org.sbml.jsbml.ext.spatial

Class SampledFieldGeometry

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase

org.sbml.jsbml.ext.spatial.GeometryDefinition

org.sbml.jsbml.ext.spatial.SampledFieldGeometry

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, SpatialNamedSBase, SBase, TreeNodeWithChangeSupport

public class SampledFieldGeometry
extends GeometryDefinition

Since:

1.0

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
SampledFieldGeometry() Creates a new SampledFieldGeometry instance.
SampledFieldGeometry(SampledFieldGeometry sampledFieldGeometry) Creates a new SampledFieldGeometry instance cloned from the given sampledFieldGeometry.
SampledFieldGeometry(String id, int level, int version) Creates a new SampledFieldGeometry instance.

Method Summary

Modifier and Type	Method and Description
boolean	addSampledVolume(SampledVolume sampledVolume) Adds a new SampledVolume to the listOfSampledVolumes.
SampledFieldGeometry	clone()
SampledVolume	createSampledVolume() Creates a new SampledVolume instance and adds it to the ListOfSampledVolumes list
SampledVolume	createSampledVolume(String id) Creates a new SampledVolume instance and adds it to the ListOfSampledVolumes list
boolean	equals(Object object)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<SampledVolume>	getListOfSampledVolumes() Returns the listOfSampledVolumes.
String	getSampledField() Returns the value of sampledField
int	hashCode()
boolean	isSetListOfSampledVolumes() Returns true, if listOfSampledVolumes contains at least one element.
boolean	isSetSampledField() Returns whether sampledField is set
boolean	readAttribute(String attributeName, String prefix, String value)
void	removeSampledVolume(int i) Removes an element from the listOfSampledVolumes at the given index.
boolean	removeSampledVolume(SampledVolume sampledVolume) Removes an element from the listOfSampledVolumes.
void	removeSampledVolume(String id) Removes an element from the listOfSampledVolumes with the given id.
void	setListOfSampledVolumes(ListOf<SampledVolume> listOfSampledVolumes) Sets the given ListOf<SampledVolume>.
void	setSampledField(String sampledField) Sets the value of sampledField
boolean	unsetListOfSampledVolumes() Returns true, if listOfSampledVolumes contain at least one element, otherwise false
boolean	unsetSampledField() Unsets the variable sampledField
Map<String,String>	writeXMLAttributes()

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

getIsActive, isActive, isSetIsActive, setIsActive, unsetIsActive

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

SampledFieldGeometry

public SampledFieldGeometry()

Creates a new SampledFieldGeometry instance.

SampledFieldGeometry

public SampledFieldGeometry(SampledFieldGeometry sampledFieldGeometry)

Creates a new SampledFieldGeometry instance cloned from the given sampledFieldGeometry.

Parameters:

sampledFieldGeometry - the SampledFieldGeometry to clone.

SampledFieldGeometry

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

Creates a new SampledFieldGeometry instance.

Parameters:

id - the element id

level - the SBML level

version - the SBML version

Method Detail

clone

public SampledFieldGeometry clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSpatialNamedSBase

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class GeometryDefinition

getSampledField

public String getSampledField()

Returns the value of sampledField

Returns:

the value of sampledField

isSetSampledField

public boolean isSetSampledField()

Returns whether sampledField is set

Returns:

whether sampledField is set

setSampledField

public void setSampledField(String sampledField)

Sets the value of sampledField

Parameters:

sampledField - the sampledField value to set

unsetSampledField

public boolean unsetSampledField()

Unsets the variable sampledField

Returns:

true, if sampledField was set before, otherwise false

isSetListOfSampledVolumes

public boolean isSetListOfSampledVolumes()

Returns true, if listOfSampledVolumes contains at least one element.

Returns:

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

getListOfSampledVolumes

public ListOf<SampledVolume> getListOfSampledVolumes()

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

Returns:

the listOfSampledVolumes

setListOfSampledVolumes

public void setListOfSampledVolumes(ListOf<SampledVolume> listOfSampledVolumes)

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

Parameters:

listOfSampledVolumes - the list of SampledVolume to set.

unsetListOfSampledVolumes

public boolean unsetListOfSampledVolumes()

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

Returns:

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

addSampledVolume

public boolean addSampledVolume(SampledVolume sampledVolume)

Adds a new SampledVolume to the listOfSampledVolumes.

The listOfSampledVolumes is initialized if necessary.

Parameters:

sampledVolume - the element to add to the list

Returns:

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

removeSampledVolume

public boolean removeSampledVolume(SampledVolume sampledVolume)

Removes an element from the listOfSampledVolumes.

Parameters:

sampledVolume - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List.remove(Object)

removeSampledVolume

public void removeSampledVolume(int i)

Removes an element from the listOfSampledVolumes at the given index.

Parameters:

i - the index where to remove the SampledVolume

Throws:

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

removeSampledVolume

public void removeSampledVolume(String id)

Removes an element from the listOfSampledVolumes with the given id.

Parameters:

id - the id of the element to remove.

createSampledVolume

public SampledVolume createSampledVolume()

Creates a new SampledVolume instance and adds it to the ListOfSampledVolumes list

Returns:

a new SampledVolume instance

createSampledVolume

public SampledVolume createSampledVolume(String id)

Creates a new SampledVolume instance and adds it to the ListOfSampledVolumes list

Parameters:

id - the id to set in the new SampledVolume instance

Returns:

a new SampledVolume instance

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 GeometryDefinition

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class GeometryDefinition

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class GeometryDefinition