Package org.sbml.jsbml.ext.fbc

Class GeneProduct

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.fbc.GeneProduct

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, org.sbml.jsbml.util.TreeNodeWithChangeSupport

public class GeneProduct
extends AbstractNamedSBase
implements UniqueNamedSBase

Defines a single gene product.

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.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor	Description
GeneProduct()	Creates a new GeneProduct instance.
GeneProduct(int level, int version)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id, int level, int version)	Creates a new GeneProduct instance.
GeneProduct(java.lang.String id, java.lang.String name, int level, int version)	Creates a new GeneProduct instance.
GeneProduct(GeneProduct nsb)	Creates a new GeneProduct instance.

Method Summary

Modifier and Type	Method	Description
GeneProduct	clone()
boolean	equals(java.lang.Object obj)
java.lang.String	getAssociatedSpecies()	Returns the value of associatedSpecies.
java.lang.String	getLabel()	Returns the value of label
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetAssociatedSpecies()	Returns whether associatedSpecies is set.
boolean	isSetLabel()	Returns whether label is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setAssociatedSpecies(java.lang.String associatedSpecies)	Sets the value of associatedSpecies
void	setLabel(java.lang.String label)	Sets the value of label
boolean	unsetAssociatedSpecies()	Unsets the variable associatedSpecies.
boolean	unsetLabel()	Unsets the variable label
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

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, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

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

Constructor Detail

GeneProduct

public GeneProduct()

Creates a new GeneProduct instance.

GeneProduct

public GeneProduct(GeneProduct nsb)

Creates a new GeneProduct instance.

Parameters:

nsb - the instance to clone

GeneProduct

public GeneProduct(int level,
                   int version)

Creates a new GeneProduct instance.

Parameters:

level - the SBML level

version - the SBML version

GeneProduct

public GeneProduct(java.lang.String id)

Creates a new GeneProduct instance.

Parameters:

id - the id

GeneProduct

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

Creates a new GeneProduct instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

GeneProduct

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

Creates a new GeneProduct instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Method Detail

getAssociatedSpecies

public java.lang.String getAssociatedSpecies()

Returns the value of associatedSpecies.

Returns:

the value of associatedSpecies.

isSetAssociatedSpecies

public boolean isSetAssociatedSpecies()

Returns whether associatedSpecies is set.

Returns:

whether associatedSpecies is set.

setAssociatedSpecies

public void setAssociatedSpecies(java.lang.String associatedSpecies)

Sets the value of associatedSpecies

Parameters:

associatedSpecies - the value of associatedSpecies to be set.

unsetAssociatedSpecies

public boolean unsetAssociatedSpecies()

Unsets the variable associatedSpecies.

Returns:

true if associatedSpecies was set before, otherwise false.

clone

public GeneProduct clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

equals

public boolean equals(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getLabel

public java.lang.String getLabel()

Returns the value of label

Returns:

the value of label

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isSetLabel

public boolean isSetLabel()

Returns whether label is set

Returns:

whether label is set

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setLabel

public void setLabel(java.lang.String label)

Sets the value of label

Parameters:

label -

unsetLabel

public boolean unsetLabel()

Unsets the variable label

Returns:

true, if label was set before, otherwise false

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase