org.sbml.jsbml.ext.fbc

Class FBCModelPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

org.sbml.jsbml.ext.fbc.FBCModelPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class FBCModelPlugin
extends AbstractFBCSBasePlugin

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

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
FBCModelPlugin(FBCModelPlugin fbcPlugin) Clone constructor
FBCModelPlugin(Model model) Creates a new FBCModelPlugin instance.

Method Summary

Modifier and Type	Method and Description
boolean	addFluxBound(FluxBound fluxBound) Deprecated. Only defined in FBC version 1.
boolean	addGeneProduct(GeneProduct geneProduct) Adds a new GeneProduct to the listOfGeneProducts.
boolean	addObjective(Objective objective) Adds a new Objective to the listOfObjectives.
FBCModelPlugin	clone()
FluxBound	createFluxBound() Deprecated. Only defined in FBC version 1.
FluxBound	createFluxBound(String id) Deprecated. Only defined in FBC version 1.
GeneProduct	createGeneProduct() Creates a new GeneProduct element and adds it to the ListOfGeneProducts list.
GeneProduct	createGeneProduct(String id) Creates a new GeneProduct element and adds it to the listOfGeneProducts list.
Objective	createObjective() Creates a new Objective element and adds it to the listOfObjectives.
Objective	createObjective(String id) Creates a new Objective element and adds it to the listOfObjectives.
Objective	createObjective(String id, Objective.Type type) Creates a new Objective element and adds it to the listOfObjectives.
Objective	createObjective(String id, String name, Objective.Type type) Creates a new Objective element and adds it to the listOfObjectives.
String	getActiveObjective() Gets the activeObjective.
Objective	getActiveObjectiveInstance()
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
FluxBound	getFluxBound(int i) Deprecated. Only defined in FBC version 1.
int	getFluxBoundCount() Deprecated. Only defined in FBC version 1.
GeneProduct	getGeneProduct(int i) Gets an element from the listOfGeneProducts at the given index.
GeneProduct	getGeneProduct(String geneProductId) Gets an element from the listOfGeneProducts, with the given id.
int	getGeneProductCount() Returns the number of GeneProducts in this FBCModelPlugin.
ListOf<FluxBound>	getListOfFluxBounds() Deprecated. Only defined in FBC version 1.
ListOf<GeneProduct>	getListOfGeneProducts() Returns the listOfGeneProducts.
ListOfObjectives	getListOfObjectives() Returns the listOfObjectives.
int	getNumFluxBound() Deprecated. Only defined in FBC version 1.
int	getNumGeneProducts() Returns the number of GeneProducts in this FBCModelPlugin.
int	getNumObjective() Return the number of Objectives 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.
Model	getParent()
Model	getParentSBMLObject()
boolean	getStrict() Returns the value of strict.
boolean	isSetActiveObjective()
boolean	isSetListOfFluxBounds() Deprecated. Only defined in FBC version 1.
boolean	isSetListOfGeneProducts() Returns true if listOfGeneProducts contains at least one element.
boolean	isSetListOfObjectives() Returns true if listOfObjectives is not null.
boolean	isSetStrict() Returns whether strict is set.
boolean	isStrict() Returns the value of strict.
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeFluxBound(FluxBound fluxBound) Deprecated. Only defined in FBC version 1.
void	removeFluxBound(int i) Deprecated. Only defined in FBC version 1.
boolean	removeGeneProduct(GeneProduct geneProduct) Removes an element from the listOfGeneProducts.
GeneProduct	removeGeneProduct(int i) Removes an element from the listOfGeneProducts at the given index.
GeneProduct	removeGeneProduct(String geneProductId) Removes an element from the listOfGeneProducts.
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) Deprecated. Only defined in FBC version 1.
void	setListOfGeneProducts(ListOf<GeneProduct> listOfGeneProducts) Sets the given ListOf<GeneProduct>.
void	setListOfObjectives(ListOf<Objective> listOfObjectives) Sets the given ListOf<Objective>.
void	setListOfObjectives(ListOfObjectives listOfObjectives) Sets the given ListOfObjectives.
void	setNotesKeyToUserObject(String key)
void	setStrict(boolean strict) Sets the value of strict
boolean	unsetListOfFluxBounds() Deprecated. Only defined in FBC version 1.
boolean	unsetListOfGeneProducts() Returns true if listOfGeneProducts contains at least one element, otherwise false.
boolean	unsetListOfObjectives() Returns true if listOfObjectives contain at least one element, otherwise false
boolean	unsetStrict() Unsets the variable strict.
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getPackageName, getPrefix, getURI

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

FBCModelPlugin

public FBCModelPlugin(FBCModelPlugin fbcPlugin)

Clone constructor

Parameters:

fbcPlugin - the instance to clone

FBCModelPlugin

public FBCModelPlugin(Model model)

Creates a new FBCModelPlugin instance.

Parameters:

model - the core Model

Method Detail

addFluxBound

@Deprecated
public boolean addFluxBound(FluxBound fluxBound)

Deprecated. Only defined in FBC version 1.

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(E))

addGeneProduct

public boolean addGeneProduct(GeneProduct geneProduct)

Adds a new GeneProduct to the listOfGeneProducts.

The listOfGeneProducts is initialized if necessary.

Parameters:

geneProduct - the element to add to the list

Returns:

true (as specified by Collection.add(E))

See Also:

Collection.add(Object)

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(E))

clone

public FBCModelPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

createFluxBound

@Deprecated
public FluxBound createFluxBound()

Deprecated. Only defined in FBC version 1.

Creates a new FluxBound element and adds it to the listOfFluxBounds list.

Returns:

a new FluxBound element

createFluxBound

@Deprecated
public FluxBound createFluxBound(String id)

Deprecated. Only defined in FBC version 1.

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

Parameters:

id - the id

Returns:

a new FluxBound element

createGeneProduct

public GeneProduct createGeneProduct()

Creates a new GeneProduct element and adds it to the ListOfGeneProducts list.

Returns:

a new GeneProduct element

createGeneProduct

public GeneProduct createGeneProduct(String id)

Creates a new GeneProduct element and adds it to the listOfGeneProducts list.

Parameters:

id - the id

Returns:

a new GeneProduct element.

createObjective

public Objective createObjective()

Creates a new Objective element and adds it to the listOfObjectives.

Returns:

the newly created Objective element or null if the operation fails.

See Also:

createObjective(String)

createObjective

public Objective createObjective(String id)

Creates a new Objective element and adds it to the listOfObjectives.

Parameters:

id - the identifier for the Objective of type SId, can be null.

Returns:

the newly created Objective element or null if the operation fails.

See Also:

createObjective(String, Objective.Type)

createObjective

public Objective createObjective(String id,
                                 Objective.Type type)

Creates a new Objective element and adds it to the listOfObjectives.

Parameters:

id - the identifier for the Objective of type SId, can be null.

type - the type of the Objective, i.e., maximize or minimize.

Returns:

the newly created Objective element or null if the operation fails.

See Also:

createObjective(String, String, Objective.Type)

createObjective

public Objective createObjective(String id,
                                 String name,
                                 Objective.Type type)

Creates a new Objective element and adds it to the listOfObjectives.

Parameters:

id - the identifier for the Objective of type SId, can be null.

name - the name of the objective that is to be created, can be null .

type - the type of the Objective, i.e., maximize or minimize.

Returns:

the newly created Objective element or null if the operation fails.

getActiveObjective

public String getActiveObjective()

Gets the activeObjective.

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

Returns:

the activeObjective or "".

getActiveObjectiveInstance

public Objective getActiveObjectiveInstance()

Returns:

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public TreeNode getChildAt(int index)

getChildCount

public int getChildCount()

getFluxBound

@Deprecated
public FluxBound getFluxBound(int i)

Deprecated. Only defined in FBC version 1.

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

@Deprecated
public int getFluxBoundCount()

Deprecated. Only defined in FBC version 1.

Return the number of FluxBound in this FBCModelPlugin.

Returns:

the number of FluxBound in this FBCModelPlugin.

getGeneProduct

public GeneProduct getGeneProduct(int i)

Gets an element from the listOfGeneProducts at the given index.

Parameters:

i - the index of the GeneProduct element to get.

Returns:

an element from the listOfGeneProducts at the given index.

Throws:

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

getGeneProduct

public GeneProduct getGeneProduct(String geneProductId)

Gets an element from the listOfGeneProducts, with the given id.

Parameters:

geneProductId - the id of the GeneProduct element to get.

Returns:

an element from the listOfGeneProducts with the given id or null.

getGeneProductCount

public int getGeneProductCount()

Returns the number of GeneProducts in this FBCModelPlugin.

Returns:

the number of GeneProducts in this FBCModelPlugin.

getListOfFluxBounds

@Deprecated
public ListOf<FluxBound> getListOfFluxBounds()

Deprecated. Only defined in FBC version 1.

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

Returns:

the listOfFluxBounds

getListOfGeneProducts

public ListOf<GeneProduct> getListOfGeneProducts()

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

Returns:

the listOfGeneProducts.

getListOfObjectives

public ListOfObjectives getListOfObjectives()

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

Returns:

the listOfObjectives

getNumFluxBound

@Deprecated
public int getNumFluxBound()

Deprecated. Only defined in FBC version 1.

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()

getNumGeneProducts

public int getNumGeneProducts()

Returns the number of GeneProducts in this FBCModelPlugin.

Returns:

the number of GeneProducts in this FBCModelPlugin.

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

same as getGeneProductCount()

getNumObjective

public int getNumObjective()

Return the number of Objectives in this FBCModelPlugin.

Returns:

the number of Objectives in this FBCModelPlugin.

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

same as getObjectiveCount()

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.

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

getStrict

public boolean getStrict()

Returns the value of strict.

Returns:

the value of strict.

isSetActiveObjective

public boolean isSetActiveObjective()

Returns:

isSetListOfFluxBounds

@Deprecated
public boolean isSetListOfFluxBounds()

Deprecated. Only defined in FBC version 1.

Returns true if listOfFluxBounds contains at least one element.

Returns:

true if listOfFluxBounds contains at least one element, otherwise false

isSetListOfGeneProducts

public boolean isSetListOfGeneProducts()

Returns true if listOfGeneProducts contains at least one element.

Returns:

true if listOfGeneProducts 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

isSetStrict

public boolean isSetStrict()

Returns whether strict is set.

Returns:

whether strict is set.

isStrict

public boolean isStrict()

Returns the value of strict.

Returns:

the value of strict.

readAttribute

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

removeFluxBound

@Deprecated
public boolean removeFluxBound(FluxBound fluxBound)

Deprecated. Only defined in FBC version 1.

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

@Deprecated
public void removeFluxBound(int i)

Deprecated. Only defined in FBC version 1.

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)

removeGeneProduct

public boolean removeGeneProduct(GeneProduct geneProduct)

Removes an element from the listOfGeneProducts.

Parameters:

geneProduct - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removeGeneProduct

public GeneProduct removeGeneProduct(int i)

Removes an element from the listOfGeneProducts at the given index.

Parameters:

i - the index where to remove the GeneProduct.

Returns:

the specified element if it was successfully found and removed.

Throws:

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

removeGeneProduct

public GeneProduct removeGeneProduct(String geneProductId)

Removes an element from the listOfGeneProducts.

Parameters:

geneProductId - the id of the element to be removed from the list.

Returns:

the removed element, if it was successfully found and removed or null.

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(Objective objective)

Parameters:

objective -

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 -

setListOfFluxBounds

@Deprecated
public void setListOfFluxBounds(ListOf<FluxBound> listOfFluxBounds)

Deprecated. Only defined in FBC version 1.

Sets the given ListOf<FluxBound>.

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

Parameters:

listOfFluxBounds -

setListOfGeneProducts

public void setListOfGeneProducts(ListOf<GeneProduct> listOfGeneProducts)

Sets the given ListOf<GeneProduct>. If listOfGeneProducts was defined before and contains some elements, they are all unset.

Parameters:

listOfGeneProducts -

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 -

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 -

setNotesKeyToUserObject

public void setNotesKeyToUserObject(String key)

Parameters:

key -

setStrict

public void setStrict(boolean strict)

Sets the value of strict

Parameters:

strict - the value of strict to be set.

unsetListOfFluxBounds

@Deprecated
public boolean unsetListOfFluxBounds()

Deprecated. Only defined in FBC version 1.

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

Returns:

true if listOfFluxBounds contain at least one element, otherwise false

unsetListOfGeneProducts

public boolean unsetListOfGeneProducts()

Returns true if listOfGeneProducts contains at least one element, otherwise false.

Returns:

true if listOfGeneProducts contains 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

unsetStrict

public boolean unsetStrict()

Unsets the variable strict.

Returns:

true if strict was set before, otherwise false.

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin