java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, Association
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class GeneProductRef extends AbstractNamedSBase implements Association, UniqueNamedSBase
GeneProduct
.
Introduced to FBC in version 2.
JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
GeneProductRef() |
Creates a new
GeneProductRef instance. |
GeneProductRef(int level,
int version) |
Creates a new
GeneProductRef instance. |
GeneProductRef(java.lang.String id) |
Creates a new
GeneProductRef instance. |
GeneProductRef(java.lang.String id,
int level,
int version) |
Creates a new
GeneProductRef instance. |
GeneProductRef(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a new
GeneProductRef instance. |
GeneProductRef(GeneProductRef gpr) |
Creates a new
GeneProductRef instance. |
Modifier and Type | Method | Description |
---|---|---|
GeneProductRef |
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) |
|
java.lang.String |
getGeneProduct() |
Returns the value of
geneProduct . |
GeneProduct |
getGeneProductInstance() |
Returns the
GeneProduct referenced by this GeneProductRef . |
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values using the namespace.
|
boolean |
isIdMandatory() |
Returns
true if the identifier of this
SBase is required to be defined (i.e., not null )
in the definition of SBML. |
boolean |
isSetGeneProduct() |
Returns whether
geneProduct is set. |
boolean |
isSetGeneProductInstance() |
Returns whether the gene product id is set and this id is a valid
GeneProduct id in this model. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
setGeneProduct(java.lang.String geneProduct) |
Sets the value of geneProduct
|
boolean |
unsetGeneProduct() |
Unsets the variable geneProduct
|
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. |
isValidId
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm
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
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
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
children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf
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
public GeneProductRef()
GeneProductRef
instance.public GeneProductRef(GeneProductRef gpr)
GeneProductRef
instance.gpr
- the instance to clonepublic GeneProductRef(int level, int version)
GeneProductRef
instance.level
- the SBML levelversion
- the SBML versionpublic GeneProductRef(java.lang.String id)
GeneProductRef
instance.id
- the idpublic GeneProductRef(java.lang.String id, int level, int version)
GeneProductRef
instance.id
- the idlevel
- the SBML levelversion
- the SBML versionpublic GeneProductRef(java.lang.String id, java.lang.String name, int level, int version)
GeneProductRef
instance.id
- the idname
- the namelevel
- the SBML levelversion
- the SBML versionpublic GeneProductRef clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public void initDefaults()
public boolean equals(java.lang.Object obj)
SBase
public java.lang.String getGeneProduct()
geneProduct
.geneProduct
.public GeneProduct getGeneProductInstance()
GeneProduct
referenced by this GeneProductRef
.GeneProduct
instance referenced by this GeneProductRef
or null.public boolean isSetGeneProductInstance()
GeneProduct
id in this model.true
the gene product id is set and this id is a valid GeneProduct
id in this model.public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
public boolean isIdMandatory()
SBase
true
if the identifier of this
SBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
isIdMandatory
in interface SBase
isIdMandatory
in class AbstractSBase
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.public boolean isSetGeneProduct()
geneProduct
is set.geneProduct
is set.public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
SBase
.
If the given attribute name is not recognized, nothing is done and
false
is returned.
readAttribute
in interface SBase
readAttribute
in class AbstractSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.public void setGeneProduct(java.lang.String geneProduct)
geneProduct
- the GeneProduct
idpublic boolean unsetGeneProduct()
true
, if geneProduct was set before,
otherwise false
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBase
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.
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractSBase
Map
containing the XML attributes of this object.