org.sbml.jsbml.ext.layout

Class ReactionGlyph

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.layout.GraphicalObject

org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

org.sbml.jsbml.ext.layout.ReactionGlyph

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class ReactionGlyph
extends AbstractReferenceGlyph

Analogous to how a 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.

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
ReactionGlyph()
ReactionGlyph(int level, int version)
ReactionGlyph(ReactionGlyph reactionGlyph)
ReactionGlyph(String id)
ReactionGlyph(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
boolean	addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph) Appends the specified element to the end of the listOfSpeciesReferencesGlyphs.
ReactionGlyph	clone()
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()
boolean	isSetCurve()
boolean	isSetListOfSpeciesReferencesGlyphs()
boolean	isSetReaction()
boolean	readAttribute(String attributeName, String prefix, String value)
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) The reaction attribute is used to specify the id of the corresponding Reaction in the Model.
void	unsetListOfSpeciesReferencesGlyph()
void	unsetReaction()
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.layout.AbstractReferenceGlyph

getNamedSBaseInstance, getReference, getReferenceInstance, isSetReference, setNamedSBase, setReference, toString, unsetReference

Methods inherited from class org.sbml.jsbml.ext.layout.GraphicalObject

createBoundingBox, createBoundingBox, createBoundingBox, createBoundingBox, getAllowsChildren, getBoundingBox, getMetaidRef, isIdMandatory, isSetBoundingBox, isSetMetaidRef, setBoundingBox, setMetaidRef, unsetBoundingBox, unsetMetaidRef

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

getId, getName, isSetId, isSetName, isValidId, setId, setName, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

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

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

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

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Constructor Detail

ReactionGlyph

public ReactionGlyph()

ReactionGlyph

public ReactionGlyph(int level,
                     int version)

Parameters:

level -

version -

ReactionGlyph

public ReactionGlyph(ReactionGlyph reactionGlyph)

Parameters:

reactionGlyph -

ReactionGlyph

public ReactionGlyph(String id)

Parameters:

id -

ReactionGlyph

public ReactionGlyph(String id,
                     int level,
                     int version)

Parameters:

id -

level -

version -

Method Detail

addSpeciesReferenceGlyph

public boolean addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph)

Appends the specified element to the end of the listOfSpeciesReferencesGlyphs.

Parameters:

glyph -

Returns:

true (as specified by Collection#add)

Throws:

NullPointerException - if the specified element is null and this list does not permit null elements

IllegalArgumentException - if some property of this element prevents it from being added to this list

clone

public ReactionGlyph clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

createSpeciesReferenceGlyph

public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id)

Creates and adds a new SpeciesReferenceGlyph

Parameters:

id - the identifier for the SpeciesReferenceGlyph to be created.

Returns:

a new SpeciesReferenceGlyph.

createSpeciesReferenceGlyph

public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id,
                                                         String speciesGlyph)

Creates and adds a new SpeciesReferenceGlyph

Parameters:

id - the identifier for the SpeciesReferenceGlyph to be created.

speciesGlyph - corresponding SpeciesGlyph ID.

Returns:

a new SpeciesReferenceGlyph that points to the given speciesGlyph.

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractReferenceGlyph

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class GraphicalObject

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class GraphicalObject

getCurve

public Curve getCurve()

Returns:

getListOfSpeciesReferenceGlyphs

public ListOf<SpeciesReferenceGlyph> getListOfSpeciesReferenceGlyphs()

If the listOfSpeciesReferencesGlyphs has not yet been initialized, this will be done by this method.

Returns:

the listOfSpeciesReferencesGlyphs

getReaction

public String getReaction()

Returns:

getReactionInstance

public 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.

Returns:

getSpeciesReferenceGlyph

public SpeciesReferenceGlyph getSpeciesReferenceGlyph(int i)

Parameters:

i -

Returns:

getSpeciesReferenceGlyph

public SpeciesReferenceGlyph getSpeciesReferenceGlyph(String srGlyphId)

Parameters:

srGlyphId -

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

isSetCurve

public boolean isSetCurve()

Returns:

isSetListOfSpeciesReferencesGlyphs

public boolean isSetListOfSpeciesReferencesGlyphs()

Returns:

isSetReaction

public boolean isSetReaction()

Returns:

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

setCurve

public void setCurve(Curve curve)

The curve describes the center section of a 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.

Parameters:

curve -

setListOfSpeciesReferencesGlyph

public 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. This is done using the listOfSpeciesReferenceGlyphs.

Parameters:

listOfSpeciesReferencesGlyph -

setReaction

public void setReaction(Reaction reaction)

See setReaction(String)

Parameters:

reaction -

setReaction

public void setReaction(String reaction)

The reaction attribute is used to specify the id of the corresponding Reaction in the Model. This reference is optional.

Parameters:

reaction -

unsetListOfSpeciesReferencesGlyph

public void unsetListOfSpeciesReferencesGlyph()

unsetReaction

public void unsetReaction()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject