org.sbml.jsbml.ext.spatial

Class AbstractSpatialNamedSBase

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SpatialNamedSBase, SBase, TreeNodeWithChangeSupport

Direct Known Subclasses:

AdjacentDomains, Boundary, CompartmentMapping, CoordinateComponent, CSGNode, CSGObject, Domain, DomainType, Geometry, GeometryDefinition, ParametricObject, SampledField, SampledVolume

public abstract class AbstractSpatialNamedSBase
extends AbstractSBase
implements SpatialNamedSBase

Since:

1.0

Author:

Alex Thomas, Andreas Dräger, Piero Dalle Pezze

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
AbstractSpatialNamedSBase() Creates a new AbstractSpatialNamedSBase instance.
AbstractSpatialNamedSBase(int level, int version) Creates a new AbstractSpatialNamedSBase instance.
AbstractSpatialNamedSBase(SpatialNamedSBase nse) Creates a new AbstractSpatialNamedSBase instance.
AbstractSpatialNamedSBase(String id) Creates a new AbstractSpatialNamedSBase instance.
AbstractSpatialNamedSBase(String id, int level, int version) Creates a new AbstractSpatialNamedSBase instance.

Method Summary

Modifier and Type	Method and Description
abstract AbstractSpatialNamedSBase	clone()
boolean	equals(Object object)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
String	getSpatialId() Returns the value of the id attribute
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isSetSpatialId() Returns whether id is set
boolean	readAttribute(String attributeName, String prefix, String value)
void	setSpatialId(String id) Sets the value of the id
boolean	unsetSpatialId() Unsets the id
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, 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, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, 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.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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, 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

AbstractSpatialNamedSBase

public AbstractSpatialNamedSBase()

Creates a new AbstractSpatialNamedSBase instance.

AbstractSpatialNamedSBase

public AbstractSpatialNamedSBase(int level,
                                 int version)

Creates a new AbstractSpatialNamedSBase instance.

Parameters:

level - the SBML level

version - the SBML version

AbstractSpatialNamedSBase

public AbstractSpatialNamedSBase(SpatialNamedSBase nse)

Creates a new AbstractSpatialNamedSBase instance.

Parameters:

nse - the instance to be clone.

AbstractSpatialNamedSBase

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

Creates a new AbstractSpatialNamedSBase instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

AbstractSpatialNamedSBase

public AbstractSpatialNamedSBase(String id)

Creates a new AbstractSpatialNamedSBase instance.

Parameters:

id - the id

Method Detail

clone

public abstract AbstractSpatialNamedSBase clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

getSpatialId

public String getSpatialId()

Description copied from interface: SpatialNamedSBase

Returns the value of the id attribute

Specified by:

getSpatialId in interface SpatialNamedSBase

Returns:

the value of id

isSetSpatialId

public boolean isSetSpatialId()

Description copied from interface: SpatialNamedSBase

Returns whether id is set

Specified by:

isSetSpatialId in interface SpatialNamedSBase

Returns:

whether id is set

setSpatialId

public void setSpatialId(String id)

Description copied from interface: SpatialNamedSBase

Sets the value of the id

Specified by:

setSpatialId in interface SpatialNamedSBase

unsetSpatialId

public boolean unsetSpatialId()

Description copied from interface: SpatialNamedSBase

Unsets the id

Specified by:

unsetSpatialId in interface SpatialNamedSBase

Returns:

true, if id was set before, otherwise false

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase