org.sbml.jsbml.ext.multi

Class MultiModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.multi.MultiModelPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class MultiModelPlugin
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 MultiSpeciesTypes.

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
MultiModelPlugin(Model model)
MultiModelPlugin(MultiModelPlugin multiModel)

Method Summary

Modifier and Type	Method and Description
boolean	addSpeciesType(MultiSpeciesType speciesType) Adds a MultiSpeciesType.
MultiModelPlugin	clone()
BindingSiteSpeciesType	createBindingSiteSpeciesType() Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.
BindingSiteSpeciesType	createBindingSiteSpeciesType(String id) Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.
IntraSpeciesReaction	createIntraSpeciesReaction() Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.
IntraSpeciesReaction	createIntraSpeciesReaction(String id) Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.
MultiSpeciesType	createSpeciesType() Creates a new MultiSpeciesType inside this MultiModelPlugin and returns it.
MultiSpeciesType	createSpeciesType(String id) Creates a new MultiSpeciesType inside this MultiModelPlugin and returns it.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
ListOf<MultiSpeciesType>	getListOfSpeciesTypes() Returns the listOfSpeciesTypes.
Model	getModel() Returns the Model
String	getPackageName()
SBMLDocument	getParent()
SBMLDocument	getParentSBMLObject()
String	getPrefix()
MultiSpeciesType	getSpeciesType(int i) Gets the ith MultiSpeciesType.
MultiSpeciesType	getSpeciesType(String id) Gets the MultiSpeciesType that has the given id.
String	getURI()
boolean	isSetListOfSpeciesTypes() Returns true if the listOfSpeciesType is set.
boolean	readAttribute(String attributeName, String prefix, String value)
void	setListOfSpeciesTypes(ListOf<MultiSpeciesType> listOfSpeciesTypes) Sets the listOfSpeciesTypes.
boolean	unsetListOfSpeciesTypes() Sets the listOfSpeciesTypes to null
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

equals, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getSBMLDocument, getVersion, hashCode, 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, 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

MultiModelPlugin

public MultiModelPlugin(Model model)

Parameters:

model -

MultiModelPlugin

public MultiModelPlugin(MultiModelPlugin multiModel)

Parameters:

multiModel -

Method Detail

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getParent

public SBMLDocument getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public SBMLDocument getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

clone

public MultiModelPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

getModel

public Model getModel()

Returns the Model

Returns:

the Model

getListOfSpeciesTypes

public ListOf<MultiSpeciesType> getListOfSpeciesTypes()

Returns the listOfSpeciesTypes.

Returns:

the listOfSpeciesTypes

addSpeciesType

public boolean addSpeciesType(MultiSpeciesType speciesType)

Adds a MultiSpeciesType.

Parameters:

speciesType - the speciesType to add

Returns:

createBindingSiteSpeciesType

public BindingSiteSpeciesType createBindingSiteSpeciesType()

Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.

Returns:

the BindingSiteSpeciesType object created

See Also:

addSpeciesType(MultiSpeciesType r)

createBindingSiteSpeciesType

public BindingSiteSpeciesType createBindingSiteSpeciesType(String id)

Creates a new BindingSiteSpeciesType inside this MultiModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the BindingSiteSpeciesType object created

createIntraSpeciesReaction

public IntraSpeciesReaction createIntraSpeciesReaction()

Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.

Returns:

the IntraSpeciesReaction object created

See Also:

createIntraSpeciesReaction(String)

createIntraSpeciesReaction

public IntraSpeciesReaction createIntraSpeciesReaction(String id)

Creates a new IntraSpeciesReaction inside this MultiModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the IntraSpeciesReaction object created

createSpeciesType

public MultiSpeciesType createSpeciesType()

Creates a new MultiSpeciesType inside this MultiModelPlugin and returns it.

Returns:

the MultiSpeciesType object created

See Also:

addSpeciesType(MultiSpeciesType r)

createSpeciesType

public MultiSpeciesType createSpeciesType(String id)

Creates a new MultiSpeciesType inside this MultiModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the MultiSpeciesType object created

getSpeciesType

public MultiSpeciesType getSpeciesType(int i)

Gets the ith MultiSpeciesType.

Parameters:

i -

Returns:

the ith MultiSpeciesType

Throws:

IndexOutOfBoundsException - if the index is invalid.

getSpeciesType

public MultiSpeciesType getSpeciesType(String id)

Gets the MultiSpeciesType that has the given id.

Parameters:

id -

Returns:

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

isSetListOfSpeciesTypes

public boolean isSetListOfSpeciesTypes()

Returns true if the listOfSpeciesType is set.

Returns:

true if the listOfSpeciesType is set.

setListOfSpeciesTypes

public void setListOfSpeciesTypes(ListOf<MultiSpeciesType> listOfSpeciesTypes)

Sets the listOfSpeciesTypes. If there was already some elements defined on listOfSpeciesTypes, they will be unset beforehand.

Parameters:

listOfSpeciesTypes - the list of MultiSpeciesTypes to set

unsetListOfSpeciesTypes

public boolean unsetListOfSpeciesTypes()

Sets the listOfSpeciesTypes to null

Returns:

true is successful

readAttribute

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

getChildAt

public SBase getChildAt(int childIndex)

getChildCount

public int getChildCount()

getAllowsChildren

public boolean getAllowsChildren()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin