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A library for working with OME-XML metadata structures.
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/*
 * #%L
 * OME-XML Java library for working with OME-XML metadata structures.
 * %%
 * Copyright (C) 2006 - 2016 Open Microscopy Environment:
 *   - Massachusetts Institute of Technology
 *   - National Institutes of Health
 *   - University of Dundee
 *   - Board of Regents of the University of Wisconsin-Madison
 *   - Glencoe Software, Inc.
 * %%
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * The views and conclusions contained in the software and documentation are
 * those of the authors and should not be interpreted as representing official
 * policies, either expressed or implied, of any organization.
 * #L%
 */

/*-----------------------------------------------------------------------------
 *
 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY.
 *
 *-----------------------------------------------------------------------------
 */

package ome.xml.model;

import java.util.ArrayList;
import java.util.List;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import ome.xml.model.enums.*;
import ome.xml.model.enums.handlers.*;
import ome.xml.model.primitives.*;
import ome.units.quantity.*;
import ome.units.unit.Unit;

public abstract class Annotation extends AbstractOMEModelObject
{
  // Base:  -- Name: Annotation -- Type: Annotation -- modelBaseType: AbstractOMEModelObject -- langBaseType: Object

  // -- Constants --

  public static final String NAMESPACE = "http://www.openmicroscopy.org/Schemas/OME/2016-06";

  /** Logger for this class. */
  private static final Logger LOGGER =
    LoggerFactory.getLogger(Annotation.class);

  // -- Instance variables --

  // ID property
  private String id;

  // Namespace property
  private String namespace;

  // Annotator property
  private String annotator;

  // Description property
  private String description;

  // AnnotationRef reference (occurs more than once)
  private List annotationLinks = new ReferenceList<>();

  // Image_BackReference back reference (occurs more than once)
  private List imageLinks = new ReferenceList<>();

  // Plane_BackReference back reference (occurs more than once)
  private List planeLinks = new ReferenceList<>();

  // Channel_BackReference back reference (occurs more than once)
  private List channelLinks = new ReferenceList<>();

  // Instrument_BackReference back reference (occurs more than once)
  private List instrumentLinks = new ReferenceList<>();

  // LightSource_BackReference back reference (occurs more than once)
  private List lightSourceLinks = new ReferenceList<>();

  // Project_BackReference back reference (occurs more than once)
  private List projectLinks = new ReferenceList<>();

  // ExperimenterGroup_BackReference back reference (occurs more than once)
  private List experimenterGroupLinks = new ReferenceList<>();

  // Dataset_BackReference back reference (occurs more than once)
  private List datasetLinks = new ReferenceList<>();

  // Experimenter_BackReference back reference (occurs more than once)
  private List experimenterLinks = new ReferenceList<>();

  // Folder_BackReference back reference (occurs more than once)
  private List folderLinks = new ReferenceList<>();

  // Objective_BackReference back reference (occurs more than once)
  private List objectiveLinks = new ReferenceList<>();

  // Detector_BackReference back reference (occurs more than once)
  private List detectorLinks = new ReferenceList<>();

  // Filter_BackReference back reference (occurs more than once)
  private List filterLinks = new ReferenceList<>();

  // Dichroic_BackReference back reference (occurs more than once)
  private List dichroicLinks = new ReferenceList<>();

  // LightPath_BackReference back reference (occurs more than once)
  private List lightPathLinks = new ReferenceList<>();

  // ROI_BackReference back reference (occurs more than once)
  private List roiLinks = new ReferenceList<>();

  // Shape_BackReference back reference (occurs more than once)
  private List shapeLinks = new ReferenceList<>();

  // Plate_BackReference back reference (occurs more than once)
  private List plateLinks = new ReferenceList<>();

  // Reagent_BackReference back reference (occurs more than once)
  private List reagentLinks = new ReferenceList<>();

  // Screen_BackReference back reference (occurs more than once)
  private List screenLinks = new ReferenceList<>();

  // PlateAcquisition_BackReference back reference (occurs more than once)
  private List plateAcquisitionLinks = new ReferenceList<>();

  // Well_BackReference back reference (occurs more than once)
  private List wellLinks = new ReferenceList<>();

  // -- Constructors --

  /** Default constructor. */
  public Annotation()
  {
  }



  /**
   * Constructs Annotation recursively from an XML DOM tree.
   * @param element Root of the XML DOM tree to construct a model object
   * graph from.
   * @param 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.
   */
  public Annotation(Element element, OMEModel model)
    throws EnumerationException
  {
    update(element, model);
  }

  /** Copy constructor. */
  public Annotation(Annotation orig)
  {
    id = orig.id;
    namespace = orig.namespace;
    annotator = orig.annotator;
    description = orig.description;
    annotationLinks = orig.annotationLinks;
    imageLinks = orig.imageLinks;
    planeLinks = orig.planeLinks;
    channelLinks = orig.channelLinks;
    instrumentLinks = orig.instrumentLinks;
    lightSourceLinks = orig.lightSourceLinks;
    projectLinks = orig.projectLinks;
    experimenterGroupLinks = orig.experimenterGroupLinks;
    datasetLinks = orig.datasetLinks;
    experimenterLinks = orig.experimenterLinks;
    folderLinks = orig.folderLinks;
    objectiveLinks = orig.objectiveLinks;
    detectorLinks = orig.detectorLinks;
    filterLinks = orig.filterLinks;
    dichroicLinks = orig.dichroicLinks;
    lightPathLinks = orig.lightPathLinks;
    roiLinks = orig.roiLinks;
    shapeLinks = orig.shapeLinks;
    plateLinks = orig.plateLinks;
    reagentLinks = orig.reagentLinks;
    screenLinks = orig.screenLinks;
    plateAcquisitionLinks = orig.plateAcquisitionLinks;
    wellLinks = orig.wellLinks;
  }

  // -- Custom content from Annotation specific template --


  // -- OMEModelObject API methods --

  /**
   * Updates Annotation recursively from an XML DOM tree. NOTE: No
   * properties are removed, only added or updated.
   * @param element Root of the XML DOM tree to construct a model object
   * graph from.
   * @param 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.
   */
  public void update(Element element, OMEModel model)
    throws EnumerationException
  {
    super.update(element, model);
    if (!element.hasAttribute("ID") && getID() == null)
    {
      // TODO: Should be its own exception
      throw new RuntimeException(
        "Annotation missing required ID property.");
    }
    if (element.hasAttribute("ID"))
    {
      // ID property
      setID(String.valueOf(
        element.getAttribute("ID")));
      // Adding this model object to the model handler
      model.addModelObject(getID(), this);
    }
    if (element.hasAttribute("Namespace"))
    {
      // Attribute property Namespace
      setNamespace(String.valueOf(
        element.getAttribute("Namespace")));
    }
    if (element.hasAttribute("Annotator"))
    {
      // Attribute property Annotator
      setAnnotator(String.valueOf(
        element.getAttribute("Annotator")));
    }
    List Description_nodeList =
      getChildrenByTagName(element, "Description");
    if (Description_nodeList.size() > 1)
    {
      // TODO: Should be its own Exception
      throw new RuntimeException(String.format(
        "Description node list size %d != 1",
        Description_nodeList.size()));
    }
    else if (Description_nodeList.size() != 0)
    {
      // Element property Description which is not complex (has no
      // sub-elements)
      setDescription(
        String.valueOf(Description_nodeList.get(0).getTextContent()));
    }
    // Element reference AnnotationRef
    List AnnotationRef_nodeList =
      getChildrenByTagName(element, "AnnotationRef");
    for (Element AnnotationRef_element : AnnotationRef_nodeList)
    {
      AnnotationRef annotationLinks_reference = new AnnotationRef();
      annotationLinks_reference.setID(AnnotationRef_element.getAttribute("ID"));
      model.addReference(this, annotationLinks_reference);
    }
  }

  // -- Annotation API methods --

  public boolean link(Reference reference, OMEModelObject o)
  {
    if (reference instanceof AnnotationRef)
    {
      Annotation o_casted = (Annotation) o;
      annotationLinks.add(o_casted);
      return true;
    }
    return super.link(reference, o);
  }

  // Property ID
  public String getID()
  {
    return id;
  }

  public void setID(String id)
  {
    this.id = id;
  }

  // Property Namespace
  public String getNamespace()
  {
    return namespace;
  }

  public void setNamespace(String namespace)
  {
    this.namespace = namespace;
  }

  // Property Annotator
  public String getAnnotator()
  {
    return annotator;
  }

  public void setAnnotator(String annotator)
  {
    this.annotator = annotator;
  }

  // Property Description
  public String getDescription()
  {
    return description;
  }

  public void setDescription(String description)
  {
    this.description = description;
  }

  // Reference which occurs more than once
  public int sizeOfLinkedAnnotationList()
  {
    return annotationLinks.size();
  }

  public List copyLinkedAnnotationList()
  {
    return new ArrayList<>(annotationLinks);
  }

  public Annotation getLinkedAnnotation(int index)
  {
    return annotationLinks.get(index);
  }

  public Annotation setLinkedAnnotation(int index, Annotation o)
  {
    return annotationLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkAnnotation(Annotation o)
  {
    return annotationLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkAnnotation(Annotation o)
  {
    return annotationLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedImageList()
  {
    return imageLinks.size();
  }

  public List copyLinkedImageList()
  {
    return new ArrayList<>(imageLinks);
  }

  public Image getLinkedImage(int index)
  {
    return imageLinks.get(index);
  }

  public Image setLinkedImage(int index, Image o)
  {
    return imageLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkImage(Image o)
  {
    return imageLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkImage(Image o)
  {
    return imageLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedPlaneList()
  {
    return planeLinks.size();
  }

  public List copyLinkedPlaneList()
  {
    return new ArrayList<>(planeLinks);
  }

  public Plane getLinkedPlane(int index)
  {
    return planeLinks.get(index);
  }

  public Plane setLinkedPlane(int index, Plane o)
  {
    return planeLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkPlane(Plane o)
  {
    return planeLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkPlane(Plane o)
  {
    return planeLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedChannelList()
  {
    return channelLinks.size();
  }

  public List copyLinkedChannelList()
  {
    return new ArrayList<>(channelLinks);
  }

  public Channel getLinkedChannel(int index)
  {
    return channelLinks.get(index);
  }

  public Channel setLinkedChannel(int index, Channel o)
  {
    return channelLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkChannel(Channel o)
  {
    return channelLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkChannel(Channel o)
  {
    return channelLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedInstrumentList()
  {
    return instrumentLinks.size();
  }

  public List copyLinkedInstrumentList()
  {
    return new ArrayList<>(instrumentLinks);
  }

  public Instrument getLinkedInstrument(int index)
  {
    return instrumentLinks.get(index);
  }

  public Instrument setLinkedInstrument(int index, Instrument o)
  {
    return instrumentLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkInstrument(Instrument o)
  {
    return instrumentLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkInstrument(Instrument o)
  {
    return instrumentLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedLightSourceList()
  {
    return lightSourceLinks.size();
  }

  public List copyLinkedLightSourceList()
  {
    return new ArrayList<>(lightSourceLinks);
  }

  public LightSource getLinkedLightSource(int index)
  {
    return lightSourceLinks.get(index);
  }

  public LightSource setLinkedLightSource(int index, LightSource o)
  {
    return lightSourceLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkLightSource(LightSource o)
  {
    return lightSourceLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkLightSource(LightSource o)
  {
    return lightSourceLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedProjectList()
  {
    return projectLinks.size();
  }

  public List copyLinkedProjectList()
  {
    return new ArrayList<>(projectLinks);
  }

  public Project getLinkedProject(int index)
  {
    return projectLinks.get(index);
  }

  public Project setLinkedProject(int index, Project o)
  {
    return projectLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkProject(Project o)
  {
    return projectLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkProject(Project o)
  {
    return projectLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedExperimenterGroupList()
  {
    return experimenterGroupLinks.size();
  }

  public List copyLinkedExperimenterGroupList()
  {
    return new ArrayList<>(experimenterGroupLinks);
  }

  public ExperimenterGroup getLinkedExperimenterGroup(int index)
  {
    return experimenterGroupLinks.get(index);
  }

  public ExperimenterGroup setLinkedExperimenterGroup(int index, ExperimenterGroup o)
  {
    return experimenterGroupLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkExperimenterGroup(ExperimenterGroup o)
  {
    return experimenterGroupLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkExperimenterGroup(ExperimenterGroup o)
  {
    return experimenterGroupLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedDatasetList()
  {
    return datasetLinks.size();
  }

  public List copyLinkedDatasetList()
  {
    return new ArrayList<>(datasetLinks);
  }

  public Dataset getLinkedDataset(int index)
  {
    return datasetLinks.get(index);
  }

  public Dataset setLinkedDataset(int index, Dataset o)
  {
    return datasetLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkDataset(Dataset o)
  {
    return datasetLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkDataset(Dataset o)
  {
    return datasetLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedExperimenterList()
  {
    return experimenterLinks.size();
  }

  public List copyLinkedExperimenterList()
  {
    return new ArrayList<>(experimenterLinks);
  }

  public Experimenter getLinkedExperimenter(int index)
  {
    return experimenterLinks.get(index);
  }

  public Experimenter setLinkedExperimenter(int index, Experimenter o)
  {
    return experimenterLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkExperimenter(Experimenter o)
  {
    return experimenterLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkExperimenter(Experimenter o)
  {
    return experimenterLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedFolderList()
  {
    return folderLinks.size();
  }

  public List copyLinkedFolderList()
  {
    return new ArrayList<>(folderLinks);
  }

  public Folder getLinkedFolder(int index)
  {
    return folderLinks.get(index);
  }

  public Folder setLinkedFolder(int index, Folder o)
  {
    return folderLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkFolder(Folder o)
  {
    return folderLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkFolder(Folder o)
  {
    return folderLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedObjectiveList()
  {
    return objectiveLinks.size();
  }

  public List copyLinkedObjectiveList()
  {
    return new ArrayList<>(objectiveLinks);
  }

  public Objective getLinkedObjective(int index)
  {
    return objectiveLinks.get(index);
  }

  public Objective setLinkedObjective(int index, Objective o)
  {
    return objectiveLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkObjective(Objective o)
  {
    return objectiveLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkObjective(Objective o)
  {
    return objectiveLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedDetectorList()
  {
    return detectorLinks.size();
  }

  public List copyLinkedDetectorList()
  {
    return new ArrayList<>(detectorLinks);
  }

  public Detector getLinkedDetector(int index)
  {
    return detectorLinks.get(index);
  }

  public Detector setLinkedDetector(int index, Detector o)
  {
    return detectorLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkDetector(Detector o)
  {
    return detectorLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkDetector(Detector o)
  {
    return detectorLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedFilterList()
  {
    return filterLinks.size();
  }

  public List copyLinkedFilterList()
  {
    return new ArrayList<>(filterLinks);
  }

  public Filter getLinkedFilter(int index)
  {
    return filterLinks.get(index);
  }

  public Filter setLinkedFilter(int index, Filter o)
  {
    return filterLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkFilter(Filter o)
  {
    return filterLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkFilter(Filter o)
  {
    return filterLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedDichroicList()
  {
    return dichroicLinks.size();
  }

  public List copyLinkedDichroicList()
  {
    return new ArrayList<>(dichroicLinks);
  }

  public Dichroic getLinkedDichroic(int index)
  {
    return dichroicLinks.get(index);
  }

  public Dichroic setLinkedDichroic(int index, Dichroic o)
  {
    return dichroicLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkDichroic(Dichroic o)
  {
    return dichroicLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkDichroic(Dichroic o)
  {
    return dichroicLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedLightPathList()
  {
    return lightPathLinks.size();
  }

  public List copyLinkedLightPathList()
  {
    return new ArrayList<>(lightPathLinks);
  }

  public LightPath getLinkedLightPath(int index)
  {
    return lightPathLinks.get(index);
  }

  public LightPath setLinkedLightPath(int index, LightPath o)
  {
    return lightPathLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkLightPath(LightPath o)
  {
    return lightPathLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkLightPath(LightPath o)
  {
    return lightPathLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedROIList()
  {
    return roiLinks.size();
  }

  public List copyLinkedROIList()
  {
    return new ArrayList<>(roiLinks);
  }

  public ROI getLinkedROI(int index)
  {
    return roiLinks.get(index);
  }

  public ROI setLinkedROI(int index, ROI o)
  {
    return roiLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkROI(ROI o)
  {
    return roiLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkROI(ROI o)
  {
    return roiLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedShapeList()
  {
    return shapeLinks.size();
  }

  public List copyLinkedShapeList()
  {
    return new ArrayList<>(shapeLinks);
  }

  public Shape getLinkedShape(int index)
  {
    return shapeLinks.get(index);
  }

  public Shape setLinkedShape(int index, Shape o)
  {
    return shapeLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkShape(Shape o)
  {
    return shapeLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkShape(Shape o)
  {
    return shapeLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedPlateList()
  {
    return plateLinks.size();
  }

  public List copyLinkedPlateList()
  {
    return new ArrayList<>(plateLinks);
  }

  public Plate getLinkedPlate(int index)
  {
    return plateLinks.get(index);
  }

  public Plate setLinkedPlate(int index, Plate o)
  {
    return plateLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkPlate(Plate o)
  {
    return plateLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkPlate(Plate o)
  {
    return plateLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedReagentList()
  {
    return reagentLinks.size();
  }

  public List copyLinkedReagentList()
  {
    return new ArrayList<>(reagentLinks);
  }

  public Reagent getLinkedReagent(int index)
  {
    return reagentLinks.get(index);
  }

  public Reagent setLinkedReagent(int index, Reagent o)
  {
    return reagentLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkReagent(Reagent o)
  {
    return reagentLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkReagent(Reagent o)
  {
    return reagentLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedScreenList()
  {
    return screenLinks.size();
  }

  public List copyLinkedScreenList()
  {
    return new ArrayList<>(screenLinks);
  }

  public Screen getLinkedScreen(int index)
  {
    return screenLinks.get(index);
  }

  public Screen setLinkedScreen(int index, Screen o)
  {
    return screenLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkScreen(Screen o)
  {
    return screenLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkScreen(Screen o)
  {
    return screenLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedPlateAcquisitionList()
  {
    return plateAcquisitionLinks.size();
  }

  public List copyLinkedPlateAcquisitionList()
  {
    return new ArrayList<>(plateAcquisitionLinks);
  }

  public PlateAcquisition getLinkedPlateAcquisition(int index)
  {
    return plateAcquisitionLinks.get(index);
  }

  public PlateAcquisition setLinkedPlateAcquisition(int index, PlateAcquisition o)
  {
    return plateAcquisitionLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkPlateAcquisition(PlateAcquisition o)
  {
    return plateAcquisitionLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkPlateAcquisition(PlateAcquisition o)
  {
    return plateAcquisitionLinks.remove(o);
  }

  // Reference which occurs more than once
  public int sizeOfLinkedWellList()
  {
    return wellLinks.size();
  }

  public List copyLinkedWellList()
  {
    return new ArrayList<>(wellLinks);
  }

  public Well getLinkedWell(int index)
  {
    return wellLinks.get(index);
  }

  public Well setLinkedWell(int index, Well o)
  {
    return wellLinks.set(index, o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean linkWell(Well o)
  {
    return wellLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkWell(Well o)
  {
    return wellLinks.remove(o);
  }

  public Element asXMLElement(Document document)
  {
    return asXMLElement(document, null);
  }

  public Element asXMLElement(Document document, Element Annotation_element)
  {
    // Creating XML block for Annotation
    if (Annotation_element == null)
    {
      Annotation_element =
        document.createElementNS(NAMESPACE, "Annotation");
    }

    // Ensure any base annotations add their Elements first
    super.asXMLElement(document, Annotation_element);

    if (id != null)
    {
      // Attribute property ID
      Annotation_element.setAttribute("ID", id);
    }
    if (namespace != null)
    {
      // Attribute property Namespace
      Annotation_element.setAttribute("Namespace", namespace);
    }
    if (annotator != null)
    {
      // Attribute property Annotator
      Annotation_element.setAttribute("Annotator", annotator);
    }
    if (description != null)
    {
    // Element property Description which is not complex (has no
    // sub-elements)
    Element description_element =
      document.createElementNS(NAMESPACE, "Description");
      description_element.setTextContent(description);
      Annotation_element.appendChild(description_element);
    }
    if (annotationLinks != null)
    {
      // Reference property AnnotationRef which occurs more than once
      for (Annotation annotationLinks_value : annotationLinks)
      {
        AnnotationRef o = new AnnotationRef();
        o.setID(annotationLinks_value.getID());
        Element child =
          document.createElementNS(NAMESPACE, "AnnotationRef");
        o.asXMLElement(document, child);
        Annotation_element.appendChild(child);
      }
    }
    // *** IGNORING *** Skipped back reference Image_BackReference
    // *** IGNORING *** Skipped back reference Plane_BackReference
    // *** IGNORING *** Skipped back reference Channel_BackReference
    // *** IGNORING *** Skipped back reference Instrument_BackReference
    // *** IGNORING *** Skipped back reference LightSource_BackReference
    // *** IGNORING *** Skipped back reference Project_BackReference
    // *** IGNORING *** Skipped back reference ExperimenterGroup_BackReference
    // *** IGNORING *** Skipped back reference Dataset_BackReference
    // *** IGNORING *** Skipped back reference Experimenter_BackReference
    // *** IGNORING *** Skipped back reference Folder_BackReference
    // *** IGNORING *** Skipped back reference Objective_BackReference
    // *** IGNORING *** Skipped back reference Detector_BackReference
    // *** IGNORING *** Skipped back reference Filter_BackReference
    // *** IGNORING *** Skipped back reference Dichroic_BackReference
    // *** IGNORING *** Skipped back reference LightPath_BackReference
    // *** IGNORING *** Skipped back reference ROI_BackReference
    // *** IGNORING *** Skipped back reference Shape_BackReference
    // *** IGNORING *** Skipped back reference Plate_BackReference
    // *** IGNORING *** Skipped back reference Reagent_BackReference
    // *** IGNORING *** Skipped back reference Screen_BackReference
    // *** IGNORING *** Skipped back reference PlateAcquisition_BackReference
    // *** IGNORING *** Skipped back reference Well_BackReference

    return Annotation_element;
  }
}