java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, IBoundingBox
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
CompartmentGlyph
, GeneralGlyph
, ReactionGlyph
, ReferenceGlyph
, SpeciesGlyph
, SpeciesReferenceGlyph
, TextGlyph
public abstract class AbstractReferenceGlyph extends GraphicalObject
NamedSBase
.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
AbstractReferenceGlyph() |
Creates a new instance of
AbstractReferenceGlyph . |
AbstractReferenceGlyph(int level,
int version) |
Creates a new instance of
AbstractReferenceGlyph . |
AbstractReferenceGlyph(java.lang.String id) |
Creates a new instance of
AbstractReferenceGlyph . |
AbstractReferenceGlyph(java.lang.String id,
int level,
int version) |
Creates a new instance of
AbstractReferenceGlyph . |
AbstractReferenceGlyph(AbstractReferenceGlyph glyph) |
Creates a new instance of
AbstractReferenceGlyph from the given glyph. |
Modifier and Type | Method | Description |
---|---|---|
abstract AbstractReferenceGlyph |
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 object) |
|
NamedSBase |
getNamedSBaseInstance() |
Gets the
NamedSBase instance corresponding to the reference id. |
java.lang.String |
getReference() |
Gets the reference.
|
NamedSBase |
getReferenceInstance() |
Gets the
NamedSBase instance corresponding to the reference id. |
SBase |
getSBaseInstance() |
Gets the
SBase instance corresponding to the reference id. |
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
boolean |
isSetReference() |
Returns
true if the reference attribute is not null and not empty. |
void |
setNamedSBase(NamedSBase namedSBase) |
Sets the reference based on the id of the given
NamedSBase . |
boolean |
setReference(java.lang.String sbase) |
Sets the reference.
|
void |
setSBase(SBase sbase) |
Sets the reference based on the id of the given
SBase . |
boolean |
unsetReference() |
Unsets the reference.
|
isValidId
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, 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
createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getChildAt, getChildCount, getMetaidRef, initDefaults, isIdMandatory, isSetBoundingBox, isSetMetaidRef, readAttribute, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef, writeXMLAttributes
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
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 AbstractReferenceGlyph()
AbstractReferenceGlyph
.public AbstractReferenceGlyph(int level, int version)
AbstractReferenceGlyph
.level
- the SBML levelversion
- the SBML versionpublic AbstractReferenceGlyph(AbstractReferenceGlyph glyph)
AbstractReferenceGlyph
from the given glyph.glyph
- the glyph to clone.public AbstractReferenceGlyph(java.lang.String id)
AbstractReferenceGlyph
.id
- the idpublic AbstractReferenceGlyph(java.lang.String id, int level, int version)
AbstractReferenceGlyph
.id
- the idlevel
- the SBML levelversion
- the SBML versionpublic abstract AbstractReferenceGlyph clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class GraphicalObject
public boolean equals(java.lang.Object object)
SBase
public java.lang.String getReference()
This attribute is used to store all the references from the different glyphs, meaning the 'compartment' for CompartmentGlyph
,
the 'species' for SpeciesGlyph
, the 'reaction' for ReactionGlyph
amd the 'reference' for GeneralGlyph
.
The optional reference attribute of type SIdRef that can be used to specify the id of the corresponding element
in the model that is represented.
If the reference attribute is used together with the metaidRef, they need to refer to the same object in the Model.
public NamedSBase getReferenceInstance()
NamedSBase
instance corresponding to the reference id.
Careful if you want to support SBML L3V2, you should use getSBaseInstance()
.
This method might be deprecated in future JSBML releases.
NamedSBase
instance corresponding to the reference id.public SBase getSBaseInstance()
SBase
instance corresponding to the reference id.SBase
instance corresponding to the reference id.public NamedSBase getNamedSBaseInstance()
NamedSBase
instance corresponding to the reference id.
Careful if you want to support SBML L3V2, you should use getSBaseInstance()
.
This method might be deprecated in future JSBML releases.
NamedSBase
instance corresponding to the reference id.getSBaseInstance()
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class GraphicalObject
SBase
instance.Object.hashCode()
public boolean isSetReference()
true
if the reference attribute is not null and not empty.true
if the reference attribute is set.public void setNamedSBase(NamedSBase namedSBase)
NamedSBase
.namedSBase
- the NamedSBase
to set as reference for this glyph.setReference(String)
public void setSBase(SBase sbase)
SBase
.sbase
- the SBase
to set as reference for this glyph.setReference(String)
public boolean setReference(java.lang.String sbase)
sbase
- the id of an SBase
.true
if this operation caused any change.public boolean unsetReference()
setReference(java.lang.String)
,
setNamedSBase(org.sbml.jsbml.NamedSBase)
and setSBase(org.sbml.jsbml.SBase)
)true
if this operation caused any change.