org.sbml.jsbml.ext.multi

Class MultiSpecies

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.multi.MultiSpecies

All Implemented Interfaces:

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

public class MultiSpecies
extends AbstractSBasePlugin

Since:

1.0

Version:

$Rev: 1639 $

Author:

Nicolas Rodriguez, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<SpeciesTypeInstance>	listOfSpeciesTypeInstances
private static long	serialVersionUID Generated serial version identifier.
private Species	species

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
MultiSpecies(MultiSpecies multiSpecies)
MultiSpecies(Species species)

Method Summary

Methods

Modifier and Type	Method and Description
void	addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)
MultiSpecies	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
SpeciesTypeInstance	createSpeciesTypeInstance(java.lang.String id)
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.
SpeciesTypeInstance	getInitialSpeciesInstance(java.lang.String id)
ListOf<SpeciesTypeInstance>	getListOfSpeciesTypeInstances()
java.lang.String	getPackageName() Returns the package name of this plugin object.
ListOf<Species>	getParent()
ListOf<Species>	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.
SpeciesTypeInstance	getSpeciesTypeInstance(int n)
java.lang.String	getURI() Gets the URI to which this element belongs to.
boolean	isSetListOfSpeciesInstances()
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.
java.lang.String	toString()
boolean	unsetListOfInitialSpeciesInstances() Removes the listOfSpeciesTypeInstances from this Model and notifies all registered instances of TreeNodeChangeListener.
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, 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

listOfSpeciesTypeInstances

private ListOf<SpeciesTypeInstance> listOfSpeciesTypeInstances

species

private Species species

Constructor Detail

MultiSpecies

public MultiSpecies(Species species)

Parameters:

species -

MultiSpecies

public MultiSpecies(MultiSpecies multiSpecies)

Parameters:

multiSpecies -

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 ListOf<Species> getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public ListOf<Species> 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 MultiSpecies 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.

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public SBase getChildAt(int childIndex)

getChildCount

public int getChildCount()

addSpeciesTypeInstance

public void addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)

Parameters:

speciesTypeInstance -

getSpeciesTypeInstance

public SpeciesTypeInstance getSpeciesTypeInstance(int n)

Parameters:

n -

Returns:

getInitialSpeciesInstance

public SpeciesTypeInstance getInitialSpeciesInstance(java.lang.String id)

Parameters:

id -

Returns:

getListOfSpeciesTypeInstances

public ListOf<SpeciesTypeInstance> getListOfSpeciesTypeInstances()

Returns:

isSetListOfSpeciesInstances

public boolean isSetListOfSpeciesInstances()

Returns:

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.

toString

public java.lang.String toString()

Overrides:

toString in class AbstractTreeNode

unsetListOfInitialSpeciesInstances

public boolean unsetListOfInitialSpeciesInstances()

Removes the listOfSpeciesTypeInstances from this Model and notifies all registered instances of TreeNodeChangeListener.

Returns:

true if calling this method lead to a change in this data structure.

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.

createSpeciesTypeInstance

public SpeciesTypeInstance createSpeciesTypeInstance(java.lang.String id)