org.sbml.jsbml.ext.fbc

Class FluxObjective

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.FluxObjective

All Implemented Interfaces:

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

public class FluxObjective
extends AbstractNamedSBase
implements UniqueNamedSBase

The FluxObjective class is a relatively simple container for a model variable weighted by a signed linear coefficient.

Since:

1.0

Author:

Nicolas Rodriguez

See Also:

Serialized Form

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

Method Summary

Modifier and Type	Method and Description
FluxObjective	clone() clones this class
boolean	equals(Object obj)
double	getCoefficient() Returns the value of coefficient
String	getReaction() Returns the value of reaction
Reaction	getReactionInstance() Returns the Reaction associated with this FluxObjective.
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetCoefficient() Returns whether coefficient is set
boolean	isSetReaction() Returns whether reaction is set
boolean	isSetReactionInstance() Returns whether reaction is set and is a valid Reaction in the model.
boolean	readAttribute(String attributeName, String prefix, String value)
void	setCoefficient(double coefficient) The coefficient attribute takes the value of the coefficient that the FluxObjective takes in the context of the enclosing Objective class.
void	setReaction(Reaction reaction) Sets the Reaction that this FluxObjective is associated with in the context of the enclosing Objective class.
void	setReaction(String reaction) Sets the reaction that this FluxObjective is associated with in the context of the enclosing Objective class.
boolean	unsetCoefficient() Unsets the variable coefficient
boolean	unsetReaction() Unsets the variable reaction
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, getChildAt, getChildCount, 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, getChildAt, getChildCount, getIndex, getParent, isLeaf

Constructor Detail

FluxObjective

public FluxObjective()

Creates an FluxObjective instance

FluxObjective

public FluxObjective(int level,
                     int version)

Creates a FluxObjective instance with a level and version.

Parameters:

level - the SBML level

version - the SBML version

FluxObjective

public FluxObjective(String id)

Creates a FluxObjective instance with an id.

Parameters:

id - the id

FluxObjective

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

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

Parameters:

id - the id

level - the SBML level

version - the SBML version

FluxObjective

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

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

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

FluxObjective

public FluxObjective(FluxObjective obj)

Clone constructor

Parameters:

obj - the instance to clone

Method Detail

clone

public FluxObjective clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getCoefficient

public double getCoefficient()

Returns the value of coefficient

Returns:

the value of coefficient

getReaction

public String getReaction()

Returns the value of reaction

Returns:

the value of reaction

getReactionInstance

public Reaction getReactionInstance()

Returns the Reaction associated with this FluxObjective.

Returns:

the Reaction associated with this FluxObjective or null if the reaction attribute is not a valid reaction id.

isSetReactionInstance

public boolean isSetReactionInstance()

Returns whether reaction is set and is a valid Reaction in the model.

Returns:

whether reaction is set and is a valid Reaction in the model.

isSetReaction

public boolean isSetReaction()

Returns whether reaction is set

Returns:

whether reaction is set

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetCoefficient

public boolean isSetCoefficient()

Returns whether coefficient is set

Returns:

whether coefficient is set

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setCoefficient

public void setCoefficient(double coefficient)

The coefficient attribute takes the value of the coefficient that the FluxObjective takes in the context of the enclosing Objective class.

Parameters:

coefficient - the coefficient to set

setReaction

public void setReaction(Reaction reaction)

Sets the Reaction that this FluxObjective is associated with in the context of the enclosing Objective class.

Parameters:

reaction - the reaction to set

setReaction

public void setReaction(String reaction)

Sets the reaction that this FluxObjective is associated with in the context of the enclosing Objective class.

Parameters:

reaction - the reaction to set

unsetCoefficient

public boolean unsetCoefficient()

Unsets the variable coefficient

Returns:

true, if coefficient was set before, otherwise false

unsetReaction

public boolean unsetReaction()

Unsets the variable reaction

Returns:

true, if reaction was set before, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase