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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 WellSample extends AbstractOMEModelObject
{
// Base: -- Name: WellSample -- Type: WellSample -- 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(WellSample.class);
// -- Instance variables --
// ID property
private String id;
// PositionX property
private Length positionX;
// PositionY property
private Length positionY;
// Timepoint property
private Timestamp timepoint;
// Index property
private NonNegativeInteger index;
// ImageRef reference
private Image image;
// PlateAcquisition_BackReference back reference (occurs more than once)
private List plateAcquisitions = new ReferenceList();
// Well_BackReference back reference
private Well well;
// -- Constructors --
/** Default constructor. */
public WellSample()
{
}
/**
* Constructs WellSample 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 WellSample(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
/** Copy constructor. */
public WellSample(WellSample orig)
{
id = orig.id;
positionX = orig.positionX;
positionY = orig.positionY;
timepoint = orig.timepoint;
index = orig.index;
image = orig.image;
plateAcquisitions = orig.plateAcquisitions;
well = orig.well;
}
// -- Custom content from WellSample specific template --
// -- OMEModelObject API methods --
/**
* Updates WellSample 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();
if (!element.hasAttribute("ID") && getID() == null)
{
// TODO: Should be its own exception
throw new RuntimeException(String.format(
"WellSample 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("PositionX"))
{
// Attribute property PositionX with unit companion PositionXUnit
String unitSymbol = element.getAttribute("PositionXUnit");
if ((unitSymbol == null) || (unitSymbol.isEmpty()))
{
// Use default value specified in the xsd model
unitSymbol = getPositionXUnitXsdDefault();
}
UnitsLength modelUnit =
UnitsLength.fromString(unitSymbol);
Double baseValue = Double.valueOf(
element.getAttribute("PositionX"));
if (baseValue != null)
{
setPositionX(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit));
}
}
if (element.hasAttribute("PositionY"))
{
// Attribute property PositionY with unit companion PositionYUnit
String unitSymbol = element.getAttribute("PositionYUnit");
if ((unitSymbol == null) || (unitSymbol.isEmpty()))
{
// Use default value specified in the xsd model
unitSymbol = getPositionYUnitXsdDefault();
}
UnitsLength modelUnit =
UnitsLength.fromString(unitSymbol);
Double baseValue = Double.valueOf(
element.getAttribute("PositionY"));
if (baseValue != null)
{
setPositionY(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit));
}
}
if (element.hasAttribute("Timepoint"))
{
// Attribute property Timepoint
setTimepoint(Timestamp.valueOf(
element.getAttribute("Timepoint")));
}
if (element.hasAttribute("Index"))
{
// Attribute property Index
setIndex(NonNegativeInteger.valueOf(
element.getAttribute("Index")));
}
// Element reference ImageRef
List ImageRef_nodeList =
getChildrenByTagName(element, "ImageRef");
for (Element ImageRef_element : ImageRef_nodeList)
{
ImageRef image_reference = new ImageRef();
image_reference.setID(ImageRef_element.getAttribute("ID"));
model.addReference(this, image_reference);
}
}
// -- WellSample API methods --
public boolean link(Reference reference, OMEModelObject o)
{
if (reference instanceof ImageRef)
{
Image o_casted = (Image) o;
o_casted.linkWellSample(this);
image = 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 PositionX with unit companion PositionXUnit
public Length getPositionX()
{
return positionX;
}
public void setPositionX(Length positionX)
{
this.positionX = positionX;
}
// Property PositionXUnit is a unit companion
public static String getPositionXUnitXsdDefault()
{
return "reference frame";
}
// Property PositionY with unit companion PositionYUnit
public Length getPositionY()
{
return positionY;
}
public void setPositionY(Length positionY)
{
this.positionY = positionY;
}
// Property PositionYUnit is a unit companion
public static String getPositionYUnitXsdDefault()
{
return "reference frame";
}
// Property Timepoint
public Timestamp getTimepoint()
{
return timepoint;
}
public void setTimepoint(Timestamp timepoint)
{
this.timepoint = timepoint;
}
// Property Index
public NonNegativeInteger getIndex()
{
return index;
}
public void setIndex(NonNegativeInteger index)
{
this.index = index;
}
// Reference
public Image getLinkedImage()
{
return image;
}
public void linkImage(Image o)
{
image = o;
}
public void unlinkImage(Image o)
{
if (image == o)
{
image = null;
}
}
// Reference which occurs more than once
public int sizeOfLinkedPlateAcquisitionList()
{
return plateAcquisitions.size();
}
public List copyLinkedPlateAcquisitionList()
{
return new ArrayList(plateAcquisitions);
}
public PlateAcquisition getLinkedPlateAcquisition(int index)
{
return plateAcquisitions.get(index);
}
public PlateAcquisition setLinkedPlateAcquisition(int index, PlateAcquisition o)
{
return plateAcquisitions.set(index, o);
}
public boolean linkPlateAcquisition(PlateAcquisition o)
{
return plateAcquisitions.add(o);
}
public boolean unlinkPlateAcquisition(PlateAcquisition o)
{
return plateAcquisitions.remove(o);
}
// Property Well_BackReference
public Well getWell()
{
return well;
}
public void setWell(Well well_BackReference)
{
this.well = well_BackReference;
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
public Element asXMLElement(Document document, Element WellSample_element)
{
// Creating XML block for WellSample
if (WellSample_element == null)
{
WellSample_element =
document.createElementNS(NAMESPACE, "WellSample");
}
// Ensure any base annotations add their Elements first
super.asXMLElement(document, WellSample_element);
if (id != null)
{
// Attribute property ID
WellSample_element.setAttribute("ID", id.toString());
}
if (positionX != null)
{
// Attribute property PositionX with units companion prop.unitsCompanion.name
if (positionX.value() != null)
{
WellSample_element.setAttribute("PositionX", positionX.value().toString());
}
if (positionX.unit() != null)
{
try
{
UnitsLength enumUnits = UnitsLength.fromString(positionX.unit().getSymbol());
WellSample_element.setAttribute("PositionXUnit", enumUnits.toString());
} catch (EnumerationException e)
{
LOGGER.debug("Unable to create xml for WellSample:PositionXUnit: {}", e.toString());
}
}
}
if (positionY != null)
{
// Attribute property PositionY with units companion prop.unitsCompanion.name
if (positionY.value() != null)
{
WellSample_element.setAttribute("PositionY", positionY.value().toString());
}
if (positionY.unit() != null)
{
try
{
UnitsLength enumUnits = UnitsLength.fromString(positionY.unit().getSymbol());
WellSample_element.setAttribute("PositionYUnit", enumUnits.toString());
} catch (EnumerationException e)
{
LOGGER.debug("Unable to create xml for WellSample:PositionYUnit: {}", e.toString());
}
}
}
if (timepoint != null)
{
// Attribute property Timepoint
WellSample_element.setAttribute("Timepoint", timepoint.toString());
}
if (index != null)
{
// Attribute property Index
WellSample_element.setAttribute("Index", index.toString());
}
if (image != null)
{
// Reference property ImageRef
ImageRef o = new ImageRef();
o.setID(image.getID());
Element child =
document.createElementNS(NAMESPACE, "ImageRef");
o.asXMLElement(document, child);
WellSample_element.appendChild(child);
}
if (plateAcquisitions != null)
{
// *** IGNORING *** Skipped back reference PlateAcquisition_BackReference
}
if (well != null)
{
// *** IGNORING *** Skipped back reference Well_BackReference
}
return WellSample_element;
}
}
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