Package ome.xml.model

Class Annotation

    • 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.
      • 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)
      • 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)
      • 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)
      • 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()
      • getLinkedExperimenterGroup

        public ExperimenterGroup getLinkedExperimenterGroup​(int index)
      • 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)
      • 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)
      • 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)
      • 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()
      • getLinkedPlateAcquisition

        public PlateAcquisition getLinkedPlateAcquisition​(int index)
      • 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,
                                    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.