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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 Experiment extends AbstractOMEModelObject
{
// Base: -- Name: Experiment -- Type: Experiment -- 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(Experiment.class);
// -- Instance variables --
// Type property
private ExperimentType type;
// ID property
private String id;
// Description property
private String description;
// ExperimenterRef reference
private Experimenter experimenter;
// MicrobeamManipulation property (occurs more than once)
private List microbeamManipulations = new ArrayList();
// Image_BackReference back reference (occurs more than once)
private List images = new ReferenceList();
// -- Constructors --
/** Default constructor. */
public Experiment()
{
}
/**
* Constructs Experiment 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 Experiment(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
/** Copy constructor. */
public Experiment(Experiment orig)
{
type = orig.type;
id = orig.id;
description = orig.description;
experimenter = orig.experimenter;
microbeamManipulations = orig.microbeamManipulations;
images = orig.images;
}
// -- Custom content from Experiment specific template --
// -- OMEModelObject API methods --
/**
* Updates Experiment 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("Type"))
{
// Attribute property which is an enumeration Type
setType(ExperimentType.fromString(
element.getAttribute("Type")));
}
if (!element.hasAttribute("ID") && getID() == null)
{
// TODO: Should be its own exception
throw new RuntimeException(String.format(
"Experiment 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);
}
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 ExperimenterRef
List ExperimenterRef_nodeList =
getChildrenByTagName(element, "ExperimenterRef");
for (Element ExperimenterRef_element : ExperimenterRef_nodeList)
{
ExperimenterRef experimenter_reference = new ExperimenterRef();
experimenter_reference.setID(ExperimenterRef_element.getAttribute("ID"));
model.addReference(this, experimenter_reference);
}
// Element property MicrobeamManipulation which is complex (has
// sub-elements) and occurs more than once
List MicrobeamManipulation_nodeList =
getChildrenByTagName(element, "MicrobeamManipulation");
for (Element MicrobeamManipulation_element : MicrobeamManipulation_nodeList)
{
addMicrobeamManipulation(
new MicrobeamManipulation(MicrobeamManipulation_element, model));
}
}
// -- Experiment API methods --
public boolean link(Reference reference, OMEModelObject o)
{
if (reference instanceof ExperimenterRef)
{
Experimenter o_casted = (Experimenter) o;
o_casted.linkExperiment(this);
experimenter = o_casted;
return true;
}
return super.link(reference, o);
}
// Property Type
public ExperimentType getType()
{
return type;
}
public void setType(ExperimentType type)
{
this.type = type;
}
// Property ID
public String getID()
{
return id;
}
public void setID(String id)
{
this.id = id;
}
// Property Description
public String getDescription()
{
return description;
}
public void setDescription(String description)
{
this.description = description;
}
// Reference
public Experimenter getLinkedExperimenter()
{
return experimenter;
}
public void linkExperimenter(Experimenter o)
{
experimenter = o;
}
public void unlinkExperimenter(Experimenter o)
{
if (experimenter == o)
{
experimenter = null;
}
}
// Property which occurs more than once
public int sizeOfMicrobeamManipulationList()
{
return microbeamManipulations.size();
}
public List copyMicrobeamManipulationList()
{
return new ArrayList(microbeamManipulations);
}
public MicrobeamManipulation getMicrobeamManipulation(int index)
{
return microbeamManipulations.get(index);
}
public MicrobeamManipulation setMicrobeamManipulation(int index, MicrobeamManipulation microbeamManipulation)
{
microbeamManipulation.setExperiment(this);
return microbeamManipulations.set(index, microbeamManipulation);
}
public void addMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
{
microbeamManipulation.setExperiment(this);
microbeamManipulations.add(microbeamManipulation);
}
public void removeMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
{
microbeamManipulations.remove(microbeamManipulation);
}
// Reference which occurs more than once
public int sizeOfLinkedImageList()
{
return images.size();
}
public List copyLinkedImageList()
{
return new ArrayList(images);
}
public Image getLinkedImage(int index)
{
return images.get(index);
}
public Image setLinkedImage(int index, Image o)
{
return images.set(index, o);
}
public boolean linkImage(Image o)
{
return images.add(o);
}
public boolean unlinkImage(Image o)
{
return images.remove(o);
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
public Element asXMLElement(Document document, Element Experiment_element)
{
// Creating XML block for Experiment
if (Experiment_element == null)
{
Experiment_element =
document.createElementNS(NAMESPACE, "Experiment");
}
// Ensure any base annotations add their Elements first
super.asXMLElement(document, Experiment_element);
if (type != null)
{
// Attribute property Type
Experiment_element.setAttribute("Type", type.toString());
}
if (id != null)
{
// Attribute property ID
Experiment_element.setAttribute("ID", id.toString());
}
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.toString());
Experiment_element.appendChild(description_element);
}
if (experimenter != null)
{
// Reference property ExperimenterRef
ExperimenterRef o = new ExperimenterRef();
o.setID(experimenter.getID());
Element child =
document.createElementNS(NAMESPACE, "ExperimenterRef");
o.asXMLElement(document, child);
Experiment_element.appendChild(child);
}
if (microbeamManipulations != null)
{
// Element property MicrobeamManipulation which is complex (has
// sub-elements) and occurs more than once
for (MicrobeamManipulation microbeamManipulations_value : microbeamManipulations)
{
Element child =
document.createElementNS(NAMESPACE, "MicrobeamManipulation");
microbeamManipulations_value.asXMLElement(document, child);
Experiment_element.appendChild(child);
}
}
if (images != null)
{
// *** IGNORING *** Skipped back reference Image_BackReference
}
return Experiment_element;
}
}
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