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, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class CompartmentGlyph
extends AbstractReferenceGlyph

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

Since:

1.0

Version:

$Rev: 1699 $

Author:

Nicolas Rodriguez, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.Double	order
private static long	serialVersionUID Generated serial version identifier.

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

Method Summary

Methods

Modifier and Type	Method and Description
CompartmentGlyph	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
java.lang.String	getCompartment()
NamedSBase	getCompartmentInstance() 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.
double	getOrder() Returns the value of order
boolean	isSetCompartment()
boolean	isSetOrder() Returns whether order is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setCompartment(Compartment compartment) The compartment attribute is used to add a reference to the id of the corresponding Compartment in the Model.
void	setCompartment(java.lang.String compartment) See annotation for setCompartment(Compartment)
void	setOrder(double order) The order attribute is an optional attribute of type Double.
void	unsetCompartment()
boolean	unsetOrder() Unsets the variable order
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.

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

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

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 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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

order

private java.lang.Double order

Constructor Detail

CompartmentGlyph

public CompartmentGlyph()

CompartmentGlyph

public CompartmentGlyph(CompartmentGlyph compartmentGlyph)

Parameters:

compartmentGlyph -

CompartmentGlyph

public CompartmentGlyph(int level,
                int version)

Parameters:

level -

version -

CompartmentGlyph

public CompartmentGlyph(java.lang.String id)

Parameters:

id -

CompartmentGlyph

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

Parameters:

id -

level -

version -

Method Detail

clone

public CompartmentGlyph clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractReferenceGlyph

Returns:

a copy of this object

getCompartment

public java.lang.String getCompartment()

Returns:

getCompartmentInstance

public NamedSBase getCompartmentInstance()

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:

getOrder

public double getOrder()

Returns the value of order

Returns:

the value of order

isSetCompartment

public boolean isSetCompartment()

Returns:

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)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GraphicalObject

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setCompartment

public void setCompartment(Compartment compartment)

The compartment attribute is used to add a reference to the id of the corresponding Compartment in the Model. Since the compartment is optional, the user can specify Compartments in the Layout that are not part of the Model. This attribute is optional.

Parameters:

compartment -

setCompartment

public void setCompartment(java.lang.String compartment)

See annotation for setCompartment(Compartment)

Parameters:

compartment -

setOrder

public void setOrder(double order)

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 -

unsetCompartment

public void unsetCompartment()

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()

Description copied from interface: SBase

Returns a map with all the attributes of this 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.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GraphicalObject

Returns:

a Map containing the XML attributes of this object.