org.sbml.jsbml.ext.layout
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.Modifier and Type | Field and Description |
---|---|
private Curve |
curve |
private ListOf<ReferenceGlyph> |
listOfReferenceGlyphs |
private ListOf<GraphicalObject> |
listOfSubGlyphs |
private static long |
serialVersionUID
Generated serial version identifier.
|
ignoredExtensions, ignoredXMLElements
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
GeneralGlyph() |
GeneralGlyph(GeneralGlyph generalGlyph) |
GeneralGlyph(int level,
int version) |
GeneralGlyph(java.lang.String id) |
GeneralGlyph(java.lang.String id,
int level,
int version) |
Modifier and Type | Method and 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() |
ListOf<ReferenceGlyph> |
getListOfReferenceGlyphs()
If the
listOfReferenceGlyphs has not yet been initialized, this
will be done by this method. |
ListOf<GraphicalObject> |
getListOfSubGlyphs()
Returns the listOfSubGlyphs.
|
int |
hashCode()
Returns a hash code value for this
SBase instance. |
boolean |
isSetCurve() |
boolean |
isSetListOfReferenceGlyphs() |
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(GraphicalObject subGlyph) |
void |
removeGeneralGlyph(int i) |
boolean |
removeSubGlyph(GraphicalObject subGlyph)
Removes an element from the listOfSubGlyphs.
|
void |
removeSubGlyph(int i)
Removes an element from the listOfSubGlyphs at the given index.
|
void |
setCurve(Curve curve)
This is an optional attribute of type
Curve . |
void |
setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph)
The listOfReferenceGlyphs is optional, since conceivable the
GeneralGlyph could
just contain a number of subglyphs. |
void |
setListOfSubGlyphs(ListOf<GraphicalObject> listOfSubGlyphs)
The listOfSubGlyphs is an optional list that can contain sub-glyphs of the
GeneralGlyph . |
private void |
unsetListOfReferenceGlyph() |
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. |
getNamedSBaseInstance, getReference, getReferenceInstance, isSetReference, setNamedSBase, setReference, setReference, toString, unsetReference
createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef
getId, getName, isSetId, isSetName, isValidId, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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
finalize, getClass, notify, notifyAll, wait, wait, wait
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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
private static final long serialVersionUID
private Curve curve
private ListOf<ReferenceGlyph> listOfReferenceGlyphs
private ListOf<GraphicalObject> listOfSubGlyphs
public GeneralGlyph()
public GeneralGlyph(int level, int version)
level
- version
- public GeneralGlyph(GeneralGlyph generalGlyph)
generalGlyph
- public GeneralGlyph(java.lang.String id)
id
- public GeneralGlyph(java.lang.String id, int level, int version)
id
- level
- version
- 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
- 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
)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)
i
- the index where to remove the SubGlyph
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)
public void removeGeneralGlyph(GraphicalObject subGlyph)
public ReferenceGlyph createReferenceGlyph()
ReferenceGlyph
element and adds it to the ListOfSubGlyphs listpublic TextGlyph createTextGlyph()
TextGlyph
element and adds it to the ListOfSubGlyphs listpublic TextGlyph createTextGlyph(java.lang.String id)
TextGlyph
element and adds it to the ListOfSubGlyphs listTextGlyph
elementpublic ReferenceGlyph createReferenceGlyphForList()
ReferenceGlyph
element and adds it to the ListOfSubGlyphs listpublic ReferenceGlyph createReferenceGlyphForList(java.lang.String id)
ReferenceGlyph
element and adds it to the ListOfSubGlyphs listReferenceGlyph
elementpublic SpeciesGlyph createSpeciesGlyph()
SpeciesGlyph
element and adds it to the ListOfSubGlyphs listpublic SpeciesGlyph createSpeciesGlyph(java.lang.String id)
SpeciesGlyph
element and adds it to the ListOfSubGlyphs listSpeciesGlyph
elementpublic SpeciesReferenceGlyph createSpeciesReferenceGlyph()
SpeciesReferenceGlyph
element and adds it to the ListOfSubGlyphs listpublic SpeciesReferenceGlyph createSpeciesReferenceGlyph(java.lang.String id)
SpeciesReferenceGlyph
element and adds it to the ListOfSubGlyphs listSpeciesReferenceGlyph
elementpublic CompartmentGlyph createCompartmentGlyph()
CompartmentGlyph
element and adds it to the ListOfSubGlyphs listpublic CompartmentGlyph createCompartmentGlyph(java.lang.String id)
CompartmentGlyph
element and adds it to the ListOfSubGlyphs listCompartmentGlyph
elementpublic GeneralGlyph createGeneralGlyph()
GeneralGlyph
element and adds it to the ListOfSubGlyphs listpublic GeneralGlyph createGeneralGlyph(java.lang.String id)
GeneralGlyph
element and adds it to the ListOfSubGlyphs listGeneralGlyph
elementpublic ReactionGlyph createReactionGlyph()
ReactionGlyph
element and adds it to the ListOfSubGlyphs listpublic ReactionGlyph createReactionGlyph(java.lang.String id)
ReactionGlyph
element and adds it to the ListOfSubGlyphs listReactionGlyph
elementpublic GraphicalObject createGraphicalObject()
GraphicalObject
element and adds it to the ListOfSubGlyphs listpublic GraphicalObject createGraphicalObject(java.lang.String id)
GraphicalObject
element and adds it to the ListOfSubGlyphs listGraphicalObject
elementpublic boolean addReferenceGlyph(ReferenceGlyph glyph)
listOfReferenceGlyphs
.glyph
- 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 Curve getCurve()
public ListOf<ReferenceGlyph> getListOfReferenceGlyphs()
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()
public boolean isSetListOfReferenceGlyphs()
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
. If this is defined, then the
BoundingBox
is to be ignored.curve
- public void setListOfReferenceGlyph(ListOf<ReferenceGlyph> listOfReferenceGlyph)
GeneralGlyph
could
just contain a number of subglyphs. When present, it must include at least one ReferenceGlyph
.listOfReferenceGlyph
- private void unsetListOfReferenceGlyph()
public void unsetReaction()
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.