org.sbml.jsbml.ext.multi

Class MultiModel

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.multi.MultiModel

All Implemented Interfaces:

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

public class MultiModel
extends AbstractSBasePlugin

In order to encode the structures needed to define and use multistate and multi-component complexes, the element model is extended to be linked to a list of SpeciesTypes and a list of Selectors.

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
(package private) ListOf<Selector>	listOfSelectors
(package private) ListOf<SpeciesType>	listOfSpeciesTypes
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
MultiModel(Model model)
MultiModel(MultiModel multiModel)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSelector(Selector selector) Adds a Selector.
void	addSpeciesType(SpeciesType speciesType) Adds a SpeciesType.
MultiModel	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
Selector	createSelector() Creates a new Selector inside this MultiModel and returns it.
Selector	createSelector(java.lang.String id) Creates a new Selector inside this MultiModel and returns it.
SpeciesType	createSpeciesType() Creates a new SpeciesType inside this MultiModel and returns it.
SpeciesType	createSpeciesType(java.lang.String id) Creates a new SpeciesType inside this MultiModel and returns it.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
ListOf<Selector>	getListOfSelectors() Returns the listOfSelectors.
ListOf<SpeciesType>	getListOfSpeciesTypes() Returns the listOfSpeciesTypes.
Model	getModel() Returns the Model
java.lang.String	getPackageName() Returns the package name of this plugin object.
SBMLDocument	getParent()
SBMLDocument	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.
Selector	getSelector(int i) Gets the ith Selector.
Selector	getSelector(java.lang.String id) Gets the Selector that has the given id.
SpeciesType	getSpeciesType(int i) Gets the ith SpeciesType.
SpeciesType	getSpeciesType(java.lang.String id) Gets the SpeciesType that has the given id.
java.lang.String	getURI() Gets the URI to which this element belongs to.
boolean	isSetListOfSelectors() Returns true if the listOfSelector is set.
boolean	isSetListOfSpeciesTypes() Returns true if the listOfSpeciesType 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.
boolean	unsetListOfSelectors() Sets the listOfSelectors to null
boolean	unsetListOfSpeciesTypes() Sets the listOfSpeciesTypes to null
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, 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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

listOfSpeciesTypes

ListOf<SpeciesType> listOfSpeciesTypes

listOfSelectors

ListOf<Selector> listOfSelectors

Constructor Detail

MultiModel

public MultiModel(Model model)

Parameters:

model -

MultiModel

public MultiModel(MultiModel multiModel)

Parameters:

model -

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 SBMLDocument getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBMLDocument 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 MultiModel clone()

Description copied from interface: SBasePlugin

Creates a new instance of SBasePlugin from this SBasePlugin.

Specified by:

clone in interface SBasePlugin

Specified by:

clone in class AbstractSBasePlugin

Returns:

a new instance of SBasePlugin from this SBasePlugin.

getModel

public Model getModel()

Returns the Model

Returns:

the Model

getListOfSpeciesTypes

public ListOf<SpeciesType> getListOfSpeciesTypes()

Returns the listOfSpeciesTypes.

Returns:

the listOfSpeciesTypes

addSpeciesType

public void addSpeciesType(SpeciesType speciesType)

Adds a SpeciesType.

Parameters:

speciesTypes - the speciesType to add

createSpeciesType

public SpeciesType createSpeciesType()

Creates a new SpeciesType inside this MultiModel and returns it.

Returns:

the SpeciesType object created

See Also:

addSpeciesType(SpeciesType r)

createSpeciesType

public SpeciesType createSpeciesType(java.lang.String id)

Creates a new SpeciesType inside this MultiModel and returns it.

Parameters:

id - the id of the new element to create

Returns:

the SpeciesType object created

getSpeciesType

public SpeciesType getSpeciesType(int i)

Gets the ith SpeciesType.

Parameters:

i -

Returns:

the ith SpeciesType

Throws:

java.lang.IndexOutOfBoundsException - if the index is invalid.

getSpeciesType

public SpeciesType getSpeciesType(java.lang.String id)

Gets the SpeciesType that has the given id.

Parameters:

id -

Returns:

the SpeciesType that has the given id or null if no SpeciesType are found that match id.

isSetListOfSpeciesTypes

public boolean isSetListOfSpeciesTypes()

Returns true if the listOfSpeciesType is set.

Returns:

true if the listOfSpeciesType is set.

unsetListOfSpeciesTypes

public boolean unsetListOfSpeciesTypes()

Sets the listOfSpeciesTypes to null

Returns:

true is successful

getListOfSelectors

public ListOf<Selector> getListOfSelectors()

Returns the listOfSelectors.

Returns:

the listOfSelectors

addSelector

public void addSelector(Selector selector)

Adds a Selector.

Parameters:

selector - the selector to add

createSelector

public Selector createSelector()

Creates a new Selector inside this MultiModel and returns it.

Returns:

the Selector object created

See Also:

addSelector(Selector r)

createSelector

public Selector createSelector(java.lang.String id)

Creates a new Selector inside this MultiModel and returns it.

Parameters:

id - the id of the new element to create

Returns:

the Selector object created

getSelector

public Selector getSelector(int i)

Gets the ith Selector.

Parameters:

i -

Returns:

the ith Selector

Throws:

java.lang.IndexOutOfBoundsException - if the index is invalid.

getSelector

public Selector getSelector(java.lang.String id)

Gets the Selector that has the given id.

Parameters:

id -

Returns:

the Selector that has the given id or null if no Selector are found that match id.

isSetListOfSelectors

public boolean isSetListOfSelectors()

Returns true if the listOfSelector is set.

Returns:

true if the listOfSelector is set.

unsetListOfSelectors

public boolean unsetListOfSelectors()

Sets the listOfSelectors to null

Returns:

true is successful

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.

getChildAt

public SBase getChildAt(int childIndex)

getChildCount

public int getChildCount()

getAllowsChildren

public boolean getAllowsChildren()

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.