Annotation (Bio-Formats API)

java.lang.Object
- ome.xml.model.AbstractOMEModelObject
- - ome.xml.model.Annotation

All Implemented Interfaces:

OMEModelObject

Direct Known Subclasses:

BasicAnnotation, ListAnnotation, MapAnnotation, TextAnnotation, TypeAnnotation
```
public abstract class Annotation
extends AbstractOMEModelObject
```

Field Summary

Fields
Modifier and Type	Field and Description
`private List<Annotation>`	`annotationLinks`
`private String`	`annotator`
`private List<Channel>`	`channelLinks`
`private List<Dataset>`	`datasetLinks`
`private String`	`description`
`private List<Detector>`	`detectorLinks`
`private List<Dichroic>`	`dichroicLinks`
`private List<ExperimenterGroup>`	`experimenterGroupLinks`
`private List<Experimenter>`	`experimenterLinks`
`private List<Filter>`	`filterLinks`
`private List<Folder>`	`folderLinks`
`private String`	`id`
`private List<Image>`	`imageLinks`
`private List<Instrument>`	`instrumentLinks`
`private List<LightPath>`	`lightPathLinks`
`private List<LightSource>`	`lightSourceLinks`
`private static org.slf4j.Logger`	`LOGGER` Logger for this class.
`private String`	`namespace`
`static String`	`NAMESPACE`
`private List<Objective>`	`objectiveLinks`
`private List<Plane>`	`planeLinks`
`private List<PlateAcquisition>`	`plateAcquisitionLinks`
`private List<Plate>`	`plateLinks`
`private List<Project>`	`projectLinks`
`private List<Reagent>`	`reagentLinks`
`private List<ROI>`	`roiLinks`
`private List<Screen>`	`screenLinks`
`private List<Shape>`	`shapeLinks`
`private List<Well>`	`wellLinks`

Constructor Summary

Constructors
Constructor and Description
`Annotation()` Default constructor.
`Annotation(Annotation orig)` Copy constructor.
`Annotation(Element element, OMEModel model)` Constructs Annotation recursively from an XML DOM tree.

Method Summary

Methods
Modifier and Type	Method and Description
`Element`	`asXMLElement(Document document)` Takes the entire object hierarchy and produces an XML DOM tree.
`protected Element`	`asXMLElement(Document document, Element Annotation_element)` Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.
`List<Annotation>`	`copyLinkedAnnotationList()`
`List<Channel>`	`copyLinkedChannelList()`
`List<Dataset>`	`copyLinkedDatasetList()`
`List<Detector>`	`copyLinkedDetectorList()`
`List<Dichroic>`	`copyLinkedDichroicList()`
`List<ExperimenterGroup>`	`copyLinkedExperimenterGroupList()`
`List<Experimenter>`	`copyLinkedExperimenterList()`
`List<Filter>`	`copyLinkedFilterList()`
`List<Folder>`	`copyLinkedFolderList()`
`List<Image>`	`copyLinkedImageList()`
`List<Instrument>`	`copyLinkedInstrumentList()`
`List<LightPath>`	`copyLinkedLightPathList()`
`List<LightSource>`	`copyLinkedLightSourceList()`
`List<Objective>`	`copyLinkedObjectiveList()`
`List<Plane>`	`copyLinkedPlaneList()`
`List<PlateAcquisition>`	`copyLinkedPlateAcquisitionList()`
`List<Plate>`	`copyLinkedPlateList()`
`List<Project>`	`copyLinkedProjectList()`
`List<Reagent>`	`copyLinkedReagentList()`
`List<ROI>`	`copyLinkedROIList()`
`List<Screen>`	`copyLinkedScreenList()`
`List<Shape>`	`copyLinkedShapeList()`
`List<Well>`	`copyLinkedWellList()`
`String`	`getAnnotator()`
`String`	`getDescription()`
`String`	`getID()`
`Annotation`	`getLinkedAnnotation(int index)`
`Channel`	`getLinkedChannel(int index)`
`Dataset`	`getLinkedDataset(int index)`
`Detector`	`getLinkedDetector(int index)`
`Dichroic`	`getLinkedDichroic(int index)`
`Experimenter`	`getLinkedExperimenter(int index)`
`ExperimenterGroup`	`getLinkedExperimenterGroup(int index)`
`Filter`	`getLinkedFilter(int index)`
`Folder`	`getLinkedFolder(int index)`
`Image`	`getLinkedImage(int index)`
`Instrument`	`getLinkedInstrument(int index)`
`LightPath`	`getLinkedLightPath(int index)`
`LightSource`	`getLinkedLightSource(int index)`
`Objective`	`getLinkedObjective(int index)`
`Plane`	`getLinkedPlane(int index)`
`Plate`	`getLinkedPlate(int index)`
`PlateAcquisition`	`getLinkedPlateAcquisition(int index)`
`Project`	`getLinkedProject(int index)`
`Reagent`	`getLinkedReagent(int index)`
`ROI`	`getLinkedROI(int index)`
`Screen`	`getLinkedScreen(int index)`
`Shape`	`getLinkedShape(int index)`
`Well`	`getLinkedWell(int index)`
`String`	`getNamespace()`
`boolean`	`link(Reference reference, OMEModelObject o)` Link a given OME model object to this model object.
`boolean`	`linkAnnotation(Annotation o)`
`boolean`	`linkChannel(Channel o)`
`boolean`	`linkDataset(Dataset o)`
`boolean`	`linkDetector(Detector o)`
`boolean`	`linkDichroic(Dichroic o)`
`boolean`	`linkExperimenter(Experimenter o)`
`boolean`	`linkExperimenterGroup(ExperimenterGroup o)`
`boolean`	`linkFilter(Filter o)`
`boolean`	`linkFolder(Folder o)`
`boolean`	`linkImage(Image o)`
`boolean`	`linkInstrument(Instrument o)`
`boolean`	`linkLightPath(LightPath o)`
`boolean`	`linkLightSource(LightSource o)`
`boolean`	`linkObjective(Objective o)`
`boolean`	`linkPlane(Plane o)`
`boolean`	`linkPlate(Plate o)`
`boolean`	`linkPlateAcquisition(PlateAcquisition o)`
`boolean`	`linkProject(Project o)`
`boolean`	`linkReagent(Reagent o)`
`boolean`	`linkROI(ROI o)`
`boolean`	`linkScreen(Screen o)`
`boolean`	`linkShape(Shape o)`
`boolean`	`linkWell(Well o)`
`void`	`setAnnotator(String annotator)`
`void`	`setDescription(String description)`
`void`	`setID(String id)`
`Annotation`	`setLinkedAnnotation(int index, Annotation o)`
`Channel`	`setLinkedChannel(int index, Channel o)`
`Dataset`	`setLinkedDataset(int index, Dataset o)`
`Detector`	`setLinkedDetector(int index, Detector o)`
`Dichroic`	`setLinkedDichroic(int index, Dichroic o)`
`Experimenter`	`setLinkedExperimenter(int index, Experimenter o)`
`ExperimenterGroup`	`setLinkedExperimenterGroup(int index, ExperimenterGroup o)`
`Filter`	`setLinkedFilter(int index, Filter o)`
`Folder`	`setLinkedFolder(int index, Folder o)`
`Image`	`setLinkedImage(int index, Image o)`
`Instrument`	`setLinkedInstrument(int index, Instrument o)`
`LightPath`	`setLinkedLightPath(int index, LightPath o)`
`LightSource`	`setLinkedLightSource(int index, LightSource o)`
`Objective`	`setLinkedObjective(int index, Objective o)`
`Plane`	`setLinkedPlane(int index, Plane o)`
`Plate`	`setLinkedPlate(int index, Plate o)`
`PlateAcquisition`	`setLinkedPlateAcquisition(int index, PlateAcquisition o)`
`Project`	`setLinkedProject(int index, Project o)`
`Reagent`	`setLinkedReagent(int index, Reagent o)`
`ROI`	`setLinkedROI(int index, ROI o)`
`Screen`	`setLinkedScreen(int index, Screen o)`
`Shape`	`setLinkedShape(int index, Shape o)`
`Well`	`setLinkedWell(int index, Well o)`
`void`	`setNamespace(String namespace)`
`int`	`sizeOfLinkedAnnotationList()`
`int`	`sizeOfLinkedChannelList()`
`int`	`sizeOfLinkedDatasetList()`
`int`	`sizeOfLinkedDetectorList()`
`int`	`sizeOfLinkedDichroicList()`
`int`	`sizeOfLinkedExperimenterGroupList()`
`int`	`sizeOfLinkedExperimenterList()`
`int`	`sizeOfLinkedFilterList()`
`int`	`sizeOfLinkedFolderList()`
`int`	`sizeOfLinkedImageList()`
`int`	`sizeOfLinkedInstrumentList()`
`int`	`sizeOfLinkedLightPathList()`
`int`	`sizeOfLinkedLightSourceList()`
`int`	`sizeOfLinkedObjectiveList()`
`int`	`sizeOfLinkedPlaneList()`
`int`	`sizeOfLinkedPlateAcquisitionList()`
`int`	`sizeOfLinkedPlateList()`
`int`	`sizeOfLinkedProjectList()`
`int`	`sizeOfLinkedReagentList()`
`int`	`sizeOfLinkedROIList()`
`int`	`sizeOfLinkedScreenList()`
`int`	`sizeOfLinkedShapeList()`
`int`	`sizeOfLinkedWellList()`
`boolean`	`unlinkAnnotation(Annotation o)`
`boolean`	`unlinkChannel(Channel o)`
`boolean`	`unlinkDataset(Dataset o)`
`boolean`	`unlinkDetector(Detector o)`
`boolean`	`unlinkDichroic(Dichroic o)`
`boolean`	`unlinkExperimenter(Experimenter o)`
`boolean`	`unlinkExperimenterGroup(ExperimenterGroup o)`
`boolean`	`unlinkFilter(Filter o)`
`boolean`	`unlinkFolder(Folder o)`
`boolean`	`unlinkImage(Image o)`
`boolean`	`unlinkInstrument(Instrument o)`
`boolean`	`unlinkLightPath(LightPath o)`
`boolean`	`unlinkLightSource(LightSource o)`
`boolean`	`unlinkObjective(Objective o)`
`boolean`	`unlinkPlane(Plane o)`
`boolean`	`unlinkPlate(Plate o)`
`boolean`	`unlinkPlateAcquisition(PlateAcquisition o)`
`boolean`	`unlinkProject(Project o)`
`boolean`	`unlinkReagent(Reagent o)`
`boolean`	`unlinkROI(ROI o)`
`boolean`	`unlinkScreen(Screen o)`
`boolean`	`unlinkShape(Shape o)`
`boolean`	`unlinkWell(Well o)`
`void`	`update(Element element, OMEModel model)` Updates Annotation recursively from an XML DOM tree.

Methods inherited from class ome.xml.model.AbstractOMEModelObject
getChildrenByTagName, stripNamespacePrefix

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NAMESPACE
```
public static final String NAMESPACE
```
See Also:
Constant Field Values

LOGGER

private static final org.slf4j.Logger LOGGER

Logger for this class.

namespace
```
private String namespace
```

id
```
private String id
```

annotator
```
private String annotator
```

description
```
private String description
```

annotationLinks

private List<Annotation> annotationLinks

imageLinks
```
private List<Image> imageLinks
```

planeLinks
```
private List<Plane> planeLinks
```

channelLinks
```
private List<Channel> channelLinks
```

instrumentLinks

private List<Instrument> instrumentLinks

lightSourceLinks

private List<LightSource> lightSourceLinks

projectLinks
```
private List<Project> projectLinks
```

experimenterGroupLinks

private List<ExperimenterGroup> experimenterGroupLinks

datasetLinks
```
private List<Dataset> datasetLinks
```

experimenterLinks

private List<Experimenter> experimenterLinks

folderLinks
```
private List<Folder> folderLinks
```

objectiveLinks
```
private List<Objective> objectiveLinks
```

detectorLinks
```
private List<Detector> detectorLinks
```

filterLinks
```
private List<Filter> filterLinks
```

dichroicLinks
```
private List<Dichroic> dichroicLinks
```

lightPathLinks
```
private List<LightPath> lightPathLinks
```

roiLinks
```
private List<ROI> roiLinks
```

shapeLinks
```
private List<Shape> shapeLinks
```

plateLinks
```
private List<Plate> plateLinks
```

reagentLinks
```
private List<Reagent> reagentLinks
```

screenLinks
```
private List<Screen> screenLinks
```

plateAcquisitionLinks

private List<PlateAcquisition> plateAcquisitionLinks

wellLinks
```
private List<Well> wellLinks
```

Constructor Detail
- Annotation
```
public Annotation()
```
  Default constructor.
- Annotation
```
public Annotation(Element element,
          OMEModel model)
           throws EnumerationException
```
  Constructs Annotation recursively from an XML DOM tree.
  
  Parameters:
  element - Root of the XML DOM tree to construct a model object graph from.
  model - Handler for the OME model which keeps track of instances and references seen during object population.
  
  Throws:
  
  EnumerationException - If there is an error instantiating an enumeration during model object creation.
- Annotation
```
public Annotation(Annotation orig)
```
  Copy constructor.

Method Detail

update
```
public void update(Element element,
          OMEModel model)
            throws EnumerationException
```
Updates Annotation recursively from an XML DOM tree. NOTE: No properties are removed, only added or updated.

Specified by:

update in interface OMEModelObject

Overrides:

update in class AbstractOMEModelObject

Parameters:
element - Root of the XML DOM tree to construct a model object graph from.
model - Handler for the OME model which keeps track of instances and references seen during object population.

Throws:

EnumerationException - If there is an error instantiating an enumeration during model object creation.

link
```
public boolean link(Reference reference,
           OMEModelObject o)
```
Description copied from interface: OMEModelObject

Link a given OME model object to this model object.

Specified by:

link in interface OMEModelObject

Overrides:

link in class AbstractOMEModelObject

Parameters:
reference - The type qualifier for the reference. This should be the corresponding reference type for o. If, for example, o is of type Image, reference MUST be of type ImageRef.
o - Model object to link to.

Returns:
true if this model object was able to handle the reference, false otherwise.

getNamespace
```
public String getNamespace()
```

setNamespace

public void setNamespace(String namespace)

getID
```
public String getID()
```

setID
```
public void setID(String id)
```

getAnnotator
```
public String getAnnotator()
```

setAnnotator

public void setAnnotator(String annotator)

getDescription
```
public String getDescription()
```

setDescription

public void setDescription(String description)

sizeOfLinkedAnnotationList

public int sizeOfLinkedAnnotationList()

copyLinkedAnnotationList

public List<Annotation> copyLinkedAnnotationList()

getLinkedAnnotation

public Annotation getLinkedAnnotation(int index)

setLinkedAnnotation

public Annotation setLinkedAnnotation(int index,
                             Annotation o)

linkAnnotation

public boolean linkAnnotation(Annotation o)

unlinkAnnotation

public boolean unlinkAnnotation(Annotation o)

sizeOfLinkedImageList
```
public int sizeOfLinkedImageList()
```

copyLinkedImageList

public List<Image> copyLinkedImageList()

getLinkedImage

public Image getLinkedImage(int index)

setLinkedImage

public Image setLinkedImage(int index,
                   Image o)

linkImage
```
public boolean linkImage(Image o)
```

unlinkImage
```
public boolean unlinkImage(Image o)
```

sizeOfLinkedPlaneList
```
public int sizeOfLinkedPlaneList()
```

copyLinkedPlaneList

public List<Plane> copyLinkedPlaneList()

getLinkedPlane

public Plane getLinkedPlane(int index)

setLinkedPlane

public Plane setLinkedPlane(int index,
                   Plane o)

linkPlane
```
public boolean linkPlane(Plane o)
```

unlinkPlane
```
public boolean unlinkPlane(Plane o)
```

sizeOfLinkedChannelList
```
public int sizeOfLinkedChannelList()
```

copyLinkedChannelList

public List<Channel> copyLinkedChannelList()

getLinkedChannel

public Channel getLinkedChannel(int index)

setLinkedChannel

public Channel setLinkedChannel(int index,
                       Channel o)

linkChannel

public boolean linkChannel(Channel o)

unlinkChannel

public boolean unlinkChannel(Channel o)

sizeOfLinkedInstrumentList

public int sizeOfLinkedInstrumentList()

copyLinkedInstrumentList

public List<Instrument> copyLinkedInstrumentList()

getLinkedInstrument

public Instrument getLinkedInstrument(int index)

setLinkedInstrument

public Instrument setLinkedInstrument(int index,
                             Instrument o)

linkInstrument

public boolean linkInstrument(Instrument o)

unlinkInstrument

public boolean unlinkInstrument(Instrument o)

sizeOfLinkedLightSourceList

public int sizeOfLinkedLightSourceList()

copyLinkedLightSourceList

public List<LightSource> copyLinkedLightSourceList()

getLinkedLightSource

public LightSource getLinkedLightSource(int index)

setLinkedLightSource

public LightSource setLinkedLightSource(int index,
                               LightSource o)

linkLightSource

public boolean linkLightSource(LightSource o)

unlinkLightSource

public boolean unlinkLightSource(LightSource o)

sizeOfLinkedProjectList
```
public int sizeOfLinkedProjectList()
```

copyLinkedProjectList

public List<Project> copyLinkedProjectList()

getLinkedProject

public Project getLinkedProject(int index)

setLinkedProject

public Project setLinkedProject(int index,
                       Project o)

linkProject

public boolean linkProject(Project o)

unlinkProject

public boolean unlinkProject(Project o)

sizeOfLinkedExperimenterGroupList

public int sizeOfLinkedExperimenterGroupList()

copyLinkedExperimenterGroupList

public List<ExperimenterGroup> copyLinkedExperimenterGroupList()

getLinkedExperimenterGroup

public ExperimenterGroup getLinkedExperimenterGroup(int index)

setLinkedExperimenterGroup

public ExperimenterGroup setLinkedExperimenterGroup(int index,
                                           ExperimenterGroup o)

linkExperimenterGroup

public boolean linkExperimenterGroup(ExperimenterGroup o)

unlinkExperimenterGroup

public boolean unlinkExperimenterGroup(ExperimenterGroup o)

sizeOfLinkedDatasetList
```
public int sizeOfLinkedDatasetList()
```

copyLinkedDatasetList

public List<Dataset> copyLinkedDatasetList()

getLinkedDataset

public Dataset getLinkedDataset(int index)

setLinkedDataset

public Dataset setLinkedDataset(int index,
                       Dataset o)

linkDataset

public boolean linkDataset(Dataset o)

unlinkDataset

public boolean unlinkDataset(Dataset o)

sizeOfLinkedExperimenterList

public int sizeOfLinkedExperimenterList()

copyLinkedExperimenterList

public List<Experimenter> copyLinkedExperimenterList()

getLinkedExperimenter

public Experimenter getLinkedExperimenter(int index)

setLinkedExperimenter

public Experimenter setLinkedExperimenter(int index,
                                 Experimenter o)

linkExperimenter

public boolean linkExperimenter(Experimenter o)

unlinkExperimenter

public boolean unlinkExperimenter(Experimenter o)

sizeOfLinkedFolderList
```
public int sizeOfLinkedFolderList()
```

copyLinkedFolderList

public List<Folder> copyLinkedFolderList()

getLinkedFolder

public Folder getLinkedFolder(int index)

setLinkedFolder

public Folder setLinkedFolder(int index,
                     Folder o)

linkFolder
```
public boolean linkFolder(Folder o)
```

unlinkFolder

public boolean unlinkFolder(Folder o)

sizeOfLinkedObjectiveList

public int sizeOfLinkedObjectiveList()

copyLinkedObjectiveList

public List<Objective> copyLinkedObjectiveList()

getLinkedObjective

public Objective getLinkedObjective(int index)

setLinkedObjective

public Objective setLinkedObjective(int index,
                           Objective o)

linkObjective

public boolean linkObjective(Objective o)

unlinkObjective

public boolean unlinkObjective(Objective o)

sizeOfLinkedDetectorList
```
public int sizeOfLinkedDetectorList()
```

copyLinkedDetectorList

public List<Detector> copyLinkedDetectorList()

getLinkedDetector

public Detector getLinkedDetector(int index)

setLinkedDetector

public Detector setLinkedDetector(int index,
                         Detector o)

linkDetector

public boolean linkDetector(Detector o)

unlinkDetector

public boolean unlinkDetector(Detector o)

sizeOfLinkedFilterList
```
public int sizeOfLinkedFilterList()
```

copyLinkedFilterList

public List<Filter> copyLinkedFilterList()

getLinkedFilter

public Filter getLinkedFilter(int index)

setLinkedFilter

public Filter setLinkedFilter(int index,
                     Filter o)

linkFilter
```
public boolean linkFilter(Filter o)
```

unlinkFilter

public boolean unlinkFilter(Filter o)

sizeOfLinkedDichroicList
```
public int sizeOfLinkedDichroicList()
```

copyLinkedDichroicList

public List<Dichroic> copyLinkedDichroicList()

getLinkedDichroic

public Dichroic getLinkedDichroic(int index)

setLinkedDichroic

public Dichroic setLinkedDichroic(int index,
                         Dichroic o)

linkDichroic

public boolean linkDichroic(Dichroic o)

unlinkDichroic

public boolean unlinkDichroic(Dichroic o)

sizeOfLinkedLightPathList

public int sizeOfLinkedLightPathList()

copyLinkedLightPathList

public List<LightPath> copyLinkedLightPathList()

getLinkedLightPath

public LightPath getLinkedLightPath(int index)

setLinkedLightPath

public LightPath setLinkedLightPath(int index,
                           LightPath o)

linkLightPath

public boolean linkLightPath(LightPath o)

unlinkLightPath

public boolean unlinkLightPath(LightPath o)

sizeOfLinkedROIList
```
public int sizeOfLinkedROIList()
```

copyLinkedROIList
```
public List<ROI> copyLinkedROIList()
```

getLinkedROI
```
public ROI getLinkedROI(int index)
```

setLinkedROI

public ROI setLinkedROI(int index,
               ROI o)

linkROI
```
public boolean linkROI(ROI o)
```

unlinkROI
```
public boolean unlinkROI(ROI o)
```

sizeOfLinkedShapeList
```
public int sizeOfLinkedShapeList()
```

copyLinkedShapeList

public List<Shape> copyLinkedShapeList()

getLinkedShape

public Shape getLinkedShape(int index)

setLinkedShape

public Shape setLinkedShape(int index,
                   Shape o)

linkShape
```
public boolean linkShape(Shape o)
```

unlinkShape
```
public boolean unlinkShape(Shape o)
```

sizeOfLinkedPlateList
```
public int sizeOfLinkedPlateList()
```

copyLinkedPlateList

public List<Plate> copyLinkedPlateList()

getLinkedPlate

public Plate getLinkedPlate(int index)

setLinkedPlate

public Plate setLinkedPlate(int index,
                   Plate o)

linkPlate
```
public boolean linkPlate(Plate o)
```

unlinkPlate
```
public boolean unlinkPlate(Plate o)
```

sizeOfLinkedReagentList
```
public int sizeOfLinkedReagentList()
```

copyLinkedReagentList

public List<Reagent> copyLinkedReagentList()

getLinkedReagent

public Reagent getLinkedReagent(int index)

setLinkedReagent

public Reagent setLinkedReagent(int index,
                       Reagent o)

linkReagent

public boolean linkReagent(Reagent o)

unlinkReagent

public boolean unlinkReagent(Reagent o)

sizeOfLinkedScreenList
```
public int sizeOfLinkedScreenList()
```

copyLinkedScreenList

public List<Screen> copyLinkedScreenList()

getLinkedScreen

public Screen getLinkedScreen(int index)

setLinkedScreen

public Screen setLinkedScreen(int index,
                     Screen o)

linkScreen
```
public boolean linkScreen(Screen o)
```

unlinkScreen

public boolean unlinkScreen(Screen o)

sizeOfLinkedPlateAcquisitionList

public int sizeOfLinkedPlateAcquisitionList()

copyLinkedPlateAcquisitionList

public List<PlateAcquisition> copyLinkedPlateAcquisitionList()

getLinkedPlateAcquisition

public PlateAcquisition getLinkedPlateAcquisition(int index)

setLinkedPlateAcquisition

public PlateAcquisition setLinkedPlateAcquisition(int index,
                                         PlateAcquisition o)

linkPlateAcquisition

public boolean linkPlateAcquisition(PlateAcquisition o)

unlinkPlateAcquisition

public boolean unlinkPlateAcquisition(PlateAcquisition o)

sizeOfLinkedWellList
```
public int sizeOfLinkedWellList()
```

copyLinkedWellList

public List<Well> copyLinkedWellList()

getLinkedWell
```
public Well getLinkedWell(int index)
```

setLinkedWell

public Well setLinkedWell(int index,
                 Well o)

linkWell
```
public boolean linkWell(Well o)
```

unlinkWell
```
public boolean unlinkWell(Well o)
```

asXMLElement
```
public Element asXMLElement(Document document)
```
Description copied from interface: OMEModelObject

Takes the entire object hierarchy and produces an XML DOM tree.

Specified by:

asXMLElement in interface OMEModelObject

Specified by:

asXMLElement in class AbstractOMEModelObject

Parameters:
document - Destination document for element creation, etc.

Returns:
XML DOM tree root element for this model object.

asXMLElement
```
protected Element asXMLElement(Document document,
                   Element Annotation_element)
```
Description copied from class: AbstractOMEModelObject

Takes the entire object hierarchy and produced an XML DOM tree taking into account class hierarchy.

Overrides:

asXMLElement in class AbstractOMEModelObject

Parameters:
document - Destination document for element creation, etc.
Annotation_element - Element from the subclass. If null a new element will be created of this class.

Returns:
element populated with properties from this class.

Class Annotation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class ome.xml.model.AbstractOMEModelObject

Methods inherited from class java.lang.Object

Field Detail

NAMESPACE

LOGGER

namespace

id

annotator

description

annotationLinks

imageLinks

planeLinks

channelLinks

instrumentLinks

lightSourceLinks

projectLinks

experimenterGroupLinks

datasetLinks

experimenterLinks

folderLinks

objectiveLinks

detectorLinks

filterLinks

dichroicLinks

lightPathLinks

roiLinks

shapeLinks

plateLinks

reagentLinks

screenLinks

plateAcquisitionLinks

wellLinks

Constructor Detail

Annotation

Annotation

Annotation

Method Detail

update

link

getNamespace

setNamespace

getID

setID

getAnnotator

setAnnotator

getDescription

setDescription

sizeOfLinkedAnnotationList

copyLinkedAnnotationList

getLinkedAnnotation

setLinkedAnnotation

linkAnnotation

unlinkAnnotation

sizeOfLinkedImageList

copyLinkedImageList

getLinkedImage

setLinkedImage

linkImage

unlinkImage

sizeOfLinkedPlaneList

copyLinkedPlaneList

getLinkedPlane

setLinkedPlane

linkPlane

unlinkPlane

sizeOfLinkedChannelList

copyLinkedChannelList

getLinkedChannel

setLinkedChannel

linkChannel

unlinkChannel

sizeOfLinkedInstrumentList

copyLinkedInstrumentList

getLinkedInstrument

setLinkedInstrument

linkInstrument