org.sbml.jsbml.ext.layout
public class ReactionGlyph extends AbstractReferenceGlyph
Reaction
object has to at least have one reactant
or product, the ReactionGlyph
has to at least have one
SpeciesReferenceGlyph
stored in the
listOfSpeciesReferencesGlyphs
. The ReactionGlyph
inherits
from GraphicalObject
.
In addition to the attributes inherited from GraphicalObject
, the
ReactionGlyph
is described by an attribute reaction, a Curve
element and a listOfSpeciesReferencesGlyphs
element.UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
Constructor and Description |
---|
ReactionGlyph() |
ReactionGlyph(int level,
int version) |
ReactionGlyph(ReactionGlyph reactionGlyph) |
ReactionGlyph(String id) |
ReactionGlyph(String id,
int level,
int version) |
Modifier and Type | Method and Description |
---|---|
boolean |
addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph)
Appends the specified element to the end of the
listOfSpeciesReferencesGlyphs . |
ReactionGlyph |
clone()
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
Curve |
createCurve()
Creates and adds a new
Curve to this ReactionGlyph. |
SpeciesReferenceGlyph |
createSpeciesReferenceGlyph(String id)
Creates and adds a new
SpeciesReferenceGlyph |
SpeciesReferenceGlyph |
createSpeciesReferenceGlyph(String id,
String speciesGlyph)
Creates and adds a new
SpeciesReferenceGlyph |
boolean |
equals(Object object)
|
TreeNode |
getChildAt(int index) |
int |
getChildCount() |
Curve |
getCurve() |
ListOf<SpeciesReferenceGlyph> |
getListOfSpeciesReferenceGlyphs()
If the
listOfSpeciesReferencesGlyphs has not yet been initialized, this
will be done by this method. |
String |
getReaction() |
NamedSBase |
getReactionInstance()
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. |
SpeciesReferenceGlyph |
getSpeciesReferenceGlyph(int i) |
SpeciesReferenceGlyph |
getSpeciesReferenceGlyph(String srGlyphId) |
int |
hashCode()
Returns a hash code value for this
SBase instance. |
void |
initDefaults()
Initializes the default values using the namespace.
|
boolean |
isSetCurve() |
boolean |
isSetListOfSpeciesReferencesGlyphs() |
boolean |
isSetReaction() |
boolean |
readAttribute(String attributeName,
String prefix,
String value)
Sets the given attribute in this
SBase . |
void |
setCurve(Curve curve)
The curve describes the center section of a
ReactionGlyph . |
void |
setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph)
Since the
Species element can have several graphical representations
in the layout there must be a way to specify which SpeciesGlyph should
be connected to the ReactionGlyph . |
void |
setReaction(Reaction reaction)
See setReaction(String)
|
void |
setReaction(String reaction)
|
void |
unsetListOfSpeciesReferencesGlyph() |
void |
unsetReaction() |
Map<String,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, 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, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setPackageVersion, 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
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, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, 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 ReactionGlyph()
public ReactionGlyph(int level, int version)
level
- version
- public ReactionGlyph(ReactionGlyph reactionGlyph)
reactionGlyph
- public ReactionGlyph(String id)
id
- public ReactionGlyph(String id, int level, int version)
id
- level
- version
- public void initDefaults()
initDefaults
in class GraphicalObject
public boolean addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph)
listOfSpeciesReferencesGlyphs
.glyph
- true
(as specified by Collection.add(E)
)NullPointerException
- if the specified element is null and this list does not
permit null elementsIllegalArgumentException
- if some property of this element prevents it from being added
to this listpublic ReactionGlyph clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractReferenceGlyph
public Curve createCurve()
Curve
to this ReactionGlyph.Curve
instance.public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id)
SpeciesReferenceGlyph
id
- the identifier for the SpeciesReferenceGlyph
to be created.SpeciesReferenceGlyph
.public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id, String speciesGlyph)
SpeciesReferenceGlyph
id
- the identifier for the SpeciesReferenceGlyph
to be created.speciesGlyph
- corresponding SpeciesGlyph
ID.SpeciesReferenceGlyph
that points to the given
speciesGlyph
.public TreeNode getChildAt(int index)
getChildAt
in interface TreeNode
getChildAt
in class GraphicalObject
public int getChildCount()
getChildCount
in interface TreeNode
getChildCount
in class GraphicalObject
public Curve getCurve()
public ListOf<SpeciesReferenceGlyph> getListOfSpeciesReferenceGlyphs()
listOfSpeciesReferencesGlyphs
has not yet been initialized, this
will be done by this method.listOfSpeciesReferencesGlyphs
public String getReaction()
public NamedSBase getReactionInstance()
NamedSBase
because it
could be possible to link some element from other packages to this glyph.public SpeciesReferenceGlyph getSpeciesReferenceGlyph(int i)
i
- public SpeciesReferenceGlyph getSpeciesReferenceGlyph(String srGlyphId)
srGlyphId
- public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractReferenceGlyph
SBase
instance.Object.hashCode()
public boolean isSetCurve()
public boolean isSetListOfSpeciesReferencesGlyphs()
public boolean isSetReaction()
public boolean readAttribute(String attributeName, String prefix, 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)
ReactionGlyph
. The center
section is frequently used by tools to separate the point where substrates arcs come together
from the point where product arcs split off. The Curve
is optional, and when not present
the dimensions of the inherited BoundingBox
describes the center section, by storing its
position and dimension.curve
- public void setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph)
Species
element can have several graphical representations
in the layout there must be a way to specify which SpeciesGlyph
should
be connected to the ReactionGlyph
. This is done using the
listOfSpeciesReferenceGlyphs.listOfSpeciesReferencesGlyph
- public void setReaction(Reaction reaction)
reaction
- public void setReaction(String reaction)
Reaction
in the Model
. This reference is optional.reaction
- public void unsetListOfSpeciesReferencesGlyph()
public void unsetReaction()
public Map<String,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.