Package ome.xml.model

Class Annotation

All Implemented Interfaces:
OMEModelObject
Direct Known Subclasses:
BasicAnnotation, ListAnnotation, MapAnnotation, TextAnnotation, TypeAnnotation

public abstract class Annotation extends AbstractOMEModelObject
  • Field Details

  • Constructor Details

    • 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 Details

    • 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.
    • getID

      public String getID()
    • setID

      public void setID(String id)
    • getNamespace

      public String getNamespace()
    • setNamespace

      public void setNamespace(String namespace)
    • 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

      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 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.