org.sbml.jsbml.ext.fbc

Class FBCReactionPlugin

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.ext.AbstractSBasePlugin

org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

org.sbml.jsbml.ext.fbc.FBCReactionPlugin

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SBasePlugin, TreeNodeWithChangeSupport

public class FBCReactionPlugin
extends AbstractFBCSBasePlugin

Extends the SBML Level 3 Version 1 Core Reaction class with the addition of a new optional element GeneProductAssociation as well as two optional attributes lowerFluxBound and upperFluxBound.

Introduced to FBC in version 2.

Since:

1.1

Author:

Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

elementNamespace, extendedSBase, packageVersion

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
FBCReactionPlugin() Creates a new FBCReactionPlugin instance.
FBCReactionPlugin(FBCReactionPlugin reactionPlugin) Creates a new FBCReactionPlugin instance.
FBCReactionPlugin(Reaction extendedSBase) Creates a new FBCReactionPlugin instance.

Method Summary

Modifier and Type	Method and Description
FBCReactionPlugin	clone()
GeneProductAssociation	createGeneProductAssociation()
GeneProductAssociation	createGeneProductAssociation(String id)
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
GeneProductAssociation	getGeneProductAssociation() Returns the value of geneProductAssociation.
String	getLowerFluxBound() Returns the value of lowerFluxBound.
Parameter	getLowerFluxBoundInstance()
String	getUpperFluxBound() Returns the value of upperFluxBound.
Parameter	getUpperFluxBoundInstance()
int	hashCode()
boolean	isSetGeneProductAssociation() Returns whether geneProductAssociation is set.
boolean	isSetLowerFluxBound() Returns whether lowerFluxBound is set.
boolean	isSetLowerFluxBoundInstance()
boolean	isSetUpperFluxBound() Returns whether upperFluxBound is set.
boolean	isSetUpperFluxBoundInstance()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setGeneProductAssociation(GeneProductAssociation geneProductAssociation) Sets the value of geneProductAssociation
void	setLowerFluxBound(Parameter boundParameter)
void	setLowerFluxBound(String lowerFluxBound) Sets the value of lowerFluxBound
void	setUpperFluxBound(Parameter boundParameter)
void	setUpperFluxBound(String upperFluxBound) Sets the value of upperFluxBound
boolean	unsetGeneProductAssociation() Unsets the variable geneProductAssociation.
boolean	unsetLowerFluxBound() Unsets the variable lowerFluxBound.
boolean	unsetUpperFluxBound() Unsets the variable upperFluxBound.
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.fbc.AbstractFBCSBasePlugin

getPackageName, getPrefix, getURI

Methods inherited from class org.sbml.jsbml.ext.AbstractSBasePlugin

fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getElementNamespace, getExtendedSBase, getLevel, getPackageVersion, getParentSBMLObject, getSBMLDocument, getVersion, isSetExtendedSBase, isSetPackageVersion, removeFromParent, setExtendedSBase, setNamespace, setPackageVersion

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getParent, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, notifyChildChange, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, 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.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Constructor Detail

FBCReactionPlugin

public FBCReactionPlugin()

Creates a new FBCReactionPlugin instance.

FBCReactionPlugin

public FBCReactionPlugin(FBCReactionPlugin reactionPlugin)

Creates a new FBCReactionPlugin instance.

Parameters:

reactionPlugin - the instance to be clone

FBCReactionPlugin

public FBCReactionPlugin(Reaction extendedSBase)

Creates a new FBCReactionPlugin instance.

Parameters:

extendedSBase - the core Reaction that is extended

Method Detail

clone

public FBCReactionPlugin clone()

Specified by:

clone in interface SBasePlugin

Overrides:

clone in class AbstractSBasePlugin

createGeneProductAssociation

public GeneProductAssociation createGeneProductAssociation()

Returns:

createGeneProductAssociation

public GeneProductAssociation createGeneProductAssociation(String id)

Parameters:

id -

Returns:

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBasePlugin

Overrides:

equals in class AbstractSBasePlugin

getAllowsChildren

public boolean getAllowsChildren()

getChildAt

public TreeNode getChildAt(int index)

getChildCount

public int getChildCount()

getGeneProductAssociation

public GeneProductAssociation getGeneProductAssociation()

Returns the value of geneProductAssociation.

Returns:

the value of geneProductAssociation.

getLowerFluxBound

public String getLowerFluxBound()

Returns the value of lowerFluxBound.

Returns:

the value of lowerFluxBound.

getLowerFluxBoundInstance

public Parameter getLowerFluxBoundInstance()

Returns:

getUpperFluxBound

public String getUpperFluxBound()

Returns the value of upperFluxBound.

Returns:

the value of upperFluxBound.

getUpperFluxBoundInstance

public Parameter getUpperFluxBoundInstance()

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBasePlugin

Overrides:

hashCode in class AbstractSBasePlugin

isSetGeneProductAssociation

public boolean isSetGeneProductAssociation()

Returns whether geneProductAssociation is set.

Returns:

whether geneProductAssociation is set.

isSetLowerFluxBound

public boolean isSetLowerFluxBound()

Returns whether lowerFluxBound is set.

Returns:

whether lowerFluxBound is set.

isSetLowerFluxBoundInstance

public boolean isSetLowerFluxBoundInstance()

Returns:

isSetUpperFluxBound

public boolean isSetUpperFluxBound()

Returns whether upperFluxBound is set.

Returns:

whether upperFluxBound is set.

isSetUpperFluxBoundInstance

public boolean isSetUpperFluxBoundInstance()

Returns:

readAttribute

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

setGeneProductAssociation

public void setGeneProductAssociation(GeneProductAssociation geneProductAssociation)

Sets the value of geneProductAssociation

Parameters:

geneProductAssociation - the value of geneProductAssociation to be set.

setLowerFluxBound

public void setLowerFluxBound(Parameter boundParameter)

Parameters:

boundParameter -

setLowerFluxBound

public void setLowerFluxBound(String lowerFluxBound)

Sets the value of lowerFluxBound

Parameters:

lowerFluxBound -

setUpperFluxBound

public void setUpperFluxBound(Parameter boundParameter)

Parameters:

boundParameter -

setUpperFluxBound

public void setUpperFluxBound(String upperFluxBound)

Sets the value of upperFluxBound

Parameters:

upperFluxBound -

unsetGeneProductAssociation

public boolean unsetGeneProductAssociation()

Unsets the variable geneProductAssociation.

Returns:

true if geneProductAssociation was set before, otherwise false.

unsetLowerFluxBound

public boolean unsetLowerFluxBound()

Unsets the variable lowerFluxBound.

Returns:

true if lowerFluxBound was set before, otherwise false.

unsetUpperFluxBound

public boolean unsetUpperFluxBound()

Unsets the variable upperFluxBound.

Returns:

true if upperFluxBound was set before, otherwise false.

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBasePlugin

Overrides:

writeXMLAttributes in class AbstractSBasePlugin