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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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: 1980 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<FluxBound>	listOfFluxBounds
private ListOfObjectives	listOfObjectives
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
FBCModelPlugin(FBCModelPlugin obj) Clone constructor
FBCModelPlugin(Model model)

Method Summary

Methods

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() Creates a new instance of SBasePlugin from this SBasePlugin.
FluxBound	createFluxBound() Creates a new FluxBound element and adds it to the ListOfFluxBounds list
FluxBound	createFluxBound(java.lang.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(java.lang.String id) Creates a new Objective element and adds it to the ListOfObjectives list
java.lang.String	getActiveObjective() Gets the activeObjective.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
java.lang.String	getElementNamespace() Returns the XML namespace (URI) of the package extension of this plugin object.
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.
java.lang.String	getPackageName() Returns the package name of this plugin object.
Model	getParent()
Model	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.
java.lang.String	getURI() Gets the URI to which this element belongs to.
boolean	isSetListOfFluxBounds() Returns true if listOfFluxBounds contains at least one element.
boolean	isSetListOfObjectives() Returns true if listOfObjectives is not null.
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.
private java.lang.String	recurseAndFind(XMLNode xmlNode, java.lang.String key)
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(java.lang.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(java.lang.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
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

listOfFluxBounds

private ListOf<FluxBound> listOfFluxBounds

listOfObjectives

private ListOfObjectives listOfObjectives

Constructor Detail

FBCModelPlugin

public FBCModelPlugin(FBCModelPlugin obj)

Clone constructor

FBCModelPlugin

public FBCModelPlugin(Model model)

Parameters:

model -

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 Model getParent()

Specified by:

getParent in interface javax.swing.tree.TreeNode

Overrides:

getParent in class AbstractTreeNode

getParentSBMLObject

public Model 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.

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()

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.

createFluxBound

public FluxBound createFluxBound()

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

createFluxBound

public FluxBound createFluxBound(java.lang.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(java.lang.String id)

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

Returns:

a new Objective element

getActiveObjective

public java.lang.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 javax.swing.tree.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:

java.lang.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:

java.lang.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.

getNumObjective

public int getNumObjective()

Return the number of FluxBound in this FBCModelPlugin.

Returns:

the number of FluxBound in this FBCModelPlugin.

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(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.

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:

java.lang.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:

java.lang.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(java.lang.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 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.

setNotesKeyToUserObject

public void setNotesKeyToUserObject(java.lang.String key)

recurseAndFind

private java.lang.String recurseAndFind(XMLNode xmlNode,
                              java.lang.String key)