org.sbml.jsbml.ext.layout
public class SpeciesReferenceGlyph extends AbstractReferenceGlyph
SpeciesReferenceGlyph
class describes the graphical connection
between a SpeciesGlyph
and a ReactionGlyph
(which would be
an arrow or some curve in most cases).Modifier and Type | Field and Description |
---|---|
private Curve |
curve |
private SpeciesReferenceRole |
role |
private static long |
serialVersionUID
Generated serial version identifier.
|
private java.lang.String |
speciesGlyph |
ignoredExtensions, ignoredXMLElements
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
SpeciesReferenceGlyph() |
SpeciesReferenceGlyph(int level,
int version) |
SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph) |
SpeciesReferenceGlyph(java.lang.String id) |
SpeciesReferenceGlyph(java.lang.String id,
int level,
int version) |
Modifier and Type | Method and Description |
---|---|
SpeciesReferenceGlyph |
clone()
Creates a deep copy of this object, i.e., a new
SBase with the same properties
like this one. |
Curve |
createCurve() |
boolean |
equals(java.lang.Object object)
|
javax.swing.tree.TreeNode |
getChildAt(int index) |
int |
getChildCount() |
Curve |
getCurve() |
java.lang.String |
getSpeciesGlyph() |
SpeciesGlyph |
getSpeciesGlyphInstance() |
java.lang.String |
getSpeciesReference() |
NamedSBase |
getSpeciesReferenceInstance()
Note that the return type of this method is
NamedSBase because it
could be possible to link some element from other packages to this glyph. |
SpeciesReferenceRole |
getSpeciesReferenceRole() |
int |
hashCode()
Returns a hash code value for this
SBase instance. |
boolean |
isSetCurve() |
boolean |
isSetSpeciesGlyph() |
boolean |
isSetSpeciesReference() |
boolean |
isSetSpeciesReferenceRole() |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value)
Sets the given attribute in this
SBase . |
void |
setCurve(Curve curve)
The curve is an optional element of type
Curve . |
void |
setRole(SpeciesReferenceRole valueOf)
The role attribute is of type
SpeciesReferenceRole and is used to specify
how the species reference should be displayed. |
void |
setSpeciesGlyph(java.lang.String speciesGlyph)
The speciesGlyph attribute contains a reference to the id of a
SpeciesGlyph
object that is to be connected to the ReactionGlyph . |
void |
setSpeciesReference(SimpleSpeciesReference speciesReference)
See setSpeciesReference(String).
|
void |
setSpeciesReference(java.lang.String speciesReference)
The speciesReference is an optional attribute that allows modelers to
connect the
SpeciesReferenceGlyph with a particular SpeciesReference
of the containing Model . |
boolean |
unsetCurve() |
void |
unsetSpeciesReference() |
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 SpeciesReferenceRole role
private java.lang.String speciesGlyph
public SpeciesReferenceGlyph()
public SpeciesReferenceGlyph(int level, int version)
level
- version
- public SpeciesReferenceGlyph(SpeciesReferenceGlyph speciesReferenceGlyph)
speciesReferenceGlyph
- public SpeciesReferenceGlyph(java.lang.String id)
id
- public SpeciesReferenceGlyph(java.lang.String id, int level, int version)
id
- level
- version
- public SpeciesReferenceGlyph clone()
SBase
SBase
with the same properties
like this one.clone
in interface SBase
clone
in class AbstractReferenceGlyph
public Curve createCurve()
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 java.lang.String getSpeciesGlyph()
public SpeciesGlyph getSpeciesGlyphInstance()
public java.lang.String getSpeciesReference()
public NamedSBase getSpeciesReferenceInstance()
NamedSBase
because it
could be possible to link some element from other packages to this glyph.public SpeciesReferenceRole getSpeciesReferenceRole()
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractReferenceGlyph
SBase
instance.Object.hashCode()
public boolean isSetCurve()
public boolean isSetSpeciesGlyph()
public boolean isSetSpeciesReference()
public boolean isSetSpeciesReferenceRole()
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
. When present, the glyphs
bounding box (as inherited from the GraphicalObject
) is to be disregarded.
So as to make the drawing of these curves as easy as possible, the line segments
should be ordered depending on the role of the SpeciesReferenceGlyph
. If
no role attribute is defined, the role to be assumed is taken from the role that
the SpeciesReference
referenced via the attribute speciesReference has,
otherwise it is undefined.curve
- public void setRole(SpeciesReferenceRole valueOf)
SpeciesReferenceRole
and is used to specify
how the species reference should be displayed. This attribute is optional and should
only be necessary if the optional speciesReference attribute is not given or if the
respective information from the model needs to be overridden.
To define more specific interactions, the recommended practice is to use the sboTerm
attribute on the SpeciesReference
. If both role and sboTerm are specified and
they conflict, it is the role that takes precedence.valueOf
- public void setSpeciesGlyph(java.lang.String speciesGlyph)
SpeciesGlyph
object that is to be connected to the ReactionGlyph
. This attribute is
mandatory so as to ensure unambiguity about which SpeciesGlyph
has to be
connected with this ReactionGlyph
.speciesGlyph
- public void setSpeciesReference(SimpleSpeciesReference speciesReference)
speciesReference
- public void setSpeciesReference(java.lang.String speciesReference)
SpeciesReferenceGlyph
with a particular SpeciesReference
of the containing Model
.speciesReference
- public boolean unsetCurve()
public void unsetSpeciesReference()
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.