Annotation (Bio-Formats API)

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

All Implemented Interfaces:

OMEModelObject

Direct Known Subclasses:

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

Field Summary

Fields
Modifier and Type Field and Description

static String NAMESPACE

Fields
Modifier and Type	Field and Description
`static String`	`NAMESPACE`

Constructor Summary

Constructors
Constructor and Description

Annotation()
Default constructor.

Annotation(Element element, OMEModel model)
Constructs Annotation recursively from an XML DOM tree.

Constructors
Constructor and Description
`Annotation()` Default 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<ExperimenterGroup>`	`copyLinkedExperimenterGroupList()`
`List<Experimenter>`	`copyLinkedExperimenterList()`
`List<Image>`	`copyLinkedImageList()`
`List<Pixels>`	`copyLinkedPixelsList()`
`List<Plane>`	`copyLinkedPlaneList()`
`List<PlateAcquisition>`	`copyLinkedPlateAcquisitionList()`
`List<Plate>`	`copyLinkedPlateList()`
`List<Project>`	`copyLinkedProjectList()`
`List<Reagent>`	`copyLinkedReagentList()`
`List<ROI>`	`copyLinkedROIList()`
`List<Screen>`	`copyLinkedScreenList()`
`List<Well>`	`copyLinkedWellList()`
`List<WellSample>`	`copyLinkedWellSampleList()`
`String`	`getDescription()`
`String`	`getID()`
`Annotation`	`getLinkedAnnotation(int index)`
`Channel`	`getLinkedChannel(int index)`
`Dataset`	`getLinkedDataset(int index)`
`Experimenter`	`getLinkedExperimenter(int index)`
`ExperimenterGroup`	`getLinkedExperimenterGroup(int index)`
`Image`	`getLinkedImage(int index)`
`Pixels`	`getLinkedPixels(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)`
`Well`	`getLinkedWell(int index)`
`WellSample`	`getLinkedWellSample(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`	`linkExperimenter(Experimenter o)`
`boolean`	`linkExperimenterGroup(ExperimenterGroup o)`
`boolean`	`linkImage(Image o)`
`boolean`	`linkPixels(Pixels 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`	`linkWell(Well o)`
`boolean`	`linkWellSample(WellSample o)`
`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)`
`Experimenter`	`setLinkedExperimenter(int index, Experimenter o)`
`ExperimenterGroup`	`setLinkedExperimenterGroup(int index, ExperimenterGroup o)`
`Image`	`setLinkedImage(int index, Image o)`
`Pixels`	`setLinkedPixels(int index, Pixels 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)`
`Well`	`setLinkedWell(int index, Well o)`
`WellSample`	`setLinkedWellSample(int index, WellSample o)`
`void`	`setNamespace(String namespace)`
`int`	`sizeOfLinkedAnnotationList()`
`int`	`sizeOfLinkedChannelList()`
`int`	`sizeOfLinkedDatasetList()`
`int`	`sizeOfLinkedExperimenterGroupList()`
`int`	`sizeOfLinkedExperimenterList()`
`int`	`sizeOfLinkedImageList()`
`int`	`sizeOfLinkedPixelsList()`
`int`	`sizeOfLinkedPlaneList()`
`int`	`sizeOfLinkedPlateAcquisitionList()`
`int`	`sizeOfLinkedPlateList()`
`int`	`sizeOfLinkedProjectList()`
`int`	`sizeOfLinkedReagentList()`
`int`	`sizeOfLinkedROIList()`
`int`	`sizeOfLinkedScreenList()`
`int`	`sizeOfLinkedWellList()`
`int`	`sizeOfLinkedWellSampleList()`
`boolean`	`unlinkAnnotation(Annotation o)`
`boolean`	`unlinkChannel(Channel o)`
`boolean`	`unlinkDataset(Dataset o)`
`boolean`	`unlinkExperimenter(Experimenter o)`
`boolean`	`unlinkExperimenterGroup(ExperimenterGroup o)`
`boolean`	`unlinkImage(Image o)`
`boolean`	`unlinkPixels(Pixels 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`	`unlinkWell(Well o)`
`boolean`	`unlinkWellSample(WellSample 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, update

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

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.

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)
```

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)
```

sizeOfLinkedPixelsList
```
public int sizeOfLinkedPixelsList()
```

copyLinkedPixelsList

public List<Pixels> copyLinkedPixelsList()

getLinkedPixels

public Pixels getLinkedPixels(int index)

setLinkedPixels

public Pixels setLinkedPixels(int index,
                     Pixels o)

linkPixels
```
public boolean linkPixels(Pixels o)
```

unlinkPixels

public boolean unlinkPixels(Pixels 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)

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)

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)
```

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)
```

sizeOfLinkedWellSampleList

public int sizeOfLinkedWellSampleList()

copyLinkedWellSampleList

public List<WellSample> copyLinkedWellSampleList()

getLinkedWellSample

public WellSample getLinkedWellSample(int index)

setLinkedWellSample

public WellSample setLinkedWellSample(int index,
                             WellSample o)

linkWellSample

public boolean linkWellSample(WellSample o)

unlinkWellSample

public boolean unlinkWellSample(WellSample 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

Constructor Detail

Annotation

Annotation

Method Detail

update

link

getNamespace

setNamespace

getID

setID

getDescription

setDescription

sizeOfLinkedAnnotationList

copyLinkedAnnotationList

getLinkedAnnotation

setLinkedAnnotation

linkAnnotation

unlinkAnnotation

sizeOfLinkedImageList

copyLinkedImageList

getLinkedImage

setLinkedImage

linkImage

unlinkImage

sizeOfLinkedPixelsList

copyLinkedPixelsList

getLinkedPixels

setLinkedPixels

linkPixels

unlinkPixels

sizeOfLinkedPlaneList

copyLinkedPlaneList

getLinkedPlane

setLinkedPlane

linkPlane

unlinkPlane

sizeOfLinkedChannelList

copyLinkedChannelList

getLinkedChannel

setLinkedChannel

linkChannel

unlinkChannel

sizeOfLinkedProjectList

copyLinkedProjectList

getLinkedProject

setLinkedProject

linkProject

unlinkProject

sizeOfLinkedExperimenterGroupList

copyLinkedExperimenterGroupList

getLinkedExperimenterGroup

setLinkedExperimenterGroup

linkExperimenterGroup

unlinkExperimenterGroup

sizeOfLinkedDatasetList

copyLinkedDatasetList

getLinkedDataset

setLinkedDataset

linkDataset

unlinkDataset

sizeOfLinkedExperimenterList

copyLinkedExperimenterList

getLinkedExperimenter

setLinkedExperimenter

linkExperimenter

unlinkExperimenter

sizeOfLinkedROIList

copyLinkedROIList

getLinkedROI

setLinkedROI

linkROI

unlinkROI