org.sbml.jsbml.ext.fbc

Class FluxBound

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.FluxBound

All Implemented Interfaces:

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

public class FluxBound
extends AbstractNamedSBase
implements UniqueNamedSBase

FluxBound is a new FBC class which holds a single (in)equality that provides the maximum or minimum value that a reaction flux can obtain at steady state.

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Last modified:

27.10.2011

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FluxBound.Operation Allowable operations for flux bounds.

Field Summary

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
FluxBound() Creates an instance of FluxBound.
FluxBound(FluxBound fb)
FluxBound(int level, int version) Creates a FluxBound instance with a level and version.
FluxBound(String id) Creates a FluxBound instance with an id.
FluxBound(String id, int level, int version) Creates a FluxBound instance with an id, level, and version.
FluxBound(String id, String name, int level, int version) Creates a FluxBound instance with an id, name, level, and version.

Method Summary

Modifier and Type	Method and Description
FluxBound	clone()
boolean	equals(Object obj)
FluxBound.Operation	getOperation() Returns the operation
String	getReaction() Returns the reaction id
double	getValue() Returns the value
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetOperation() Returns whether operation is set
boolean	isSetReaction() Returns whether reaction is set
boolean	isSetValue()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setOperation(FluxBound.Operation operation)
void	setReaction(Reaction reaction)
void	setReaction(String reaction) Sets the the reaction id
void	setValue(double value)
boolean	unsetOperation() Unsets the variable operation
boolean	unsetReaction() Unsets the variable reaction
boolean	unsetValue() Unsets the variable value
Map<String,String>	writeXMLAttributes()

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, getChildAt, getChildCount, 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, getChildAt, getChildCount, getIndex, getParent, isLeaf

Constructor Detail

FluxBound

public FluxBound()

Creates an instance of FluxBound.

FluxBound

public FluxBound(FluxBound fb)

Parameters:

fb -

FluxBound

public FluxBound(int level,
                 int version)

Creates a FluxBound instance with a level and version.

Parameters:

level -

version -

FluxBound

public FluxBound(String id)

Creates a FluxBound instance with an id.

Parameters:

id -

FluxBound

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

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

Parameters:

id -

level -

version -

FluxBound

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

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

Parameters:

id -

name -

level -

version -

Method Detail

clone

public FluxBound clone()

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 AbstractNamedSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase

getOperation

public FluxBound.Operation getOperation()

Returns the operation

Returns:

the operation

getReaction

public String getReaction()

Returns the reaction id

Returns:

the reaction id

getValue

public double getValue()

Returns the value

Returns:

the value

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

isSetValue

public boolean isSetValue()

Returns:

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

setOperation

public void setOperation(FluxBound.Operation operation)

Parameters:

operation - the operation to set

setReaction

public void setReaction(Reaction reaction)

Parameters:

reaction -

setReaction

public void setReaction(String reaction)

Sets the the reaction id

Parameters:

reaction - the reaction id to set

setValue

public void setValue(double value)

Parameters:

value - the value to set

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

unsetValue

public boolean unsetValue()

Unsets the variable value

Returns:

true, if value was set before, otherwise false

isSetOperation

public boolean isSetOperation()

Returns whether operation is set

Returns:

whether operation is set

unsetOperation

public boolean unsetOperation()

Unsets the variable operation

Returns:

true, if operation was set before, otherwise false

isSetReaction

public boolean isSetReaction()

Returns whether reaction is set

Returns:

whether reaction is set

unsetReaction

public boolean unsetReaction()

Unsets the variable reaction

Returns:

true, if reaction was set before, otherwise false