Package org.sbml.jsbml.ext.layout

Class CompartmentGlyph

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.CompartmentGlyph

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CompartmentalizedSBase, IBoundingBox, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class CompartmentGlyph
extends AbstractReferenceGlyph
implements CompartmentalizedSBase

The CompartmentGlyph class is derived from GraphicalObject and inherits its attributes. Additionally it has tow optional attributes: compartment and order.

Since:

1.0

Author:

Nicolas Rodriguez, 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	Description
CompartmentGlyph()	Creates a new instance of CompartmentGlyph.
CompartmentGlyph(int level, int version)	Creates a new instance of CompartmentGlyph.
CompartmentGlyph(java.lang.String id)	Creates a new instance of CompartmentGlyph.
CompartmentGlyph(java.lang.String id, int level, int version)	Creates a new instance of CompartmentGlyph.
CompartmentGlyph(CompartmentGlyph compartmentGlyph)	Creates a new instance of CompartmentGlyph.

Method Summary

Modifier and Type	Method	Description
CompartmentGlyph	clone()
java.lang.String	getCompartment()
NamedSBase	getCompartmentInstance()
double	getOrder()	Returns the value of order
void	initDefaults()	Initializes the default values using the namespace.
boolean	isCompartmentMandatory()
boolean	isSetCompartment()
boolean	isSetCompartmentInstance()
boolean	isSetOrder()	Returns whether order is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
boolean	setCompartment(java.lang.String compartment)
boolean	setCompartment(Compartment compartment)
void	setOrder(double order)	Sets the oder.
boolean	unsetCompartment()
boolean	unsetOrder()	Unsets the variable order
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

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

equals, getNamedSBaseInstance, getReference, getReferenceInstance, getSBaseInstance, hashCode, isSetReference, setNamedSBase, setReference, setSBase, unsetReference

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 org.sbml.jsbml.ext.layout.GraphicalObject

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

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, 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, hasExtension, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

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

Constructor Detail

CompartmentGlyph

public CompartmentGlyph()

Creates a new instance of CompartmentGlyph.

CompartmentGlyph

public CompartmentGlyph(CompartmentGlyph compartmentGlyph)

Creates a new instance of CompartmentGlyph.

Parameters:

compartmentGlyph - the CompartmentGlyph to clone.

CompartmentGlyph

public CompartmentGlyph(int level,
                        int version)

Creates a new instance of CompartmentGlyph.

Parameters:

level - the SBML level

version - the SBML version

CompartmentGlyph

public CompartmentGlyph(java.lang.String id)

Creates a new instance of CompartmentGlyph.

Parameters:

id - the id

CompartmentGlyph

public CompartmentGlyph(java.lang.String id,
                        int level,
                        int version)

Creates a new instance of CompartmentGlyph.

Parameters:

id - the id

level - the SBML level

version - the SBML version

Method Detail

clone

public CompartmentGlyph clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

Overrides:

initDefaults in class GraphicalObject

getCompartment

public java.lang.String getCompartment()

Specified by:

getCompartment in interface CompartmentalizedSBase

getCompartmentInstance

public NamedSBase getCompartmentInstance()

Specified by:

getCompartmentInstance in interface CompartmentalizedSBase

getOrder

public double getOrder()

Returns the value of order

Returns:

the value of order

isCompartmentMandatory

public boolean isCompartmentMandatory()

Specified by:

isCompartmentMandatory in interface CompartmentalizedSBase

isSetCompartment

public boolean isSetCompartment()

Specified by:

isSetCompartment in interface CompartmentalizedSBase

isSetCompartmentInstance

public boolean isSetCompartmentInstance()

Specified by:

isSetCompartmentInstance in interface CompartmentalizedSBase

isSetOrder

public boolean isSetOrder()

Returns whether order is set

Returns:

whether order is set

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

setCompartment

public boolean setCompartment(Compartment compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

setCompartment

public boolean setCompartment(java.lang.String compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

setOrder

public void setOrder(double order)

Sets the oder.

The order attribute is an optional attribute of type Double. It is there to handle the case where compartments in a layout overlap, and tools want to clearly disambiguate which CompartmentGlyph is on top of the other. The order attribute follows the coordinate system. There are z dimension points into a screen; thus, an element with a lower order value will be in front of an elements with a higher value. If not specified, the order is undefined and tools are free to display the compartment glyphs in the order that best fits their needs.

Note: if z coordinates are used (and this order is seemingly redundant), the order can still be used to disambiguate drawing order.

Parameters:

order - the oder

unsetCompartment

public boolean unsetCompartment()

Specified by:

unsetCompartment in interface CompartmentalizedSBase

unsetOrder

public boolean unsetOrder()

Unsets the variable order

Returns:

true, if order was set before, otherwise false

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject