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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 class Well extends AbstractOMEModelObject
{
  // Base:  -- Name: Well -- Type: Well -- 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(Well.class);

  // -- Instance variables --

  // ID property
  private String id;

  // Column property
  private NonNegativeInteger column;

  // Row property
  private NonNegativeInteger row;

  // ExternalDescription property
  private String externalDescription;

  // ExternalIdentifier property
  private String externalIdentifier;

  // Type property
  private String type;

  // Color property
  private Color color;

  // WellSample property (occurs more than once)
  private List wellSamples = new ArrayList<>();

  // ReagentRef reference
  private Reagent reagent;

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

  // Plate_BackReference back reference
  private Plate plate;

  // -- Constructors --

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



  /**
   * Constructs Well 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 Well(Element element, OMEModel model)
    throws EnumerationException
  {
    update(element, model);
  }

  /** Copy constructor. */
  public Well(Well orig)
  {
    id = orig.id;
    column = orig.column;
    row = orig.row;
    externalDescription = orig.externalDescription;
    externalIdentifier = orig.externalIdentifier;
    type = orig.type;
    color = orig.color;
    wellSamples = orig.wellSamples;
    reagent = orig.reagent;
    annotationLinks = orig.annotationLinks;
    plate = orig.plate;
  }

  // -- Custom content from Well specific template --


  // -- OMEModelObject API methods --

  /**
   * Updates Well 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(
        "Well 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("Column"))
    {
      // Attribute property Column
      setColumn(NonNegativeInteger.valueOf(
        element.getAttribute("Column")));
    }
    if (element.hasAttribute("Row"))
    {
      // Attribute property Row
      setRow(NonNegativeInteger.valueOf(
        element.getAttribute("Row")));
    }
    if (element.hasAttribute("ExternalDescription"))
    {
      // Attribute property ExternalDescription
      setExternalDescription(String.valueOf(
        element.getAttribute("ExternalDescription")));
    }
    if (element.hasAttribute("ExternalIdentifier"))
    {
      // Attribute property ExternalIdentifier
      setExternalIdentifier(String.valueOf(
        element.getAttribute("ExternalIdentifier")));
    }
    if (element.hasAttribute("Type"))
    {
      // Attribute property Type
      setType(String.valueOf(
        element.getAttribute("Type")));
    }
    if (element.hasAttribute("Color"))
    {
      // Attribute property Color
      setColor(Color.valueOf(
        element.getAttribute("Color")));
    }
    // Element property WellSample which is complex (has
    // sub-elements) and occurs more than once
    List WellSample_nodeList =
      getChildrenByTagName(element, "WellSample");
    for (Element WellSample_element : WellSample_nodeList)
    {
      addWellSample(
        new WellSample(WellSample_element, model));
    }
    // Element reference ReagentRef
    List ReagentRef_nodeList =
      getChildrenByTagName(element, "ReagentRef");
    for (Element ReagentRef_element : ReagentRef_nodeList)
    {
      ReagentRef reagent_reference = new ReagentRef();
      reagent_reference.setID(ReagentRef_element.getAttribute("ID"));
      model.addReference(this, reagent_reference);
    }
    // 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);
    }
  }

  // -- Well API methods --

  public boolean link(Reference reference, OMEModelObject o)
  {
    if (reference instanceof ReagentRef)
    {
      Reagent o_casted = (Reagent) o;
      o_casted.linkWell(this);
      reagent = o_casted;
      return true;
    }
    if (reference instanceof AnnotationRef)
    {
      Annotation o_casted = (Annotation) o;
      o_casted.linkWell(this);
      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 Column
  public NonNegativeInteger getColumn()
  {
    return column;
  }

  public void setColumn(NonNegativeInteger column)
  {
    this.column = column;
  }

  // Property Row
  public NonNegativeInteger getRow()
  {
    return row;
  }

  public void setRow(NonNegativeInteger row)
  {
    this.row = row;
  }

  // Property ExternalDescription
  public String getExternalDescription()
  {
    return externalDescription;
  }

  public void setExternalDescription(String externalDescription)
  {
    this.externalDescription = externalDescription;
  }

  // Property ExternalIdentifier
  public String getExternalIdentifier()
  {
    return externalIdentifier;
  }

  public void setExternalIdentifier(String externalIdentifier)
  {
    this.externalIdentifier = externalIdentifier;
  }

  // Property Type
  public String getType()
  {
    return type;
  }

  public void setType(String type)
  {
    this.type = type;
  }

  // Property Color
  public Color getColor()
  {
    return color;
  }

  public void setColor(Color color)
  {
    this.color = color;
  }

  // Property which occurs more than once
  public int sizeOfWellSampleList()
  {
    return wellSamples.size();
  }

  public List copyWellSampleList()
  {
    return new ArrayList<>(wellSamples);
  }

  public void clearWellSampleList()
  {
    wellSamples.clear();
  }

  public WellSample getWellSample(int index)
  {
    return wellSamples.get(index);
  }

  public WellSample setWellSample(int index, WellSample wellSample)
  {
    wellSample.setWell(this);
    return wellSamples.set(index, wellSample);
  }

  public void addWellSample(WellSample wellSample)
  {
    wellSample.setWell(this);
    wellSamples.add(wellSample);
  }

  public void removeWellSample(WellSample wellSample)
  {
    wellSamples.remove(wellSample);
  }

  // Reference
  public Reagent getLinkedReagent()
  {
    return reagent;
  }

  public void linkReagent(Reagent o)
  {
    reagent = o;
  }

  public void unlinkReagent(Reagent o)
  {
    if (reagent == o)
    {
      reagent = null;
    }
  }

  // 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)
  {

    o.linkWell(this);
    return annotationLinks.add(o);
  }

  @SuppressWarnings("UnusedReturnValue")
  public boolean unlinkAnnotation(Annotation o)
  {

    o.unlinkWell(this);
    return annotationLinks.remove(o);
  }

  // Property Plate_BackReference
  public Plate getPlate()
  {
    return plate;
  }

  public void setPlate(Plate plate_BackReference)
  {
    this.plate = plate_BackReference;
  }

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

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

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

    if (id != null)
    {
      // Attribute property ID
      Well_element.setAttribute("ID", id);
    }
    if (column != null)
    {
      // Attribute property Column
      Well_element.setAttribute("Column", column.toString());
    }
    if (row != null)
    {
      // Attribute property Row
      Well_element.setAttribute("Row", row.toString());
    }
    if (externalDescription != null)
    {
      // Attribute property ExternalDescription
      Well_element.setAttribute("ExternalDescription", externalDescription);
    }
    if (externalIdentifier != null)
    {
      // Attribute property ExternalIdentifier
      Well_element.setAttribute("ExternalIdentifier", externalIdentifier);
    }
    if (type != null)
    {
      // Attribute property Type
      Well_element.setAttribute("Type", type);
    }
    if (color != null)
    {
      // Attribute property Color
      Well_element.setAttribute("Color", color.toString());
    }
    if (wellSamples != null)
    {
      // Element property WellSample which is complex (has
      // sub-elements) and occurs more than once
      for (WellSample wellSamples_value : wellSamples)
      {
        Element child =
          document.createElementNS(NAMESPACE, "WellSample");
        wellSamples_value.asXMLElement(document, child);
        Well_element.appendChild(child);
      }
    }
    if (reagent != null)
    {
      // Reference property ReagentRef
      ReagentRef o = new ReagentRef();
      o.setID(reagent.getID());
      Element child =
        document.createElementNS(NAMESPACE, "ReagentRef");
      o.asXMLElement(document, child);
      Well_element.appendChild(child);
    }
    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);
        Well_element.appendChild(child);
      }
    }
    // *** IGNORING *** Skipped back reference Plate_BackReference

    return Well_element;
  }
}