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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, 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

Version:

$Rev: 1706 $

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

Modifier and Type	Field and Description
private ListOf<FluxObjective>	listOfFluxObjectives
private static long	serialVersionUID
private Objective.Type	type

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

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(java.lang.String id) Creates a Objective instance with an id.
Objective(java.lang.String id, int level, int version) Creates a Objective instance with an id, level, and version.
Objective(java.lang.String id, java.lang.String name, int level, int version) Creates a Objective instance with an id, name, level, and version.

Method Summary

Methods

Modifier and Type	Method and Description
void	addFluxObjective(FluxObjective fluxObjective) Adds a new FluxObjective to the listOfFluxObjectives.
Objective	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
FluxObjective	createFluxObjective() Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
FluxObjective	createFluxObjective(java.lang.String id) Creates a new FluxObjective element and adds it to the ListOfFluxObjectives list
FluxObjective	createFluxObjective(java.lang.String id, java.lang.String name)
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<FluxObjective>	getListOfFluxObjectives() Returns the listOfFluxObjectives
Objective.Type	getType() Returns the type.
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetListOfFluxObjectives()
boolean	isSetType() Returns whether type is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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(java.lang.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(java.lang.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
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

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

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, isLeaf, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

listOfFluxObjectives

private ListOf<FluxObjective> listOfFluxObjectives

type

private Objective.Type type

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

Objective

public Objective(java.lang.String id)

Creates a Objective instance with an id.

Parameters:

id -

Objective

public Objective(java.lang.String id,
         int level,
         int version)

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

Parameters:

id -

level -

version -

Objective

public Objective(java.lang.String id,
         java.lang.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 void 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

clone

public Objective clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

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(java.lang.String id)

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

Parameters:

id - the id for the new FluxObjective

Returns:

a new FluxObjective element

createFluxObjective

public FluxObjective createFluxObjective(java.lang.String id,
                                java.lang.String name)

Parameters:

id -

name -

Returns:

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

equals

public boolean equals(java.lang.Object obj)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase

Parameters:

obj - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

getListOfFluxObjectives

public ListOf<FluxObjective> getListOfFluxObjectives()

Returns the listOfFluxObjectives

Returns:

the listOfFluxObjectives

getType

public Objective.Type getType()

Returns the type.

Returns:

the type

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

isSetListOfFluxObjectives

public boolean isSetListOfFluxObjectives()

Returns:

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

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.

setType

public void setType(java.lang.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

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.

isSetType

public boolean isSetType()

Returns whether type is set

Returns:

whether type is set

unsetType

public boolean unsetType()

Unsets the variable type

Returns:

true, if type was set before, otherwise false

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 -

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

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:

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

removeFluxObjective

public void removeFluxObjective(java.lang.String id)

Removes an element from the listOfFluxObjectives with the given id.

Parameters:

id - the id of the FluxObjective to remove.

Throws:

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