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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, SpatialNamedSBase, SBase, TreeNodeWithChangeSupport

public class SampledFieldGeometry
extends GeometryDefinition

Since:

1.0

Version:

$Rev: 1981 $

Author:

Alex Thomas, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<SampledVolume>	listOfSampledVolumes
private java.lang.String	sampledField
private static long	serialVersionUID Generated serial version identifier.

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

spatialId

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
SampledFieldGeometry()
SampledFieldGeometry(SampledFieldGeometry sampledFieldGeometry)
SampledFieldGeometry(java.lang.String id, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addSampledVolume(SampledVolume sampledVolume) Adds a new SampledVolume to the listOfSampledVolumes.
SampledFieldGeometry	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
SampledVolume	createSampledVolume() Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list
SampledVolume	createSampledVolume(java.lang.String id) Creates a new SampledVolume element and adds it to the ListOfSampledVolumes list
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<SampledVolume>	getListOfSampledVolumes() Returns the listOfSampledVolumes.
java.lang.String	getSampledField() Returns the value of sampledField
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isSetListOfSampledVolumes() Returns true, if listOfSampledVolumes contains at least one element.
boolean	isSetSampledField() Returns whether sampledField is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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(java.lang.String id)
void	setListOfSampledVolumes(ListOf<SampledVolume> listOfSampledVolumes) Sets the given ListOf<SampledVolume>.
void	setSampledField(java.lang.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
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.spatial.GeometryDefinition

getIsActive, isActive, isSetIsActive, setIsActive, toString, unsetIsActive

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

getSpatialId, isSetSpatialId, setSpatialId, unsetSpatialId

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.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

listOfSampledVolumes

private ListOf<SampledVolume> listOfSampledVolumes

sampledField

private java.lang.String sampledField

Constructor Detail

SampledFieldGeometry

public SampledFieldGeometry()

SampledFieldGeometry

public SampledFieldGeometry(SampledFieldGeometry sampledFieldGeometry)

Parameters:

sampledFieldGeometry -

SampledFieldGeometry

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

Method Detail

clone

public SampledFieldGeometry 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 AbstractSBase

Returns:

a copy of this object

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class GeometryDefinition

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getSampledField

public java.lang.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(java.lang.String sampledField)

Sets the value of sampledField

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 -

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)

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:

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

removeSampledVolume

public void removeSampledVolume(java.lang.String id)

createSampledVolume

public SampledVolume createSampledVolume()

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

createSampledVolume

public SampledVolume createSampledVolume(java.lang.String id)

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

Returns:

a new SampledVolume element

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSpatialNamedSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSpatialNamedSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSpatialNamedSBase

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class GeometryDefinition

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

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 GeometryDefinition

Returns:

a Map containing the XML attributes of this object.

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 GeometryDefinition

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.