org.sbml.jsbml.ext.fbc

Class Objective

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.Objective

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class Objective
extends AbstractNamedSBase
implements UniqueNamedSBase

An integral component in a complete description of a steady-state model is the so-called 'objective function' which generally consists of a linear combination of model variables (fluxes) and a sense (direction). In the FBC package this concept is succinctly captured in the Objective class.

Since:

1.0

Author:

Nicolas Rodriguez, Andreas Dräger

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Objective.Type

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Objective() Creates an Objective instance
Objective(int level, int version) Creates a Objective instance with a level and version.
Objective(Objective obj) Clone constructor
Objective(String id) Creates a Objective instance with an id.
Objective(String id, int level, int version) Creates a Objective instance with an id, level, and version.
Objective(String id, String name, int level, int version) Creates a Objective instance with an id, name, level, and version.

Method Summary

Modifier and Type	Method and Description
boolean	addFluxObjective(FluxObjective fluxObjective) Adds a new FluxObjective to the listOfFluxObjectives.
Objective	clone()
FluxObjective	createFluxObjective() Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
FluxObjective	createFluxObjective(String id) Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
FluxObjective	createFluxObjective(String id, String name)
FluxObjective	createFluxObjective(String id, String name, double coefficient, Reaction reaction)
FluxObjective	createFluxObjective(String id, String name, double coefficient, String rId)
boolean	equals(Object obj)
TreeNode	getChildAt(int index)
int	getChildCount()
int	getFluxObjectiveCount()
ListOf<FluxObjective>	getListOfFluxObjectives() Returns the listOfFluxObjectives
int	getNumFluxObjectives() Deprecated. use getFluxObjectiveCount()
Objective.Type	getType() Returns the type.
int	hashCode()
boolean	isIdMandatory()
boolean	isSetListOfFluxObjectives()
boolean	isSetType() Returns whether type is set
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeFluxObjective(FluxObjective fluxObjective) Removes an element from the listOfFluxObjectives.
void	removeFluxObjective(int i) Removes an element from the listOfFluxObjectives at the given index.
void	removeFluxObjective(String id) Removes an element from the listOfFluxObjectives with the given id.
void	setListOfFluxObjectives(ListOf<FluxObjective> listOfFluxObjectives) This list houses the actual fluxes to partake in this objective function, which are encoded by FluxObjective Sets the given ListOf<FluxObjective>.
void	setType(Objective.Type type) Sets the value of type
void	setType(String type) The required type attribute contains a Objective.Type which represents the sense of the optimality constraint and can take one of two values, minimize or maximize.
boolean	unsetListOfFluxObjectives() Unsets the listOfFluxObjectives.
boolean	unsetType() Unsets the variable type
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getIndex, getParent, isLeaf

Constructor Detail

Objective

public Objective()

Creates an Objective instance

Objective

public Objective(int level,
                 int version)

Creates a Objective instance with a level and version.

Parameters:

level -

version -

Objective

public Objective(Objective obj)

Clone constructor

Parameters:

obj -

Objective

public Objective(String id)

Creates a Objective instance with an id.

Parameters:

id -

Objective

public Objective(String id,
                 int level,
                 int version)

Creates a Objective instance with an id, level, and version.

Parameters:

id -

level -

version -

Objective

public Objective(String id,
                 String name,
                 int level,
                 int version)

Creates a Objective instance with an id, name, level, and version.

Parameters:

id -

name -

level -

version -

Method Detail

addFluxObjective

public boolean addFluxObjective(FluxObjective fluxObjective)

Adds a new FluxObjective to the listOfFluxObjectives.

The listOfFluxObjectives is initialized if necessary.

Parameters:

fluxObjective - the element to add to the list

Returns:

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

clone

public Objective clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

createFluxObjective

public FluxObjective createFluxObjective()

Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list

Returns:

a new FluxObjective element

createFluxObjective

public FluxObjective createFluxObjective(String id)

Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list

Parameters:

id - the id for the new FluxObjective

Returns:

the newly created FluxObjective element or null if the operation failed.

createFluxObjective

public FluxObjective createFluxObjective(String id,
                                         String name)

Parameters:

id -

name -

Returns:

the newly created FluxObjective element or null if the operation failed.

createFluxObjective

public FluxObjective createFluxObjective(String id,
                                         String name,
                                         double coefficient,
                                         Reaction reaction)

Parameters:

id -

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

coefficient -

reaction -

Returns:

the newly created FluxObjective element or null if the operation failed.

createFluxObjective

public FluxObjective createFluxObjective(String id,
                                         String name,
                                         double coefficient,
                                         String rId)

Parameters:

id -

name -

coefficient -

rId -

Returns:

the newly created FluxObjective element or null if the operation failed.

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getFluxObjectiveCount

public int getFluxObjectiveCount()

Returns:

getListOfFluxObjectives

public ListOf<FluxObjective> getListOfFluxObjectives()

Returns the listOfFluxObjectives

Returns:

the listOfFluxObjectives

getNumFluxObjectives

@Deprecated
public int getNumFluxObjectives()

Deprecated. use getFluxObjectiveCount()

Returns:

getType

public Objective.Type getType()

Returns the type.

Returns:

the type

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetListOfFluxObjectives

public boolean isSetListOfFluxObjectives()

Returns:

isSetType

public boolean isSetType()

Returns whether type is set

Returns:

whether type is set

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

removeFluxObjective

public boolean removeFluxObjective(FluxObjective fluxObjective)

Removes an element from the listOfFluxObjectives.

Parameters:

fluxObjective - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeFluxObjective

public void removeFluxObjective(int i)

Removes an element from the listOfFluxObjectives at the given index.

Parameters:

i - the index where to remove the FluxObjective

Throws:

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

removeFluxObjective

public void removeFluxObjective(String id)

Removes an element from the listOfFluxObjectives with the given id.

Parameters:

id - the id of the FluxObjective to remove.

Throws:

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

setListOfFluxObjectives

public void setListOfFluxObjectives(ListOf<FluxObjective> listOfFluxObjectives)

This list houses the actual fluxes to partake in this objective function, which are encoded by FluxObjective Sets the given ListOf<FluxObjective>. If listOfFluxObjectives was defined before and contains some elements, they are all unset.

Parameters:

listOfFluxObjectives -

setType

public void setType(String type)

The required type attribute contains a Objective.Type which represents the sense of the optimality constraint and can take one of two values, minimize or maximize. Sets the type from a String.

Parameters:

type - the type to set

setType

public void setType(Objective.Type type)

Sets the value of type

Parameters:

type -

unsetListOfFluxObjectives

public boolean unsetListOfFluxObjectives()

Unsets the listOfFluxObjectives.

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

Returns:

true, if listOfFluxObjectives contain at least one element, otherwise false

unsetType

public boolean unsetType()

Unsets the variable type

Returns:

true, if type was set before, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase