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, IBoundingBox, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, 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 listOfSpeciesReferenceGlyphs. 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 listOfSpeciesReferenceGlyphs element.

Since:

1.0

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

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 listOfSpeciesReferenceGlyphs.
ReactionGlyph	clone()
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() Returns the list of SpeciesReferenceGlyphs.
int	getNumSpeciesReferenceGlyphs() Deprecated. use getSpeciesReferenceGlyphCount()
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	getSpeciesReferenceGlyphCount()
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetCurve()
boolean	isSetListOfSpeciesReferenceGlyphs() Returns true is the list of SpeciesReferenceGlyph is set.
boolean	isSetListOfSpeciesReferencesGlyphs() Deprecated. use isSetListOfSpeciesReferenceGlyphs()
boolean	isSetReaction()
boolean	isSetReactionInstance()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setCurve(Curve curve) The curve describes the center section of a ReactionGlyph.
void	setListOfSpeciesReferenceGlyphs(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph) Sets the list of SpeciesReferenceGlyphs.
void	setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph) Deprecated. use setListOfSpeciesReferenceGlyphs(ListOf)
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	unsetListOfSpeciesReferenceGlyphs() Unsets the list of SpeciesReferenceGlyphs.
void	unsetListOfSpeciesReferencesGlyph() Deprecated. use unsetListOfSpeciesReferenceGlyphs()
void	unsetReaction()
Map<String,String>	writeXMLAttributes()

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

getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, isSetReference, setNamedSBase, setReference, setSBase, 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

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, 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, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, 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, 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, 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

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

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class GraphicalObject

addSpeciesReferenceGlyph

public boolean addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph)

Appends the specified element to the end of the listOfSpeciesReferenceGlyphs.

Parameters:

glyph -

Returns:

true (as specified by Collection.add(E))

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

createCurve

public Curve createCurve()

Creates and adds a new Curve to this ReactionGlyph.

Returns:

a new Curve instance.

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()

Returns the list of SpeciesReferenceGlyphs.

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

Returns:

the listOfSpeciesReferenceGlyphs

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:

getSpeciesReferenceGlyphCount

public int getSpeciesReferenceGlyphCount()

Returns:

getNumSpeciesReferenceGlyphs

@Deprecated
public int getNumSpeciesReferenceGlyphs()

Deprecated. use getSpeciesReferenceGlyphCount()

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractReferenceGlyph

isSetCurve

public boolean isSetCurve()

Returns:

isSetListOfSpeciesReferenceGlyphs

public boolean isSetListOfSpeciesReferenceGlyphs()

Returns true is the list of SpeciesReferenceGlyph is set.

Returns:

true is the list of SpeciesReferenceGlyph is set.

isSetListOfSpeciesReferencesGlyphs

@Deprecated
public boolean isSetListOfSpeciesReferencesGlyphs()

Deprecated. use isSetListOfSpeciesReferenceGlyphs()

Returns true is the list of SpeciesReferenceGlyph is set.

Returns:

true is the list of SpeciesReferenceGlyph is set.

isSetReaction

public boolean isSetReaction()

Returns:

isSetReactionInstance

public boolean isSetReactionInstance()

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 -

setListOfSpeciesReferenceGlyphs

public void setListOfSpeciesReferenceGlyphs(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph)

Sets the list of SpeciesReferenceGlyphs.

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 - the list of SpeciesReferenceGlyphs to set.

setListOfSpeciesReferencesGlyph

@Deprecated
public void setListOfSpeciesReferencesGlyph(ListOf<SpeciesReferenceGlyph> listOfSpeciesReferencesGlyph)

Deprecated. use setListOfSpeciesReferenceGlyphs(ListOf)

Sets the list of SpeciesReferenceGlyphs.

Parameters:

listOfSpeciesReferencesGlyph - the list of SpeciesReferenceGlyphs to set.

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

@Deprecated
public void unsetListOfSpeciesReferencesGlyph()

Deprecated. use unsetListOfSpeciesReferenceGlyphs()

Unsets the list of SpeciesReferenceGlyphs.

unsetListOfSpeciesReferenceGlyphs

public void unsetListOfSpeciesReferenceGlyphs()

Unsets the list of SpeciesReferenceGlyphs.

unsetReaction

public void unsetReaction()

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject