org.sbml.jsbml.ext.qual

Class QualModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.qual.QualModelPlugin

All Implemented Interfaces:

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

Direct Known Subclasses:

QualitativeModel

public class QualModelPlugin
extends AbstractSBasePlugin

The QualModelPlugin adds two lists, one for holding QualitativeSpecies and the other for holding Transitions.

Since:

1.0

Version:

$Rev: 1725 $

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag, Clemens Wrzodek, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<QualitativeSpecies>	listOfQualitativeSpecies
private ListOf<Transition>	listOfTransitions
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
QualModelPlugin(Model model)
QualModelPlugin(QualModelPlugin qualitativeModel)

Method Summary

Methods

Modifier and Type	Method and Description
void	addQualitativeSpecies(QualitativeSpecies qualitativeSpecies) Adds a QualitativeSpecies to the model.
boolean	addSpecies(QualitativeSpecies spec) Adds a QualitativeSpecies instance to the listOfSpecies of this Model.
void	addTransition(Transition transition)
QualModelPlugin	clone() Creates a new instance of SBasePlugin from this SBasePlugin.
boolean	containsQualitativeSpecies(QualitativeSpecies qs) Returns true if qs is already part of this QualModelPlugin
QualitativeSpecies	createQualitativeSpecies() Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(java.lang.String id) Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(java.lang.String id, Compartment c) Creates a new Species inside this Model and returns it.
QualitativeSpecies	createQualitativeSpecies(java.lang.String id, Compartment compartment, boolean constant)
QualitativeSpecies	createQualitativeSpecies(java.lang.String id, java.lang.String compartment, boolean constant) Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(java.lang.String id, java.lang.String metaId, Species species) Creates a new QualitativeSpecies, based on an existing Species, adds it to this QualModelPlugin and returns it.
Transition	createTransition() Creates a new Transition inside this QualModelPlugin and returns it.
Transition	createTransition(java.lang.String id) Creates a new Transition inside this QualModelPlugin and returns it.
Transition	createTransition(java.lang.String id, Input in, Output out)
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<QualitativeSpecies>	getListOfQualitativeSpecies()
ListOf<Transition>	getListOfTransitions()
Model	getModel() Returns the Model
int	getNumQualitativeSpecies() Returns the number of QualitativeSpecies of this QualModelPlugin.
int	getNumTransitions() Returns the number of Transition of this QualModelPlugin.
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.
QualitativeSpecies	getQualitativeSpecies(int i) Gets the ith QualitativeSpecies.
QualitativeSpecies	getQualitativeSpecies(java.lang.String id) Gets the QualitativeSpecies that has the given id.
int	getQualitativeSpeciesCount() Returns the number of QualitativeSpecies objects in this QualModelPlugin.
Transition	getTransition(int i) Gets the ith Transition.
Transition	getTransition(java.lang.String id) Gets the Transition that has the given id.
int	getTransitionCount() Returns the number of Transition objects in this QualModelPlugin.
java.lang.String	getURI() Gets the URI to which this element belongs to.
boolean	isSetListOfQualitativeSpecies() Returns true if the listOfQualitativeSpecies is set.
boolean	isSetListOfTransitions() Returns true if the listOfTransitions 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	removeQualitativeSpecies(QualitativeSpecies qualitativeSpecies)
boolean	removeTransition(Transition transition)
void	setListOfQualitativeSpecies(ListOf<QualitativeSpecies> listOfQualitativeSpecies) QualModelPlugin may contain at most one listOfQualitativeSpecies which must contain at least on QualitativeSpecies.
void	setListOfTransitions(ListOf<Transition> listOfTransitions) QualModelPlugin can contain at most one listOfTransitions which must contain at least one Transition.
boolean	unsetListOfQualitativeSpecies()
boolean	unsetListOfTransitions()
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

listOfQualitativeSpecies

private ListOf<QualitativeSpecies> listOfQualitativeSpecies

listOfTransitions

private ListOf<Transition> listOfTransitions

Constructor Detail

QualModelPlugin

public QualModelPlugin(Model model)

Parameters:

model -

QualModelPlugin

public QualModelPlugin(QualModelPlugin qualitativeModel)

Parameters:

qualitativeModel -

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.

addQualitativeSpecies

public void addQualitativeSpecies(QualitativeSpecies qualitativeSpecies)

Adds a QualitativeSpecies to the model.

Parameters:

qualitativeSpecies - the qualitativeSpecies to add.

addTransition

public void addTransition(Transition transition)

Parameters:

transition -

clone

public QualModelPlugin 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()

createTransition

public Transition createTransition()

Creates a new Transition inside this QualModelPlugin and returns it.

Returns:

the Transition object created

See Also:

addTransition(Transition r)

createTransition

public Transition createTransition(java.lang.String id)

Creates a new Transition inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the Transition object created

createTransition

public Transition createTransition(java.lang.String id,
                          Input in,
                          Output out)

Parameters:

id -

in -

out -

Returns:

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies()

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

Returns:

the QualitativeSpecies object created

See Also:

addSpecies(QualitativeSpecies s)

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(java.lang.String id)

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the QualitativeSpecies object created

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(java.lang.String id,
                                          java.lang.String compartment,
                                          boolean constant)

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

Returns:

the QualitativeSpecies object created

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(java.lang.String id,
                                          Compartment compartment,
                                          boolean constant)

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(java.lang.String id,
                                          java.lang.String metaId,
                                          Species species)

Creates a new QualitativeSpecies, based on an existing Species, adds it to this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

metaId - the metaId of the new element to create

species - a template to copy fields from

Returns:

the QualitativeSpecies object created

addSpecies

public boolean addSpecies(QualitativeSpecies spec)

Adds a QualitativeSpecies instance to the listOfSpecies of this Model.

Parameters:

spec -

Returns:

true if the QualitativeSpecies was added successfully.

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(java.lang.String id,
                                          Compartment c)

Creates a new Species inside this Model and returns it.

Parameters:

id - the id of the new element to create

c - the Compartment of the new Species

Returns:

the Species object created

getListOfQualitativeSpecies

public ListOf<QualitativeSpecies> getListOfQualitativeSpecies()

Returns:

the listOfQualitativeSpecies

getListOfTransitions

public ListOf<Transition> getListOfTransitions()

Returns:

the listOTransitions

removeTransition

public boolean removeTransition(Transition transition)

Parameters:

transition - to remove from the listOfTransitions

Returns:

TRUE if the operation was successful

removeQualitativeSpecies

public boolean removeQualitativeSpecies(QualitativeSpecies qualitativeSpecies)

Parameters:

QualitativeSpecies - to remove from the listOfQualitativeSpecies

Returns:

TRUE if the operation was successful

getModel

public Model getModel()

Returns the Model

Returns:

the Model

getNumQualitativeSpecies

public int getNumQualitativeSpecies()

Returns the number of QualitativeSpecies of this QualModelPlugin.

Returns:

the number of QualitativeSpecies of this QualModelPlugin.

getNumTransitions

public int getNumTransitions()

Returns the number of Transition of this QualModelPlugin.

Returns:

the number of Transition of this QualModelPlugin.

getQualitativeSpecies

public QualitativeSpecies getQualitativeSpecies(int i)

Gets the ith QualitativeSpecies.

Parameters:

i -

Returns:

the ith QualitativeSpecies

Throws:

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

getQualitativeSpecies

public QualitativeSpecies getQualitativeSpecies(java.lang.String id)

Gets the QualitativeSpecies that has the given id.

Parameters:

id -

Returns:

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

getQualitativeSpeciesCount

public int getQualitativeSpeciesCount()

Returns the number of QualitativeSpecies objects in this QualModelPlugin.

Returns:

the number of QualitativeSpecies objects in this QualModelPlugin.

containsQualitativeSpecies

public boolean containsQualitativeSpecies(QualitativeSpecies qs)

Returns true if qs is already part of this QualModelPlugin

Parameters:

qs -

Returns:

true if qs is already part of this QualModelPlugin

getTransition

public Transition getTransition(int i)

Gets the ith Transition.

Parameters:

i -

Returns:

the ith Transition.

Throws:

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

getTransition

public Transition getTransition(java.lang.String id)

Gets the Transition that has the given id.

Parameters:

id -

Returns:

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

getTransitionCount

public int getTransitionCount()

Returns the number of Transition objects in this QualModelPlugin.

Returns:

the number of Transition objects in this QualModelPlugin.

isSetListOfQualitativeSpecies

public boolean isSetListOfQualitativeSpecies()

Returns true if the listOfQualitativeSpecies is set.

Returns:

true if the listOfQualitativeSpecies is set.

isSetListOfTransitions

public boolean isSetListOfTransitions()

Returns true if the listOfTransitions is set.

Returns:

true if the listOfTransitions is set.

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.

setListOfQualitativeSpecies

public void setListOfQualitativeSpecies(ListOf<QualitativeSpecies> listOfQualitativeSpecies)

QualModelPlugin may contain at most one listOfQualitativeSpecies which must contain at least on QualitativeSpecies.

Parameters:

listOfQualitativeSpecies -

setListOfTransitions

public void setListOfTransitions(ListOf<Transition> listOfTransitions)

QualModelPlugin can contain at most one listOfTransitions which must contain at least one Transition. s

Parameters:

listOfTransitions -

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.

unsetListOfTransitions

public boolean unsetListOfTransitions()

Returns:

true is successful

unsetListOfQualitativeSpecies

public boolean unsetListOfQualitativeSpecies()

Returns:

true is successful