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, UniqueSId, TreeNodeWithChangeSupport

Deprecated.

Only defined in FBC Version 1.

@Deprecated
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 Deprecated. Only defined in FBC version 1.

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
FluxBound() Deprecated. Only defined in FBC version 1.
FluxBound(FluxBound fb) Deprecated. Only defined in FBC version 1.
FluxBound(int level, int version) Deprecated. Only defined in FBC version 1.
FluxBound(String id) Deprecated. Only defined in FBC version 1.
FluxBound(String id, int level, int version) Deprecated. Only defined in FBC version 1.
FluxBound(String id, String name, int level, int version) Deprecated. Only defined in FBC version 1.

Method Summary

Modifier and Type	Method and Description
FluxBound	clone() Deprecated.
boolean	equals(Object obj) Deprecated.
FluxBound.Operation	getOperation() Deprecated.
String	getReaction() Deprecated. Only defined in FBC version 1.
Reaction	getReactionInstance() Deprecated. Only defined in FBC version 1.
double	getValue() Deprecated. Only defined in FBC version 1.
int	hashCode() Deprecated.
void	initDefaults() Deprecated. Only defined in FBC version 1.
boolean	isIdMandatory() Deprecated.
boolean	isSetOperation() Deprecated. Only defined in FBC version 1.
boolean	isSetReaction() Deprecated. Only defined in FBC version 1.
boolean	isSetReactionInstance() Deprecated. Only defined in FBC version 1.
boolean	isSetValue() Deprecated. Only defined in FBC version 1.
boolean	readAttribute(String attributeName, String prefix, String value) Deprecated.
void	setOperation(FluxBound.Operation operation) Deprecated. Only defined in FBC version 1.
void	setReaction(Reaction reaction) Deprecated. Only defined in FBC version 1.
void	setReaction(String reaction) Deprecated. Only defined in FBC version 1.
void	setValue(double value) Deprecated. Only defined in FBC version 1.
boolean	unsetOperation() Deprecated. Only defined in FBC version 1.
boolean	unsetReaction() Deprecated. Only defined in FBC version 1.
boolean	unsetValue() Deprecated. Only defined in FBC version 1.
Map<String,String>	writeXMLAttributes() Deprecated.

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, 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, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, 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.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

FluxBound

@Deprecated
public FluxBound()

Deprecated. Only defined in FBC version 1.

Creates an instance of FluxBound.

FluxBound

@Deprecated
public FluxBound(FluxBound fb)

Deprecated. Only defined in FBC version 1.

Parameters:

fb -

FluxBound

@Deprecated
public FluxBound(int level,
                             int version)

Deprecated. Only defined in FBC version 1.

Creates a FluxBound instance with a level and version.

Parameters:

level -

version -

FluxBound

@Deprecated
public FluxBound(String id)

Deprecated. Only defined in FBC version 1.

Creates a FluxBound instance with an id.

Parameters:

id -

FluxBound

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

Deprecated. Only defined in FBC version 1.

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

Parameters:

id -

level -

version -

FluxBound

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

Deprecated. Only defined in FBC version 1.

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

Parameters:

id -

name -

level -

version -

Method Detail

clone

@Deprecated
public FluxBound clone()

Deprecated.

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

equals

@Deprecated
public boolean equals(Object obj)

Deprecated.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getOperation

@Deprecated
public FluxBound.Operation getOperation()

Deprecated.

Returns the operation

Returns:

the operation

getReaction

@Deprecated
public String getReaction()

Deprecated. Only defined in FBC version 1.

Returns the reaction id

Returns:

the reaction id

getReactionInstance

@Deprecated
public Reaction getReactionInstance()

Deprecated. Only defined in FBC version 1.

Returns:

The Reaction to which this flux bound belongs.

getValue

@Deprecated
public double getValue()

Deprecated. Only defined in FBC version 1.

Returns the value

Returns:

the value

hashCode

@Deprecated
public int hashCode()

Deprecated.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

initDefaults

@Deprecated
public void initDefaults()

Deprecated. Only defined in FBC version 1.

Initializes the default values using the namespace.

isIdMandatory

@Deprecated
public boolean isIdMandatory()

Deprecated.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetOperation

@Deprecated
public boolean isSetOperation()

Deprecated. Only defined in FBC version 1.

Returns whether operation is set

Returns:

whether operation is set

isSetReaction

@Deprecated
public boolean isSetReaction()

Deprecated. Only defined in FBC version 1.

Returns whether reaction is set

Returns:

whether reaction is set

isSetReactionInstance

@Deprecated
public boolean isSetReactionInstance()

Deprecated. Only defined in FBC version 1.

Returns:

true if a Reaction with the id given by getReaction() exists in the Model, false otherwise.

isSetValue

@Deprecated
public boolean isSetValue()

Deprecated. Only defined in FBC version 1.

Returns:

readAttribute

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

Deprecated.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setOperation

@Deprecated
public void setOperation(FluxBound.Operation operation)

Deprecated. Only defined in FBC version 1.

Parameters:

operation - the operation to set

setReaction

@Deprecated
public void setReaction(Reaction reaction)

Deprecated. Only defined in FBC version 1.

Parameters:

reaction -

setReaction

@Deprecated
public void setReaction(String reaction)

Deprecated. Only defined in FBC version 1.

Sets the the reaction id

Parameters:

reaction - the reaction id to set

setValue

@Deprecated
public void setValue(double value)

Deprecated. Only defined in FBC version 1.

Parameters:

value - the value to set

unsetOperation

@Deprecated
public boolean unsetOperation()

Deprecated. Only defined in FBC version 1.

Unsets the variable operation

Returns:

true, if operation was set before, otherwise false

unsetReaction

@Deprecated
public boolean unsetReaction()

Deprecated. Only defined in FBC version 1.

Unsets the variable reaction

Returns:

true, if reaction was set before, otherwise false

unsetValue

@Deprecated
public boolean unsetValue()

Deprecated. Only defined in FBC version 1.

Unsets the variable value

Returns:

true, if value was set before, otherwise false

writeXMLAttributes

@Deprecated
public Map<String,String> writeXMLAttributes()

Deprecated.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase