org.sbml.jsbml.ext.spatial

Class Domain

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

org.sbml.jsbml.ext.spatial.Domain

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SpatialNamedSBase, SBase, TreeNodeWithChangeSupport

public class Domain
extends AbstractSpatialNamedSBase

Since:

1.0

Version:

$Rev$

Author:

Alex Thomas, 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
Domain()
Domain(Domain dm)
Domain(int level, int version)
Domain(String id, int level, int version)

Method Summary

Modifier and Type	Method and Description
boolean	addInteriorPoint(InteriorPoint interiorPoint) Adds a new InteriorPoint to the listOfInteriorPoints.
Domain	clone()
InteriorPoint	createInteriorPoint() Creates a new InteriorPoint element and adds it to the ListOfInteriorPoints list
boolean	equals(Object object)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
String	getDomainType() Returns the value of domainType
ListOf<InteriorPoint>	getListOfInteriorPoints() Returns the listOfInteriorPoints.
int	hashCode()
boolean	isSetDomainType() Returns whether domainType is set
boolean	isSetListOfInteriorPoints() Returns true, if listOfInteriorPoints contains at least one element.
boolean	readAttribute(String attributeName, String prefix, String value)
void	removeInteriorPoint(int i) Removes an element from the listOfInteriorPoints at the given index.
boolean	removeInteriorPoint(InteriorPoint interiorPoint) Removes an element from the listOfInteriorPoints.
void	setDomainType(String domainType) Sets the value of domainType
void	setListOfInteriorPoints(ListOf<InteriorPoint> listOfInteriorPoints) Sets the given ListOf<InteriorPoint>.
boolean	unsetDomainType() Unsets the variable domainType
boolean	unsetListOfInteriorPoints() Returns true, if listOfInteriorPoints contain at least one element, otherwise false
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

getSpatialId, initDefaults, isSetSpatialId, setSpatialId, unsetSpatialId

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, isIdMandatory, 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, 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, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet

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, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, 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

Domain

public Domain()

Domain

public Domain(int level,
              int version)

Parameters:

level -

version -

Domain

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

Parameters:

id -

level -

version -

Domain

public Domain(Domain dm)

Parameters:

dm -

Method Detail

clone

public Domain clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSpatialNamedSBase

getDomainType

public String getDomainType()

Returns the value of domainType

Returns:

the value of domainType

isSetDomainType

public boolean isSetDomainType()

Returns whether domainType is set

Returns:

whether domainType is set

setDomainType

public void setDomainType(String domainType)

Sets the value of domainType

Parameters:

domainType -

unsetDomainType

public boolean unsetDomainType()

Unsets the variable domainType

Returns:

true, if domainType was set before, otherwise false

isSetListOfInteriorPoints

public boolean isSetListOfInteriorPoints()

Returns true, if listOfInteriorPoints contains at least one element.

Returns:

true, if listOfInteriorPoints contains at least one element, otherwise false

getListOfInteriorPoints

public ListOf<InteriorPoint> getListOfInteriorPoints()

Returns the listOfInteriorPoints. Creates it if it is not already existing.

Returns:

the listOfInteriorPoints

setListOfInteriorPoints

public void setListOfInteriorPoints(ListOf<InteriorPoint> listOfInteriorPoints)

Sets the given ListOf<InteriorPoint>. If listOfInteriorPoints was defined before and contains some elements, they are all unset.

Parameters:

listOfInteriorPoints -

unsetListOfInteriorPoints

public boolean unsetListOfInteriorPoints()

Returns true, if listOfInteriorPoints contain at least one element, otherwise false

Returns:

true, if listOfInteriorPoints contain at least one element, otherwise false

addInteriorPoint

public boolean addInteriorPoint(InteriorPoint interiorPoint)

Adds a new InteriorPoint to the listOfInteriorPoints.

The listOfInteriorPoints is initialized if necessary.

Parameters:

interiorPoint - the element to add to the list

Returns:

true (as specified by Collection#add)

removeInteriorPoint

public boolean removeInteriorPoint(InteriorPoint interiorPoint)

Removes an element from the listOfInteriorPoints.

Parameters:

interiorPoint - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeInteriorPoint

public void removeInteriorPoint(int i)

Removes an element from the listOfInteriorPoints at the given index.

Parameters:

i - the index where to remove the InteriorPoint

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

createInteriorPoint

public InteriorPoint createInteriorPoint()

Creates a new InteriorPoint element and adds it to the ListOfInteriorPoints list

Returns:

a new InteriorPoint element

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSpatialNamedSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSpatialNamedSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSpatialNamedSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSpatialNamedSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSpatialNamedSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSpatialNamedSBase

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSpatialNamedSBase