org.sbml.jsbml.ext.fbc

Class FBCModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.fbc.FBCModelPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class FBCModelPlugin
extends AbstractSBasePlugin

FBCModelPlugin is the extended Model class for the FBC package. It is extended by the addition of two children, list of FluxBound and list of Objective

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Last modified:

27.10.2011

Field Summary

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
FBCModelPlugin(FBCModelPlugin obj) Clone constructor
FBCModelPlugin(Model model)

Method Summary

Modifier and Type	Method and Description
boolean	addFluxBound(FluxBound fluxBound) Adds a new FluxBound to the listOfFluxBounds.
boolean	addObjective(Objective objective) Adds a new Objective to the listOfObjectives.
FBCModelPlugin	clone()
FluxBound	createFluxBound() Creates a new FluxBound element and adds it to the ListOfFluxBounds list
FluxBound	createFluxBound(String id) Creates a new FluxBound element and adds it to the ListOfFluxBounds list
Objective	createObjective() Creates a new Objective element and adds it to the ListOfObjectives list
Objective	createObjective(String id) Creates a new Objective element and adds it to the ListOfObjectives list
String	getActiveObjective() Gets the activeObjective.
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
String	getElementNamespace()
FluxBound	getFluxBound(int i) Gets an element from the listOfFluxBounds at the given index.
int	getFluxBoundCount() Return the number of FluxBound in this FBCModelPlugin.
ListOf<FluxBound>	getListOfFluxBounds() Returns the listOfFluxBounds.
ListOfObjectives	getListOfObjectives() Returns the listOfObjectives.
int	getNumFluxBound() Return the number of FluxBound in this FBCModelPlugin.
int	getNumObjective() Return the number of FluxBound in this FBCModelPlugin.
Objective	getObjective(int i) Gets an element from the listOfObjectives at the given index.
int	getObjectiveCount() Return the number of Objective in this FBCModelPlugin.
String	getPackageName()
Model	getParent()
Model	getParentSBMLObject()
String	getPrefix()
String	getURI()
boolean	isSetListOfFluxBounds() Returns true if listOfFluxBounds contains at least one element.
boolean	isSetListOfObjectives() Returns true if listOfObjectives is not null.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeFluxBound(FluxBound fluxBound) Removes an element from the listOfFluxBounds.
void	removeFluxBound(int i) Removes an element from the listOfFluxBounds at the given index.
void	removeObjective(int i) Removes an element from the listOfObjectives at the given index.
boolean	removeObjective(Objective objective) Removes an element from the listOfObjectives.
void	setActiveObjective(Objective objective)
void	setActiveObjective(String activeObjective) The activeObjective refers to the id of an existing objective.
void	setListOfFluxBounds(ListOf<FluxBound> listOfFluxBounds) Sets the given ListOf<FluxBound>.
void	setListOfObjectives(ListOf<Objective> listOfObjectives) Sets the given ListOf<Objective>.
void	setListOfObjectives(ListOfObjectives listOfObjectives) Sets the given ListOfObjectives.
void	setNotesKeyToUserObject(String key)
boolean	unsetListOfFluxBounds() Returns true if listOfFluxBounds contain at least one element, otherwise false
boolean	unsetListOfObjectives() Returns true if listOfObjectives contain at least one element, otherwise false
Map<String,String>	writeXMLAttributes()

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

Constructor Detail

FBCModelPlugin

public FBCModelPlugin(FBCModelPlugin obj)

Clone constructor

FBCModelPlugin

public FBCModelPlugin(Model model)

Parameters:

model -

Method Detail

getElementNamespace

public String getElementNamespace()

getPackageName

public String getPackageName()

getPrefix

public String getPrefix()

getURI

public String getURI()

getParent

public Model getParent()

Specified by:

getParent in interface TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public Model getParentSBMLObject()

Specified by:

getParentSBMLObject in interface SBasePlugin

Overrides:

getParentSBMLObject in class AbstractSBasePlugin

addFluxBound

public boolean addFluxBound(FluxBound fluxBound)

Adds a new FluxBound to the listOfFluxBounds.

The listOfFluxBounds is initialized if necessary.

Parameters:

fluxBound - the element to add to the list

Returns:

true (as specified by Collection#add)

addObjective

public boolean addObjective(Objective objective)

Adds a new Objective to the listOfObjectives.

The listOfObjectives is initialized if necessary.

Parameters:

objective - the element to add to the list

Returns:

true (as specified by Collection#add)

clone

public FBCModelPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

createFluxBound

public FluxBound createFluxBound()

Creates a new FluxBound element and adds it to the ListOfFluxBounds list

createFluxBound

public FluxBound createFluxBound(String id)

Creates a new FluxBound element and adds it to the ListOfFluxBounds list

Returns:

a new FluxBound element

createObjective

public Objective createObjective()

Creates a new Objective element and adds it to the ListOfObjectives list

createObjective

public Objective createObjective(String id)

Creates a new Objective element and adds it to the ListOfObjectives list

Returns:

a new Objective element

getActiveObjective

public String getActiveObjective()

Gets the activeObjective.

If the activeObjective is not defined, an empty String is returned.

Returns:

the activeObjective or "".

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public TreeNode getChildAt(int index)

getChildCount

public int getChildCount()

getFluxBound

public FluxBound getFluxBound(int i)

Gets an element from the listOfFluxBounds at the given index.

Parameters:

i - the index where to get the FluxBound

Returns:

an element from the listOfFluxBounds at the given index.

Throws:

IndexOutOfBoundsException - if the index is out of bound (index < 0 || index > list.size)

getFluxBoundCount

public int getFluxBoundCount()

Return the number of FluxBound in this FBCModelPlugin.

Returns:

the number of FluxBound in this FBCModelPlugin.

getListOfFluxBounds

public ListOf<FluxBound> getListOfFluxBounds()

Returns the listOfFluxBounds. Creates it if it is not already existing.

Returns:

the listOfFluxBounds

getListOfObjectives

public ListOfObjectives getListOfObjectives()

Returns the listOfObjectives. Creates it if it is not already existing.

Returns:

the listOfObjectives

getObjective

public Objective getObjective(int i)

Gets an element from the listOfObjectives at the given index.

Parameters:

i - the index where to get the Objective

Returns:

an element from the listOfObjectives at the given index.

Throws:

IndexOutOfBoundsException - if the index is out of bound (index < 0 || index > list.size)

getObjectiveCount

public int getObjectiveCount()

Return the number of Objective in this FBCModelPlugin.

Returns:

the number of Objective in this FBCModelPlugin.

getNumFluxBound

public int getNumFluxBound()

Return the number of FluxBound in this FBCModelPlugin.

Returns:

the number of FluxBound in this FBCModelPlugin.

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

same as getFluxBoundCount()

getNumObjective

public int getNumObjective()

Return the number of FluxBound in this FBCModelPlugin.

Returns:

the number of FluxBound in this FBCModelPlugin.

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

same as getObjectiveCount()

isSetListOfFluxBounds

public boolean isSetListOfFluxBounds()

Returns true if listOfFluxBounds contains at least one element.

Returns:

true if listOfFluxBounds contains at least one element, otherwise false

isSetListOfObjectives

public boolean isSetListOfObjectives()

Returns true if listOfObjectives is not null.

Returns:

true if listOfObjectives is not null, otherwise false

readAttribute

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

removeFluxBound

public boolean removeFluxBound(FluxBound fluxBound)

Removes an element from the listOfFluxBounds.

Parameters:

fluxBound - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeFluxBound

public void removeFluxBound(int i)

Removes an element from the listOfFluxBounds at the given index.

Parameters:

i - the index where to remove the FluxBound

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size)

removeObjective

public void removeObjective(int i)

Removes an element from the listOfObjectives at the given index.

Parameters:

i - the index where to remove the Objective

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size)

removeObjective

public boolean removeObjective(Objective objective)

Removes an element from the listOfObjectives.

Parameters:

objective - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

setActiveObjective

public void setActiveObjective(String activeObjective)

The activeObjective refers to the id of an existing objective. This required attribute exists so that if there are multiple objectives included in the model, the model will still be well-described.

Parameters:

activeObjective -

setActiveObjective

public void setActiveObjective(Objective objective)

Parameters:

objective -

setListOfFluxBounds

public void setListOfFluxBounds(ListOf<FluxBound> listOfFluxBounds)

Sets the given ListOf<FluxBound>.

If listOfFluxBounds was defined before and contained some elements, they are all unset.

Parameters:

listOfFluxBounds -

setListOfObjectives

public void setListOfObjectives(ListOfObjectives listOfObjectives)

Sets the given ListOfObjectives.

If listOfObjectives was defined before and contained some elements, they are all unset.

Parameters:

listOfObjectives -

setListOfObjectives

public void setListOfObjectives(ListOf<Objective> listOfObjectives)

Sets the given ListOf<Objective>.

If the given list is an instance of ListOfObjectives, a call of this method is identical to directly calling setListOfObjectives(ListOfObjectives). Otherwise, a new ListOfObjectives will be created from the given ListOf. Note that in the second case there is no active objective defined.

Parameters:

listOfObjectives -

unsetListOfFluxBounds

public boolean unsetListOfFluxBounds()

Returns true if listOfFluxBounds contain at least one element, otherwise false

Returns:

true if listOfFluxBounds contain at least one element, otherwise false

unsetListOfObjectives

public boolean unsetListOfObjectives()

Returns true if listOfObjectives contain at least one element, otherwise false

Returns:

true if listOfObjectives contain at least one element, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin

setNotesKeyToUserObject

public void setNotesKeyToUserObject(String key)