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:

Serializable, Cloneable, 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

Author:

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

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
QualModelPlugin(Model model) Creates a new QualModelPlugin instance
QualModelPlugin(QualModelPlugin qualitativeModel) Clone constructor

Method Summary

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()
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(String id) Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(String id, Compartment c) Creates a new Species inside this Model and returns it.
QualitativeSpecies	createQualitativeSpecies(String id, Compartment compartment, boolean constant) Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(String id, String compartment, boolean constant) Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.
QualitativeSpecies	createQualitativeSpecies(String id, 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(String id) Creates a new Transition inside this QualModelPlugin and returns it.
Transition	createTransition(String id, Input in, Output out) Creates a new Transition inside this QualModelPlugin and returns it.
boolean	getAllowsChildren()
SBase	getChildAt(int childIndex)
int	getChildCount()
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.
String	getPackageName()
SBMLDocument	getParent()
SBMLDocument	getParentSBMLObject()
String	getPrefix()
QualitativeSpecies	getQualitativeSpecies(int i) Gets the ith QualitativeSpecies.
QualitativeSpecies	getQualitativeSpecies(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(String id) Gets the Transition that has the given id.
int	getTransitionCount() Returns the number of Transition objects in this QualModelPlugin.
String	getURI()
boolean	isSetListOfQualitativeSpecies() Returns true if the listOfQualitativeSpecies is set.
boolean	isSetListOfTransitions() Returns true if the listOfTransitions is set.
boolean	readAttribute(String attributeName, String prefix, String value)
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()
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, 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

QualModelPlugin

public QualModelPlugin(Model model)

Creates a new QualModelPlugin instance

Parameters:

model - the Model to extends

QualModelPlugin

public QualModelPlugin(QualModelPlugin qualitativeModel)

Clone constructor

Parameters:

qualitativeModel - the QualModelPlugin to be cloned

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

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()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

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(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(String id,
                                   Input in,
                                   Output out)

Creates a new Transition inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

in -

out -

Returns:

the Transition object created

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(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(String id,
                                                   String compartment,
                                                   boolean constant)

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

compartment -

constant -

Returns:

the QualitativeSpecies object created

createQualitativeSpecies

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

Creates a new QualitativeSpecies inside this QualModelPlugin and returns it.

Parameters:

id - the id of the new element to create

compartment -

constant -

Returns:

the QualitativeSpecies object created

createQualitativeSpecies

public QualitativeSpecies createQualitativeSpecies(String id,
                                                   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(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.

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

same as getQualitativeSpeciesCount()

getNumTransitions

public int getNumTransitions()

Returns the number of Transition of this QualModelPlugin.

Returns:

the number of Transition of this QualModelPlugin.

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

same as getTransitionCount()

getQualitativeSpecies

public QualitativeSpecies getQualitativeSpecies(int i)

Gets the ith QualitativeSpecies.

Parameters:

i -

Returns:

the ith QualitativeSpecies

Throws:

IndexOutOfBoundsException - is the index is invalid.

getQualitativeSpecies

public QualitativeSpecies getQualitativeSpecies(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:

IndexOutOfBoundsException - is the index is invalid.

getTransition

public Transition getTransition(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(String attributeName,
                             String prefix,
                             String value)

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 Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

unsetListOfTransitions

public boolean unsetListOfTransitions()

Returns:

true is successful

unsetListOfQualitativeSpecies

public boolean unsetListOfQualitativeSpecies()

Returns:

true is successful