java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, IBoundingBox
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class GeneralGlyph extends AbstractReferenceGlyph
GeneralGlyph
is used to facilitate the representation of elements
other than Compartment
, Species
and Reaction
and thus
can be used for the display of relationships of Rule
or
elements defined by other SBML packages. It closely follows the structure of
the ReactionGlyph
. GeneralGlyph
is defined to have an
optional attribute reference as well as the elements curve,
listOfReferenceGlyphs and listOfSubGlyphs.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
GeneralGlyph() |
|
GeneralGlyph(int level,
int version) |
Creates a new instance of
GeneralGlyph . |
GeneralGlyph(java.lang.String id) |
Creates a new instance of
GeneralGlyph . |
GeneralGlyph(java.lang.String id,
int level,
int version) |
Creates a new instance of
GeneralGlyph . |
GeneralGlyph(GeneralGlyph generalGlyph) |
Creates a new instance of
GeneralGlyph cloned from the given element. |
Modifier and Type | Method | Description |
---|---|---|
boolean |
addReferenceGlyph(ReferenceGlyph glyph) |
Appends the specified element to the end of the
listOfReferenceGlyphs . |
boolean |
addSubGlyph(GraphicalObject subGlyph) |
Adds a new
GraphicalObject to the listOfSubGlyphs. |
GeneralGlyph |
clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
CompartmentGlyph |
createCompartmentGlyph() |
Creates a new
CompartmentGlyph element and adds it to the ListOfSubGlyphs list. |
CompartmentGlyph |
createCompartmentGlyph(java.lang.String id) |
Creates a new
CompartmentGlyph element and adds it to the ListOfSubGlyphs list. |
GeneralGlyph |
createGeneralGlyph() |
Creates a new
GeneralGlyph element and adds it to the ListOfSubGlyphs list. |
GeneralGlyph |
createGeneralGlyph(java.lang.String id) |
Creates a new
GeneralGlyph element and adds it to the ListOfSubGlyphs list. |
GraphicalObject |
createGraphicalObject() |
Creates a new
GraphicalObject element and adds it to the ListOfSubGlyphs list. |
GraphicalObject |
createGraphicalObject(java.lang.String id) |
Creates a new
GraphicalObject element and adds it to the ListOfSubGlyphs list. |
ReactionGlyph |
createReactionGlyph() |
Creates a new
ReactionGlyph element and adds it to the ListOfSubGlyphs list. |
ReactionGlyph |
createReactionGlyph(java.lang.String id) |
Creates a new
ReactionGlyph element and adds it to the ListOfSubGlyphs list. |
ReferenceGlyph |
createReferenceGlyph() |
Creates a new
ReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
ReferenceGlyph |
createReferenceGlyph(java.lang.String id) |
Creates and adds a new
ReferenceGlyph . |
ReferenceGlyph |
createReferenceGlyphForList() |
Creates a new
ReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
ReferenceGlyph |
createReferenceGlyphForList(java.lang.String id) |
Creates a new
ReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesGlyph |
createSpeciesGlyph() |
Creates a new
SpeciesGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesGlyph |
createSpeciesGlyph(java.lang.String id) |
Creates a new
SpeciesGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesReferenceGlyph |
createSpeciesReferenceGlyph() |
Creates a new
SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
SpeciesReferenceGlyph |
createSpeciesReferenceGlyph(java.lang.String id) |
Creates a new
SpeciesReferenceGlyph element and adds it to the ListOfSubGlyphs list. |
TextGlyph |
createTextGlyph() |
Creates a new
TextGlyph element and adds it to the ListOfSubGlyphs list. |
TextGlyph |
createTextGlyph(java.lang.String id) |
Creates a new
TextGlyph element and adds it to the ListOfSubGlyphs list. |
boolean |
equals(java.lang.Object object) |
|
javax.swing.tree.TreeNode |
getChildAt(int index) |
|
int |
getChildCount() |
|
Curve |
getCurve() |
Gets the
Curve . |
ListOf<ReferenceGlyph> |
getListOfReferenceGlyphs() |
Returns the
listOfReferenceGlyphs . |
ListOf<GraphicalObject> |
getListOfSubGlyphs() |
Returns the listOfSubGlyphs.
|
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values using the namespace.
|
boolean |
isSetCurve() |
Returns
true if the Curve element is not null. |
boolean |
isSetListOfReferenceGlyphs() |
Returns
true if the listOfReferenceGlyphs element is not null. |
boolean |
isSetListOfSubGlyphs() |
Returns
true , if listOfSubGlyphs contains at least one element. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
removeGeneralGlyph(int i) |
Removes an element from the
listOfSubGlyphs at the given index. |
boolean |
removeGeneralGlyph(GraphicalObject subGlyph) |
Removes an element from the listOfSubGlyphs.
|
void |
removeSubGlyph(int i) |
Removes an element from the
listOfSubGlyphs at the given index. |
boolean |
removeSubGlyph(GraphicalObject subGlyph) |
Removes an element from the listOfSubGlyphs.
|
void |
setCurve(Curve curve) |
Sets the
Curve . |
void |
setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph) |
Sets the
listOfReferenceGlyphs . |
void |
setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs) |
The listOfSubGlyphs is an optional list that can contain sub-glyphs of the
GeneralGlyph . |
void |
unsetCurve() |
Unsets the curve (and fires appropriate Event)
|
boolean |
unsetListOfSubGlyphs() |
Returns
true , if listOfSubGlyphs contain at least one element,
otherwise false |
void |
unsetReaction() |
|
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
getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, isSetReference, setNamedSBase, setReference, setSBase, unsetReference
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, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef
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 GeneralGlyph()
public GeneralGlyph(int level, int version)
GeneralGlyph
.level
- the SBML levelversion
- the SBML versionpublic GeneralGlyph(GeneralGlyph generalGlyph)
GeneralGlyph
cloned from the given element.generalGlyph
- the GeneralGlyph
to clone.public GeneralGlyph(java.lang.String id)
GeneralGlyph
.id
- the idpublic GeneralGlyph(java.lang.String id, int level, int version)
GeneralGlyph
.id
- the idlevel
- the SBML levelversion
- the SBML versionpublic void initDefaults()
initDefaults
in class GraphicalObject
public boolean isSetListOfSubGlyphs()
true
, if listOfSubGlyphs contains at least one element.true
, if listOfSubGlyphs contains at least one element,
otherwise false
public ListOf<GraphicalObject> getListOfSubGlyphs()
public void setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs)
GeneralGlyph
.
One example of its use could be a sub-module containing SpeciesGlyph
s and ReactionGlyph
s
that are not necessarily part of the enclosing Model
. Another example is an Event
, visualized
with its Trigger
and additional GeneralGlyph
s for its EventAssignment
. The
listOfSubGlyphs consists of GraphicalObject
s or derived classes. Thus, unlike
the listOfAdditionalGraphicalObjects (which may only contain GraphicalObject
or GeneralGlyph
s),
the listOfSubGlyphs may contain any derived class, such as for example TextGlyph
elements.
Sets the given ListOf<GraphicalObject
>. If listOfSubGlyphs
was defined before and contains some elements, they are all unset.listOfSubGlyphs
- the list of SubGlyphs to set.public boolean unsetListOfSubGlyphs()
true
, if listOfSubGlyphs contain at least one element,
otherwise false
true
, if listOfSubGlyphs contain at least one element,
otherwise false
public boolean addSubGlyph(GraphicalObject subGlyph)
GraphicalObject
to the listOfSubGlyphs.
The listOfSubGlyphs is initialized if necessary.
subGlyph
- the element to add to the listtrue
(as specified by Collection.add(E)
)public boolean removeSubGlyph(GraphicalObject subGlyph)
subGlyph
- the element to be removed from the listtrue
if the list contained the specified elementList.remove(Object)
public void removeSubGlyph(int i)
listOfSubGlyphs
at the given index.i
- the index where to remove the glyph.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size)public void removeGeneralGlyph(int i)
listOfSubGlyphs
at the given index.i
- the index where to remove the glyph.public boolean removeGeneralGlyph(GraphicalObject subGlyph)
subGlyph
- the element to be removed from the listtrue
if the list contained the specified elementList.remove(Object)
public ReferenceGlyph createReferenceGlyph()
ReferenceGlyph
element and adds it to the ListOfSubGlyphs list.ReferenceGlyph
instance.public TextGlyph createTextGlyph()
TextGlyph
element and adds it to the ListOfSubGlyphs list.TextGlyph
instance.public TextGlyph createTextGlyph(java.lang.String id)
TextGlyph
element and adds it to the ListOfSubGlyphs list.public ReferenceGlyph createReferenceGlyphForList()
ReferenceGlyph
element and adds it to the ListOfSubGlyphs list.ReferenceGlyph
element.public ReferenceGlyph createReferenceGlyphForList(java.lang.String id)
ReferenceGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new ReferenceGlyph
instance.ReferenceGlyph
element.public SpeciesGlyph createSpeciesGlyph()
SpeciesGlyph
element and adds it to the ListOfSubGlyphs list.SpeciesGlyph
element.public SpeciesGlyph createSpeciesGlyph(java.lang.String id)
SpeciesGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new SpeciesGlyph
instance.SpeciesGlyph
element.public SpeciesReferenceGlyph createSpeciesReferenceGlyph()
SpeciesReferenceGlyph
element and adds it to the ListOfSubGlyphs list.SpeciesReferenceGlyph
element.public SpeciesReferenceGlyph createSpeciesReferenceGlyph(java.lang.String id)
SpeciesReferenceGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new SpeciesReferenceGlyph
instance.SpeciesReferenceGlyph
element.public CompartmentGlyph createCompartmentGlyph()
CompartmentGlyph
element and adds it to the ListOfSubGlyphs list.CompartmentGlyph
element.public CompartmentGlyph createCompartmentGlyph(java.lang.String id)
CompartmentGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new CompartmentGlyph
instance.CompartmentGlyph
element.public GeneralGlyph createGeneralGlyph()
GeneralGlyph
element and adds it to the ListOfSubGlyphs list.GeneralGlyph
.public GeneralGlyph createGeneralGlyph(java.lang.String id)
GeneralGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new GeneralGlyph
instance.GeneralGlyph
element.public ReactionGlyph createReactionGlyph()
ReactionGlyph
element and adds it to the ListOfSubGlyphs list.ReactionGlyph
element.public ReactionGlyph createReactionGlyph(java.lang.String id)
ReactionGlyph
element and adds it to the ListOfSubGlyphs list.id
- the id of the new ReactionGlyph
instance.ReactionGlyph
element.public GraphicalObject createGraphicalObject()
GraphicalObject
element and adds it to the ListOfSubGlyphs list.GraphicalObject
element.public GraphicalObject createGraphicalObject(java.lang.String id)
GraphicalObject
element and adds it to the ListOfSubGlyphs list.id
- the id of the new GraphicalObject
instance.GraphicalObject
element.public boolean addReferenceGlyph(ReferenceGlyph glyph)
listOfReferenceGlyphs
.glyph
- the glyph to be added.true
(as specified by Collection.add(E)
)java.lang.NullPointerException
- if the specified element is null and this list does not
permit null elementsjava.lang.IllegalArgumentException
- if some property of this element prevents it from being added
to this listpublic GeneralGlyph clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractReferenceGlyph
public ReferenceGlyph createReferenceGlyph(java.lang.String id)
ReferenceGlyph
.id
- the identifier for the ReferenceGlyph
to be created.ReferenceGlyph
.public boolean equals(java.lang.Object object)
SBase
public javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
in class GraphicalObject
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class GraphicalObject
public ListOf<ReferenceGlyph> getListOfReferenceGlyphs()
listOfReferenceGlyphs
.
If the listOfReferenceGlyphs
has not yet been initialized, this
will be done by this method.
listOfReferenceGlyphs
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractReferenceGlyph
SBase
instance.Object.hashCode()
public boolean isSetCurve()
true
if the Curve
element is not null.true
if the Curve
element is set.public boolean isSetListOfReferenceGlyphs()
true
if the listOfReferenceGlyphs
element is not null.true
if the listOfReferenceGlyphs
element 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 GraphicalObject
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 setCurve(Curve curve)
Curve
.
This is an optional attribute of type Curve
. If this is defined, then the
BoundingBox
is to be ignored.
curve
- the Curve
instance to set.public void setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph)
listOfReferenceGlyphs
.
The listOfReferenceGlyphs is optional, since conceivable the GeneralGlyph
could
just contain a number of subglyphs. When present, it must include at least one ReferenceGlyph
.
listOfReferenceGlyph
- the list of ReferenceGlyph
to set.public void unsetReaction()
public void unsetCurve()
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 GraphicalObject
Map
containing the XML attributes of this object.