Package ome.xml.model
Class Annotation
- java.lang.Object
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- ome.xml.model.AbstractOMEModelObject
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- ome.xml.model.Annotation
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- All Implemented Interfaces:
OMEModelObject
- Direct Known Subclasses:
BasicAnnotation
,ListAnnotation
,MapAnnotation
,TextAnnotation
,TypeAnnotation
public abstract class Annotation extends AbstractOMEModelObject
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Constructor Summary
Constructors Constructor Description Annotation()
Default constructor.Annotation(Annotation orig)
Copy constructor.Annotation(Element element, OMEModel model)
Constructs Annotation recursively from an XML DOM tree.
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Method Summary
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Methods inherited from class ome.xml.model.AbstractOMEModelObject
getChildrenByTagName, stripNamespacePrefix
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Field Detail
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NAMESPACE
public static final String NAMESPACE
- See Also:
- Constant Field Values
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Constructor Detail
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Annotation
public Annotation()
Default constructor.
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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.
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Annotation
public Annotation(Annotation orig)
Copy constructor.
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Method Detail
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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 interfaceOMEModelObject
- Overrides:
update
in classAbstractOMEModelObject
- 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.
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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 interfaceOMEModelObject
- Overrides:
link
in classAbstractOMEModelObject
- Parameters:
reference
- The type qualifier for the reference. This should be the corresponding reference type foro
. If, for example,o
is of typeImage
,reference
MUST be of typeImageRef
.o
- Model object to link to.- Returns:
true
if this model object was able to handle the reference,false
otherwise.
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getID
public String getID()
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setID
public void setID(String id)
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getNamespace
public String getNamespace()
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setNamespace
public void setNamespace(String namespace)
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getAnnotator
public String getAnnotator()
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setAnnotator
public void setAnnotator(String annotator)
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getDescription
public String getDescription()
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setDescription
public void setDescription(String description)
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sizeOfLinkedAnnotationList
public int sizeOfLinkedAnnotationList()
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copyLinkedAnnotationList
public List<Annotation> copyLinkedAnnotationList()
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getLinkedAnnotation
public Annotation getLinkedAnnotation(int index)
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setLinkedAnnotation
public Annotation setLinkedAnnotation(int index, Annotation o)
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linkAnnotation
public boolean linkAnnotation(Annotation o)
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unlinkAnnotation
public boolean unlinkAnnotation(Annotation o)
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sizeOfLinkedImageList
public int sizeOfLinkedImageList()
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getLinkedImage
public Image getLinkedImage(int index)
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linkImage
public boolean linkImage(Image o)
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unlinkImage
public boolean unlinkImage(Image o)
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sizeOfLinkedPlaneList
public int sizeOfLinkedPlaneList()
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getLinkedPlane
public Plane getLinkedPlane(int index)
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linkPlane
public boolean linkPlane(Plane o)
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unlinkPlane
public boolean unlinkPlane(Plane o)
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sizeOfLinkedChannelList
public int sizeOfLinkedChannelList()
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getLinkedChannel
public Channel getLinkedChannel(int index)
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linkChannel
public boolean linkChannel(Channel o)
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unlinkChannel
public boolean unlinkChannel(Channel o)
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sizeOfLinkedInstrumentList
public int sizeOfLinkedInstrumentList()
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copyLinkedInstrumentList
public List<Instrument> copyLinkedInstrumentList()
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getLinkedInstrument
public Instrument getLinkedInstrument(int index)
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setLinkedInstrument
public Instrument setLinkedInstrument(int index, Instrument o)
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linkInstrument
public boolean linkInstrument(Instrument o)
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unlinkInstrument
public boolean unlinkInstrument(Instrument o)
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sizeOfLinkedLightSourceList
public int sizeOfLinkedLightSourceList()
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copyLinkedLightSourceList
public List<LightSource> copyLinkedLightSourceList()
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getLinkedLightSource
public LightSource getLinkedLightSource(int index)
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setLinkedLightSource
public LightSource setLinkedLightSource(int index, LightSource o)
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linkLightSource
public boolean linkLightSource(LightSource o)
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unlinkLightSource
public boolean unlinkLightSource(LightSource o)
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sizeOfLinkedProjectList
public int sizeOfLinkedProjectList()
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getLinkedProject
public Project getLinkedProject(int index)
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linkProject
public boolean linkProject(Project o)
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unlinkProject
public boolean unlinkProject(Project o)
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sizeOfLinkedExperimenterGroupList
public int sizeOfLinkedExperimenterGroupList()
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copyLinkedExperimenterGroupList
public List<ExperimenterGroup> copyLinkedExperimenterGroupList()
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getLinkedExperimenterGroup
public ExperimenterGroup getLinkedExperimenterGroup(int index)
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setLinkedExperimenterGroup
public ExperimenterGroup setLinkedExperimenterGroup(int index, ExperimenterGroup o)
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linkExperimenterGroup
public boolean linkExperimenterGroup(ExperimenterGroup o)
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unlinkExperimenterGroup
public boolean unlinkExperimenterGroup(ExperimenterGroup o)
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sizeOfLinkedDatasetList
public int sizeOfLinkedDatasetList()
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getLinkedDataset
public Dataset getLinkedDataset(int index)
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linkDataset
public boolean linkDataset(Dataset o)
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unlinkDataset
public boolean unlinkDataset(Dataset o)
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sizeOfLinkedExperimenterList
public int sizeOfLinkedExperimenterList()
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copyLinkedExperimenterList
public List<Experimenter> copyLinkedExperimenterList()
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getLinkedExperimenter
public Experimenter getLinkedExperimenter(int index)
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setLinkedExperimenter
public Experimenter setLinkedExperimenter(int index, Experimenter o)
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linkExperimenter
public boolean linkExperimenter(Experimenter o)
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unlinkExperimenter
public boolean unlinkExperimenter(Experimenter o)
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sizeOfLinkedFolderList
public int sizeOfLinkedFolderList()
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getLinkedFolder
public Folder getLinkedFolder(int index)
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linkFolder
public boolean linkFolder(Folder o)
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unlinkFolder
public boolean unlinkFolder(Folder o)
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sizeOfLinkedObjectiveList
public int sizeOfLinkedObjectiveList()
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getLinkedObjective
public Objective getLinkedObjective(int index)
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linkObjective
public boolean linkObjective(Objective o)
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unlinkObjective
public boolean unlinkObjective(Objective o)
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sizeOfLinkedDetectorList
public int sizeOfLinkedDetectorList()
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getLinkedDetector
public Detector getLinkedDetector(int index)
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linkDetector
public boolean linkDetector(Detector o)
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unlinkDetector
public boolean unlinkDetector(Detector o)
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sizeOfLinkedFilterList
public int sizeOfLinkedFilterList()
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getLinkedFilter
public Filter getLinkedFilter(int index)
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linkFilter
public boolean linkFilter(Filter o)
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unlinkFilter
public boolean unlinkFilter(Filter o)
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sizeOfLinkedDichroicList
public int sizeOfLinkedDichroicList()
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getLinkedDichroic
public Dichroic getLinkedDichroic(int index)
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linkDichroic
public boolean linkDichroic(Dichroic o)
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unlinkDichroic
public boolean unlinkDichroic(Dichroic o)
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sizeOfLinkedLightPathList
public int sizeOfLinkedLightPathList()
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getLinkedLightPath
public LightPath getLinkedLightPath(int index)
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linkLightPath
public boolean linkLightPath(LightPath o)
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unlinkLightPath
public boolean unlinkLightPath(LightPath o)
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sizeOfLinkedROIList
public int sizeOfLinkedROIList()
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getLinkedROI
public ROI getLinkedROI(int index)
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linkROI
public boolean linkROI(ROI o)
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unlinkROI
public boolean unlinkROI(ROI o)
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sizeOfLinkedShapeList
public int sizeOfLinkedShapeList()
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getLinkedShape
public Shape getLinkedShape(int index)
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linkShape
public boolean linkShape(Shape o)
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unlinkShape
public boolean unlinkShape(Shape o)
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sizeOfLinkedPlateList
public int sizeOfLinkedPlateList()
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getLinkedPlate
public Plate getLinkedPlate(int index)
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linkPlate
public boolean linkPlate(Plate o)
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unlinkPlate
public boolean unlinkPlate(Plate o)
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sizeOfLinkedReagentList
public int sizeOfLinkedReagentList()
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getLinkedReagent
public Reagent getLinkedReagent(int index)
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linkReagent
public boolean linkReagent(Reagent o)
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unlinkReagent
public boolean unlinkReagent(Reagent o)
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sizeOfLinkedScreenList
public int sizeOfLinkedScreenList()
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getLinkedScreen
public Screen getLinkedScreen(int index)
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linkScreen
public boolean linkScreen(Screen o)
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unlinkScreen
public boolean unlinkScreen(Screen o)
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sizeOfLinkedPlateAcquisitionList
public int sizeOfLinkedPlateAcquisitionList()
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copyLinkedPlateAcquisitionList
public List<PlateAcquisition> copyLinkedPlateAcquisitionList()
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getLinkedPlateAcquisition
public PlateAcquisition getLinkedPlateAcquisition(int index)
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setLinkedPlateAcquisition
public PlateAcquisition setLinkedPlateAcquisition(int index, PlateAcquisition o)
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linkPlateAcquisition
public boolean linkPlateAcquisition(PlateAcquisition o)
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unlinkPlateAcquisition
public boolean unlinkPlateAcquisition(PlateAcquisition o)
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sizeOfLinkedWellList
public int sizeOfLinkedWellList()
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getLinkedWell
public Well getLinkedWell(int index)
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linkWell
public boolean linkWell(Well o)
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unlinkWell
public boolean unlinkWell(Well o)
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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 interfaceOMEModelObject
- Specified by:
asXMLElement
in classAbstractOMEModelObject
- Parameters:
document
- Destination document for element creation, etc.- Returns:
- XML DOM tree root element for this model object.
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asXMLElement
public 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 classAbstractOMEModelObject
- Parameters:
document
- Destination document for element creation, etc.Annotation_element
- Element from the subclass. Ifnull
a new element will be created of this class.- Returns:
element
populated with properties from this class.
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