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OME XML model and metadata classes
/*
* #%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.units.quantity.Angle;
import ome.units.quantity.ElectricPotential;
import ome.units.quantity.Frequency;
import ome.units.quantity.Length;
import ome.units.quantity.Power;
import ome.units.quantity.Pressure;
import ome.units.quantity.Temperature;
import ome.units.quantity.Time;
import ome.units.unit.Unit;
import ome.xml.model.enums.*;
import ome.xml.model.enums.handlers.*;
import ome.xml.model.primitives.*;
public class StructuredAnnotations extends AbstractOMEModelObject
{
// Base: -- Name: StructuredAnnotations -- Type: StructuredAnnotations -- 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(StructuredAnnotations.class);
// -- Instance variables --
// XMLAnnotation property (occurs more than once)
private List xmlAnnotations = new ArrayList();
// FileAnnotation property (occurs more than once)
private List fileAnnotations = new ArrayList();
// ListAnnotation property (occurs more than once)
private List listAnnotations = new ArrayList();
// LongAnnotation property (occurs more than once)
private List longAnnotations = new ArrayList();
// DoubleAnnotation property (occurs more than once)
private List doubleAnnotations = new ArrayList();
// CommentAnnotation property (occurs more than once)
private List commentAnnotations = new ArrayList();
// BooleanAnnotation property (occurs more than once)
private List booleanAnnotations = new ArrayList();
// TimestampAnnotation property (occurs more than once)
private List timestampAnnotations = new ArrayList();
// TagAnnotation property (occurs more than once)
private List tagAnnotations = new ArrayList();
// TermAnnotation property (occurs more than once)
private List termAnnotations = new ArrayList();
// MapAnnotation property (occurs more than once)
private List mapAnnotations = new ArrayList();
// -- Constructors --
/** Default constructor. */
public StructuredAnnotations()
{
}
/**
* Constructs StructuredAnnotations 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 StructuredAnnotations(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
/** Copy constructor. */
public StructuredAnnotations(StructuredAnnotations orig)
{
xmlAnnotations = orig.xmlAnnotations;
fileAnnotations = orig.fileAnnotations;
listAnnotations = orig.listAnnotations;
longAnnotations = orig.longAnnotations;
doubleAnnotations = orig.doubleAnnotations;
commentAnnotations = orig.commentAnnotations;
booleanAnnotations = orig.booleanAnnotations;
timestampAnnotations = orig.timestampAnnotations;
tagAnnotations = orig.tagAnnotations;
termAnnotations = orig.termAnnotations;
mapAnnotations = orig.mapAnnotations;
}
// -- Custom content from StructuredAnnotations specific template --
// -- OMEModelObject API methods --
/**
* Updates StructuredAnnotations 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);
String tagName = element.getTagName();
// Element property XMLAnnotation which is complex (has
// sub-elements) and occurs more than once
List XMLAnnotation_nodeList =
getChildrenByTagName(element, "XMLAnnotation");
for (Element XMLAnnotation_element : XMLAnnotation_nodeList)
{
addXMLAnnotation(
new XMLAnnotation(XMLAnnotation_element, model));
}
// Element property FileAnnotation which is complex (has
// sub-elements) and occurs more than once
List FileAnnotation_nodeList =
getChildrenByTagName(element, "FileAnnotation");
for (Element FileAnnotation_element : FileAnnotation_nodeList)
{
addFileAnnotation(
new FileAnnotation(FileAnnotation_element, model));
}
// Element property ListAnnotation which is complex (has
// sub-elements) and occurs more than once
List ListAnnotation_nodeList =
getChildrenByTagName(element, "ListAnnotation");
for (Element ListAnnotation_element : ListAnnotation_nodeList)
{
addListAnnotation(
new ListAnnotation(ListAnnotation_element, model));
}
// Element property LongAnnotation which is complex (has
// sub-elements) and occurs more than once
List LongAnnotation_nodeList =
getChildrenByTagName(element, "LongAnnotation");
for (Element LongAnnotation_element : LongAnnotation_nodeList)
{
addLongAnnotation(
new LongAnnotation(LongAnnotation_element, model));
}
// Element property DoubleAnnotation which is complex (has
// sub-elements) and occurs more than once
List DoubleAnnotation_nodeList =
getChildrenByTagName(element, "DoubleAnnotation");
for (Element DoubleAnnotation_element : DoubleAnnotation_nodeList)
{
addDoubleAnnotation(
new DoubleAnnotation(DoubleAnnotation_element, model));
}
// Element property CommentAnnotation which is complex (has
// sub-elements) and occurs more than once
List CommentAnnotation_nodeList =
getChildrenByTagName(element, "CommentAnnotation");
for (Element CommentAnnotation_element : CommentAnnotation_nodeList)
{
addCommentAnnotation(
new CommentAnnotation(CommentAnnotation_element, model));
}
// Element property BooleanAnnotation which is complex (has
// sub-elements) and occurs more than once
List BooleanAnnotation_nodeList =
getChildrenByTagName(element, "BooleanAnnotation");
for (Element BooleanAnnotation_element : BooleanAnnotation_nodeList)
{
addBooleanAnnotation(
new BooleanAnnotation(BooleanAnnotation_element, model));
}
// Element property TimestampAnnotation which is complex (has
// sub-elements) and occurs more than once
List TimestampAnnotation_nodeList =
getChildrenByTagName(element, "TimestampAnnotation");
for (Element TimestampAnnotation_element : TimestampAnnotation_nodeList)
{
addTimestampAnnotation(
new TimestampAnnotation(TimestampAnnotation_element, model));
}
// Element property TagAnnotation which is complex (has
// sub-elements) and occurs more than once
List TagAnnotation_nodeList =
getChildrenByTagName(element, "TagAnnotation");
for (Element TagAnnotation_element : TagAnnotation_nodeList)
{
addTagAnnotation(
new TagAnnotation(TagAnnotation_element, model));
}
// Element property TermAnnotation which is complex (has
// sub-elements) and occurs more than once
List TermAnnotation_nodeList =
getChildrenByTagName(element, "TermAnnotation");
for (Element TermAnnotation_element : TermAnnotation_nodeList)
{
addTermAnnotation(
new TermAnnotation(TermAnnotation_element, model));
}
// Element property MapAnnotation which is complex (has
// sub-elements) and occurs more than once
List MapAnnotation_nodeList =
getChildrenByTagName(element, "MapAnnotation");
for (Element MapAnnotation_element : MapAnnotation_nodeList)
{
addMapAnnotation(
new MapAnnotation(MapAnnotation_element, model));
}
}
// -- StructuredAnnotations API methods --
public boolean link(Reference reference, OMEModelObject o)
{
return super.link(reference, o);
}
// Property which occurs more than once
public int sizeOfXMLAnnotationList()
{
return xmlAnnotations.size();
}
public List copyXMLAnnotationList()
{
return new ArrayList(xmlAnnotations);
}
public XMLAnnotation getXMLAnnotation(int index)
{
return xmlAnnotations.get(index);
}
public XMLAnnotation setXMLAnnotation(int index, XMLAnnotation xmlAnnotation)
{
xmlAnnotation.setStructuredAnnotations(this);
return xmlAnnotations.set(index, xmlAnnotation);
}
public void addXMLAnnotation(XMLAnnotation xmlAnnotation)
{
xmlAnnotation.setStructuredAnnotations(this);
xmlAnnotations.add(xmlAnnotation);
}
public void removeXMLAnnotation(XMLAnnotation xmlAnnotation)
{
xmlAnnotations.remove(xmlAnnotation);
}
// Property which occurs more than once
public int sizeOfFileAnnotationList()
{
return fileAnnotations.size();
}
public List copyFileAnnotationList()
{
return new ArrayList(fileAnnotations);
}
public FileAnnotation getFileAnnotation(int index)
{
return fileAnnotations.get(index);
}
public FileAnnotation setFileAnnotation(int index, FileAnnotation fileAnnotation)
{
fileAnnotation.setStructuredAnnotations(this);
return fileAnnotations.set(index, fileAnnotation);
}
public void addFileAnnotation(FileAnnotation fileAnnotation)
{
fileAnnotation.setStructuredAnnotations(this);
fileAnnotations.add(fileAnnotation);
}
public void removeFileAnnotation(FileAnnotation fileAnnotation)
{
fileAnnotations.remove(fileAnnotation);
}
// Property which occurs more than once
public int sizeOfListAnnotationList()
{
return listAnnotations.size();
}
public List copyListAnnotationList()
{
return new ArrayList(listAnnotations);
}
public ListAnnotation getListAnnotation(int index)
{
return listAnnotations.get(index);
}
public ListAnnotation setListAnnotation(int index, ListAnnotation listAnnotation)
{
listAnnotation.setStructuredAnnotations(this);
return listAnnotations.set(index, listAnnotation);
}
public void addListAnnotation(ListAnnotation listAnnotation)
{
listAnnotation.setStructuredAnnotations(this);
listAnnotations.add(listAnnotation);
}
public void removeListAnnotation(ListAnnotation listAnnotation)
{
listAnnotations.remove(listAnnotation);
}
// Property which occurs more than once
public int sizeOfLongAnnotationList()
{
return longAnnotations.size();
}
public List copyLongAnnotationList()
{
return new ArrayList(longAnnotations);
}
public LongAnnotation getLongAnnotation(int index)
{
return longAnnotations.get(index);
}
public LongAnnotation setLongAnnotation(int index, LongAnnotation longAnnotation)
{
longAnnotation.setStructuredAnnotations(this);
return longAnnotations.set(index, longAnnotation);
}
public void addLongAnnotation(LongAnnotation longAnnotation)
{
longAnnotation.setStructuredAnnotations(this);
longAnnotations.add(longAnnotation);
}
public void removeLongAnnotation(LongAnnotation longAnnotation)
{
longAnnotations.remove(longAnnotation);
}
// Property which occurs more than once
public int sizeOfDoubleAnnotationList()
{
return doubleAnnotations.size();
}
public List copyDoubleAnnotationList()
{
return new ArrayList(doubleAnnotations);
}
public DoubleAnnotation getDoubleAnnotation(int index)
{
return doubleAnnotations.get(index);
}
public DoubleAnnotation setDoubleAnnotation(int index, DoubleAnnotation doubleAnnotation)
{
doubleAnnotation.setStructuredAnnotations(this);
return doubleAnnotations.set(index, doubleAnnotation);
}
public void addDoubleAnnotation(DoubleAnnotation doubleAnnotation)
{
doubleAnnotation.setStructuredAnnotations(this);
doubleAnnotations.add(doubleAnnotation);
}
public void removeDoubleAnnotation(DoubleAnnotation doubleAnnotation)
{
doubleAnnotations.remove(doubleAnnotation);
}
// Property which occurs more than once
public int sizeOfCommentAnnotationList()
{
return commentAnnotations.size();
}
public List copyCommentAnnotationList()
{
return new ArrayList(commentAnnotations);
}
public CommentAnnotation getCommentAnnotation(int index)
{
return commentAnnotations.get(index);
}
public CommentAnnotation setCommentAnnotation(int index, CommentAnnotation commentAnnotation)
{
commentAnnotation.setStructuredAnnotations(this);
return commentAnnotations.set(index, commentAnnotation);
}
public void addCommentAnnotation(CommentAnnotation commentAnnotation)
{
commentAnnotation.setStructuredAnnotations(this);
commentAnnotations.add(commentAnnotation);
}
public void removeCommentAnnotation(CommentAnnotation commentAnnotation)
{
commentAnnotations.remove(commentAnnotation);
}
// Property which occurs more than once
public int sizeOfBooleanAnnotationList()
{
return booleanAnnotations.size();
}
public List copyBooleanAnnotationList()
{
return new ArrayList(booleanAnnotations);
}
public BooleanAnnotation getBooleanAnnotation(int index)
{
return booleanAnnotations.get(index);
}
public BooleanAnnotation setBooleanAnnotation(int index, BooleanAnnotation booleanAnnotation)
{
booleanAnnotation.setStructuredAnnotations(this);
return booleanAnnotations.set(index, booleanAnnotation);
}
public void addBooleanAnnotation(BooleanAnnotation booleanAnnotation)
{
booleanAnnotation.setStructuredAnnotations(this);
booleanAnnotations.add(booleanAnnotation);
}
public void removeBooleanAnnotation(BooleanAnnotation booleanAnnotation)
{
booleanAnnotations.remove(booleanAnnotation);
}
// Property which occurs more than once
public int sizeOfTimestampAnnotationList()
{
return timestampAnnotations.size();
}
public List copyTimestampAnnotationList()
{
return new ArrayList(timestampAnnotations);
}
public TimestampAnnotation getTimestampAnnotation(int index)
{
return timestampAnnotations.get(index);
}
public TimestampAnnotation setTimestampAnnotation(int index, TimestampAnnotation timestampAnnotation)
{
timestampAnnotation.setStructuredAnnotations(this);
return timestampAnnotations.set(index, timestampAnnotation);
}
public void addTimestampAnnotation(TimestampAnnotation timestampAnnotation)
{
timestampAnnotation.setStructuredAnnotations(this);
timestampAnnotations.add(timestampAnnotation);
}
public void removeTimestampAnnotation(TimestampAnnotation timestampAnnotation)
{
timestampAnnotations.remove(timestampAnnotation);
}
// Property which occurs more than once
public int sizeOfTagAnnotationList()
{
return tagAnnotations.size();
}
public List copyTagAnnotationList()
{
return new ArrayList(tagAnnotations);
}
public TagAnnotation getTagAnnotation(int index)
{
return tagAnnotations.get(index);
}
public TagAnnotation setTagAnnotation(int index, TagAnnotation tagAnnotation)
{
tagAnnotation.setStructuredAnnotations(this);
return tagAnnotations.set(index, tagAnnotation);
}
public void addTagAnnotation(TagAnnotation tagAnnotation)
{
tagAnnotation.setStructuredAnnotations(this);
tagAnnotations.add(tagAnnotation);
}
public void removeTagAnnotation(TagAnnotation tagAnnotation)
{
tagAnnotations.remove(tagAnnotation);
}
// Property which occurs more than once
public int sizeOfTermAnnotationList()
{
return termAnnotations.size();
}
public List copyTermAnnotationList()
{
return new ArrayList(termAnnotations);
}
public TermAnnotation getTermAnnotation(int index)
{
return termAnnotations.get(index);
}
public TermAnnotation setTermAnnotation(int index, TermAnnotation termAnnotation)
{
termAnnotation.setStructuredAnnotations(this);
return termAnnotations.set(index, termAnnotation);
}
public void addTermAnnotation(TermAnnotation termAnnotation)
{
termAnnotation.setStructuredAnnotations(this);
termAnnotations.add(termAnnotation);
}
public void removeTermAnnotation(TermAnnotation termAnnotation)
{
termAnnotations.remove(termAnnotation);
}
// Property which occurs more than once
public int sizeOfMapAnnotationList()
{
return mapAnnotations.size();
}
public List copyMapAnnotationList()
{
return new ArrayList(mapAnnotations);
}
public MapAnnotation getMapAnnotation(int index)
{
return mapAnnotations.get(index);
}
public MapAnnotation setMapAnnotation(int index, MapAnnotation mapAnnotation)
{
mapAnnotation.setStructuredAnnotations(this);
return mapAnnotations.set(index, mapAnnotation);
}
public void addMapAnnotation(MapAnnotation mapAnnotation)
{
mapAnnotation.setStructuredAnnotations(this);
mapAnnotations.add(mapAnnotation);
}
public void removeMapAnnotation(MapAnnotation mapAnnotation)
{
mapAnnotations.remove(mapAnnotation);
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
public Element asXMLElement(Document document, Element StructuredAnnotations_element)
{
// Creating XML block for StructuredAnnotations
if (StructuredAnnotations_element == null)
{
StructuredAnnotations_element =
document.createElementNS(NAMESPACE, "StructuredAnnotations");
}
// Ensure any base annotations add their Elements first
super.asXMLElement(document, StructuredAnnotations_element);
if (xmlAnnotations != null)
{
// Element property XMLAnnotation which is complex (has
// sub-elements) and occurs more than once
for (XMLAnnotation xmlAnnotations_value : xmlAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "XMLAnnotation");
xmlAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (fileAnnotations != null)
{
// Element property FileAnnotation which is complex (has
// sub-elements) and occurs more than once
for (FileAnnotation fileAnnotations_value : fileAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "FileAnnotation");
fileAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (listAnnotations != null)
{
// Element property ListAnnotation which is complex (has
// sub-elements) and occurs more than once
for (ListAnnotation listAnnotations_value : listAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "ListAnnotation");
listAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (longAnnotations != null)
{
// Element property LongAnnotation which is complex (has
// sub-elements) and occurs more than once
for (LongAnnotation longAnnotations_value : longAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "LongAnnotation");
longAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (doubleAnnotations != null)
{
// Element property DoubleAnnotation which is complex (has
// sub-elements) and occurs more than once
for (DoubleAnnotation doubleAnnotations_value : doubleAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "DoubleAnnotation");
doubleAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (commentAnnotations != null)
{
// Element property CommentAnnotation which is complex (has
// sub-elements) and occurs more than once
for (CommentAnnotation commentAnnotations_value : commentAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "CommentAnnotation");
commentAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (booleanAnnotations != null)
{
// Element property BooleanAnnotation which is complex (has
// sub-elements) and occurs more than once
for (BooleanAnnotation booleanAnnotations_value : booleanAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "BooleanAnnotation");
booleanAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (timestampAnnotations != null)
{
// Element property TimestampAnnotation which is complex (has
// sub-elements) and occurs more than once
for (TimestampAnnotation timestampAnnotations_value : timestampAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "TimestampAnnotation");
timestampAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (tagAnnotations != null)
{
// Element property TagAnnotation which is complex (has
// sub-elements) and occurs more than once
for (TagAnnotation tagAnnotations_value : tagAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "TagAnnotation");
tagAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (termAnnotations != null)
{
// Element property TermAnnotation which is complex (has
// sub-elements) and occurs more than once
for (TermAnnotation termAnnotations_value : termAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "TermAnnotation");
termAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
if (mapAnnotations != null)
{
// Element property MapAnnotation which is complex (has
// sub-elements) and occurs more than once
for (MapAnnotation mapAnnotations_value : mapAnnotations)
{
Element child =
document.createElementNS(NAMESPACE, "MapAnnotation");
mapAnnotations_value.asXMLElement(document, child);
StructuredAnnotations_element.appendChild(child);
}
}
return StructuredAnnotations_element;
}
}
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