDefinition(ExternalModelDefinition externalModelDefinition) Adds a new ExternalModelDefinition to the listOfExternalModelDefinitions.
boolean	addModelDefinition(ModelDefinition modelDefinition) Adds a new ModelDefinition to the listOfModelDefinitions.
CompSBMLDocumentPlugin	clone() clones this class
ExternalModelDefinition	createExternalModelDefinition() Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list
ExternalModelDefinition	createExternalModelDefinition(String id) Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list
Model	createModelDefinition() Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list
Model	createModelDefinition(String id) Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int childIndex)
int	getChildCount()
ExternalModelDefinition	getExternalModelDefinition(int index) Returns the n-th ExternalModelDefinition object in this CompSBMLDocumentPlugin.
ExternalModelDefinition	getExternalModelDefinition(String id) Returns a ExternalModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.
int	getExternalModelDefinitionCount() Returns the number of ExternalModelDefinition objects in this CompSBMLDocumentPlugin.
ListOf<ExternalModelDefinition>	getListOfExternalModelDefinitions() Returns the listOfExternalModelDefinitions.
ListOf<ModelDefinition>	getListOfModelDefinitions() Returns the listOfModelDefinitions.
ModelDefinition	getModelDefinition(int index) Returns the n-th ModelDefinition object in this CompSBMLDocumentPlugin.
ModelDefinition	getModelDefinition(String id) Returns a ModelDefinition element that has the given 'id' within this CompSBMLDocumentPlugin or null if no such element can be found.
int	getModelDefinitionCount() Returns the number of ModelDefinition objects in this CompSBMLDocumentPlugin.
int	getNumExternalModelDefinitions() Returns the number of ExternalModelDefinition of this CompSBMLDocumentPlugin.
int	getNumModelDefinitions() Returns the number of ModelDefinition of this CompSBMLDocumentPlugin.
int	hashCode()
boolean	isSetListOfExternalModelDefinitions() Returns true, if listOfExternalModelDefinitions contains at least one element.
boolean	isSetListOfModelDefinitions() Returns true, if listOfModelDefinitions contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeExternalModelDefinition(ExternalModelDefinition externalModelDefinition) Removes an element from the listOfExternalModelDefinitions.
void	removeExternalModelDefinition(int i) Removes an element from the listOfExternalModelDefinitions at the given index.
void	removeExternalModelDefinition(String id) Removes an element from the listOfExternalModelDefinitions with the given id.
void	removeModelDefinition(int i) Removes an element from the listOfModelDefinitions at the given index.
boolean	removeModelDefinition(ModelDefinition modelDefinition) Removes an element from the listOfModelDefinitions.
void	removeModelDefinition(String id) Removes an element from the listOfModelDefinitions with the given id.
void	setListOfExternalModelDefinitions(ListOf<ExternalModelDefinition> listOfExternalModelDefinitions) The listOfExternamModelDefinitions is an optional element of CompSBMLDocumentPlugin and defines external SBML document references within the ExternalModelDefinition object.
void	setListOfModelDefinitions(ListOf<ModelDefinition> listOfModelDefinitions) listOfModelDefinitions is an optional list of CompSBMLDocumentPlugin which specifies ModelDefinitions for the SBML document.
boolean	unsetListOfExternalModelDefinitions() Returns true, if listOfExternalModelDefinitions contain at least one element, otherwise false
boolean	unsetListOfModelDefinitions() Returns true, if listOfModelDefinitions 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

CompSBMLDocumentPlugin

public CompSBMLDocumentPlugin(SBMLDocument doc)

Creates a new CompSBMLDocumentPlugin instance.

Parameters:

doc - the core SBMLDocument to is extended

CompSBMLDocumentPlugin

public CompSBMLDocumentPlugin(CompSBMLDocumentPlugin compSBMLDocumentPlugin)

Creates a new CompSBMLDocumentPlugin instance.

Parameters:

compSBMLDocumentPlugin - the instance to clone

Method Detail

getExternalModelDefinition

public ExternalModelDefinition getExternalModelDefinition(int index)

Returns the n-th ExternalModelDefinition object in this CompSBMLDocumentPlugin.

Parameters:

index - an index

Returns:

the ExternalModelDefinition with the given index if it exists.

Throws:

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

getExternalModelDefinition

public ExternalModelDefinition getExternalModelDefinition(String id)

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

Parameters:

id - an id indicating a ExternalModelDefinition element of the CompSBMLDocumentPlugin.

Returns:

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

getExternalModelDefinitionCount

public int getExternalModelDefinitionCount()

Returns the number of ExternalModelDefinition objects in this CompSBMLDocumentPlugin.

Returns:

the number of ExternalModelDefinition objects in this CompSBMLDocumentPlugin.

getListOfExternalModelDefinitions

public ListOf<ExternalModelDefinition> getListOfExternalModelDefinitions()

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

Returns:

the listOfExternalModelDefinitions

clone

public CompSBMLDocumentPlugin 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

isSetListOfExternalModelDefinitions

public boolean isSetListOfExternalModelDefinitions()

Returns true, if listOfExternalModelDefinitions contains at least one element.

Returns:

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

setListOfExternalModelDefinitions

public void setListOfExternalModelDefinitions(ListOf<ExternalModelDefinition> listOfExternalModelDefinitions)

The listOfExternamModelDefinitions is an optional element of CompSBMLDocumentPlugin and defines external SBML document references within the ExternalModelDefinition object. Sets the given ListOf<ExternalModelDefinition>. If listOfExternalModelDefinitions was defined before and contains some elements, they are all unset.

Parameters:

listOfExternalModelDefinitions - the list of ExternalModelDefinitions

unsetListOfExternalModelDefinitions

public boolean unsetListOfExternalModelDefinitions()

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

Returns:

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

addExternalModelDefinition

public boolean addExternalModelDefinition(ExternalModelDefinition externalModelDefinition)

Adds a new ExternalModelDefinition to the listOfExternalModelDefinitions.

The listOfExternalModelDefinitions is initialized if necessary.

Parameters:

externalModelDefinition - the element to add to the list

Returns:

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

removeExternalModelDefinition

public boolean removeExternalModelDefinition(ExternalModelDefinition externalModelDefinition)

Removes an element from the listOfExternalModelDefinitions.

Parameters:

externalModelDefinition - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeExternalModelDefinition

public void removeExternalModelDefinition(int i)

Removes an element from the listOfExternalModelDefinitions at the given index.

Parameters:

i - the index where to remove the ExternalModelDefinition

Throws:

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

removeExternalModelDefinition

public void removeExternalModelDefinition(String id)

Removes an element from the listOfExternalModelDefinitions with the given id.

Parameters:

id - the id of the ExternalModelDefinition to remove

getModelDefinition

public ModelDefinition getModelDefinition(int index)

Returns the n-th ModelDefinition object in this CompSBMLDocumentPlugin.

Parameters:

index - an index

Returns:

the ModelDefinition with the given index if it exists.

Throws:

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

getModelDefinition

public ModelDefinition getModelDefinition(String id)

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

Parameters:

id - an id indicating a ModelDefinition element of the CompSBMLDocumentPlugin.

Returns:

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

getModelDefinitionCount

public int getModelDefinitionCount()

Returns the number of ModelDefinition objects in this CompSBMLDocumentPlugin.

Returns:

the number of ModelDefinition objects in this CompSBMLDocumentPlugin.

getNumExternalModelDefinitions

public int getNumExternalModelDefinitions()

Returns the number of ExternalModelDefinition of this CompSBMLDocumentPlugin.

Returns:

the number of ExternalModelDefinition of this CompSBMLDocumentPlugin.

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

use getExternalModelDefinitionCount()

getNumModelDefinitions

public int getNumModelDefinitions()

Returns the number of ModelDefinition of this CompSBMLDocumentPlugin.

Returns:

the number of ModelDefinition of this CompSBMLDocumentPlugin.

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

use getModelDefinitionCount()

createExternalModelDefinition

public ExternalModelDefinition createExternalModelDefinition()

Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list

Returns:

a new ExternalModelDefinition element

createExternalModelDefinition

public ExternalModelDefinition createExternalModelDefinition(String id)

Creates a new ExternalModelDefinition element and adds it to the ListOfExternalModelDefinitions list

Parameters:

id - the id

Returns:

a new ExternalModelDefinition element

isSetListOfModelDefinitions

public boolean isSetListOfModelDefinitions()

Returns true, if listOfModelDefinitions contains at least one element.

Returns:

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

getListOfModelDefinitions

public ListOf<ModelDefinition> getListOfModelDefinitions()

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

Returns:

the listOfModelDefinitions

setListOfModelDefinitions

public void setListOfModelDefinitions(ListOf<ModelDefinition> listOfModelDefinitions)

listOfModelDefinitions is an optional list of CompSBMLDocumentPlugin which specifies ModelDefinitions for the SBML document. Sets the given ListOf<ModelDefinition>. If listOfModelDefinitions was defined before and contains some elements, they are all unset.

Parameters:

listOfModelDefinitions - the list of ModelDefinitions

unsetListOfModelDefinitions

public boolean unsetListOfModelDefinitions()

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

Returns:

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

addModelDefinition

public boolean addModelDefinition(ModelDefinition modelDefinition)

Adds a new ModelDefinition to the listOfModelDefinitions.

The listOfModelDefinitions is initialized if necessary.

Parameters:

modelDefinition - the element to add to the list

Returns:

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

removeModelDefinition

public boolean removeModelDefinition(ModelDefinition modelDefinition)

Removes an element from the listOfModelDefinitions.

Parameters:

modelDefinition - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeModelDefinition

public void removeModelDefinition(int i)

Removes an element from the listOfModelDefinitions at the given index.

Parameters:

i - the index where to remove the ModelDefinition

Throws:

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

removeModelDefinition

public void removeModelDefinition(String id)

Removes an element from the listOfModelDefinitions with the given id.

Parameters:

id - the id of the ModelDefinition to remove

createModelDefinition

public Model createModelDefinition()

Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list

Returns:

a new ModelDefinition element

createModelDefinition

public Model createModelDefinition(String id)

Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list

Parameters:

id - the id

Returns:

a new ModelDefinition element

readAttribute

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

Specified by:

readAttribute in interface SBasePlugin

Overrides:

readAttribute in class CompSBasePlugin

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes 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

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class CompSBasePlugin