Package ome.xml.model

Class Annotation

    • Constructor Detail

      • Annotation

        public Annotation()
        Default constructor.

      • Annotation

        public Annotation​(org.w3c.dom.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​(org.w3c.dom.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 java.lang.String getID()

      • setID

        public void setID​(java.lang.String id)

      • getNamespace

        public java.lang.String getNamespace()

      • setNamespace

        public void setNamespace​(java.lang.String namespace)

      • getAnnotator

        public java.lang.String getAnnotator()

      • setAnnotator

        public void setAnnotator​(java.lang.String annotator)

      • getDescription

        public java.lang.String getDescription()

      • setDescription

        public void setDescription​(java.lang.String description)

      • sizeOfLinkedAnnotationList

        public int sizeOfLinkedAnnotationList()

      • copyLinkedAnnotationList

        public java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.List<ExperimenterGroup> copyLinkedExperimenterGroupList()

      • getLinkedExperimenterGroup

        public ExperimenterGroup getLinkedExperimenterGroup​(int index)

      • linkExperimenterGroup

        public boolean linkExperimenterGroup​(ExperimenterGroup o)

      • unlinkExperimenterGroup

        public boolean unlinkExperimenterGroup​(ExperimenterGroup o)

      • sizeOfLinkedDatasetList

        public int sizeOfLinkedDatasetList()

      • copyLinkedDatasetList

        public java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.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 java.util.List<PlateAcquisition> copyLinkedPlateAcquisitionList()

      • getLinkedPlateAcquisition

        public PlateAcquisition getLinkedPlateAcquisition​(int index)

      • linkPlateAcquisition

        public boolean linkPlateAcquisition​(PlateAcquisition o)

      • unlinkPlateAcquisition

        public boolean unlinkPlateAcquisition​(PlateAcquisition o)

      • sizeOfLinkedWellList

        public int sizeOfLinkedWellList()

      • copyLinkedWellList

        public java.util.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 org.w3c.dom.Element asXMLElement​(org.w3c.dom.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 org.w3c.dom.Element asXMLElement​(org.w3c.dom.Document document,
                                        org.w3c.dom.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.