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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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: 1706 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	isSetValue
private FluxBound.Operation	operation
private java.lang.String	reaction
private static long	serialVersionUID Generated serial version identifier.
private java.lang.Double	value

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

Method Summary

Methods

Modifier and Type	Method and Description
FluxBound	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
FluxBound.Operation	getOperation() Returns the operation
java.lang.String	getReaction() Returns the reaction id
double	getValue() Returns the value
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	isSetOperation() Returns whether operation is set
boolean	isSetReaction() Returns whether reaction is set
boolean	isSetValue()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setOperation(FluxBound.Operation operation)
void	setReaction(Reaction reaction)
void	setReaction(java.lang.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
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, 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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

isSetValue

private boolean isSetValue

operation

private FluxBound.Operation operation

reaction

private java.lang.String reaction

value

private java.lang.Double value

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(java.lang.String id)

Creates a FluxBound instance with an id.

Parameters:

id -

FluxBound

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

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

Parameters:

id -

level -

version -

FluxBound

public FluxBound(java.lang.String id,
         java.lang.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()

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

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.

getOperation

public FluxBound.Operation getOperation()

Returns the operation

Returns:

the operation

getReaction

public java.lang.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()

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.

isSetValue

public boolean isSetValue()

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.

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(java.lang.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 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.

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