/*
* ome.xml.model.Experiment
*
*-----------------------------------------------------------------------------
*
* Copyright (C) @year@ Open Microscopy Environment
* Massachusetts Institute of Technology,
* National Institutes of Health,
* University of Dundee,
* University of Wisconsin-Madison
*
*
*
* This library is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public
* License as published by the Free Software Foundation; either
* version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this library; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*-----------------------------------------------------------------------------
*/
/*-----------------------------------------------------------------------------
*
* THIS IS AUTOMATICALLY GENERATED CODE. DO NOT MODIFY.
* Created by melissa via xsd-fu on 2011-11-09 10:55:09-0500
*
*-----------------------------------------------------------------------------
*/
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.primitives.*;
public class Experiment extends AbstractOMEModelObject
{
// Base: -- Name: Experiment -- Type: Experiment -- javaBase: AbstractOMEModelObject -- javaType: Object
// -- Constants --
public static final String NAMESPACE = "http://www.openmicroscopy.org/Schemas/OME/2011-06";
/** Logger for this class. */
private static final Logger LOGGER =
LoggerFactory.getLogger(Experiment.class);
// -- Instance variables --
// Property
private ExperimentType type;
// Property
private String id;
// Property
private String description;
// Property
private Experimenter experimenter;
// Property which occurs more than once
private List<MicrobeamManipulation> microbeamManipulationList = new ArrayList<MicrobeamManipulation>();
// Back reference Image_BackReference
private List<Image> image_BackReferenceList = new ArrayList<Image>();
// -- Constructors --
/** Default constructor. */
public Experiment()
{
super();
}
/**
* 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);
}
// -- Custom content from Experiment specific template --
// -- OMEModelObject API methods --
/**
* Updates Experiment recursively from an XML DOM tree. <b>NOTE:</b> 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 (!"Experiment".equals(tagName))
{
LOGGER.debug("Expecting node name of Experiment got {}", tagName);
}
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<Element> 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<Element> 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<Element> MicrobeamManipulation_nodeList =
getChildrenByTagName(element, "MicrobeamManipulation");
for (Element MicrobeamManipulation_element : MicrobeamManipulation_nodeList)
{
addMicrobeamManipulation(
new MicrobeamManipulation(MicrobeamManipulation_element, model));
}
// *** IGNORING *** Skipped back reference Image_BackReference
}
// -- Experiment API methods --
public boolean link(Reference reference, OMEModelObject o)
{
boolean wasHandledBySuperClass = super.link(reference, o);
if (wasHandledBySuperClass)
{
return true;
}
if (reference instanceof ExperimenterRef)
{
Experimenter o_casted = (Experimenter) o;
o_casted.linkExperiment(this);
experimenter = o_casted;
return true;
}
LOGGER.debug("Unable to handle reference of type: {}", reference.getClass());
return false;
}
// Property
public ExperimentType getType()
{
return type;
}
public void setType(ExperimentType type)
{
this.type = type;
}
// Property
public String getID()
{
return id;
}
public void setID(String id)
{
this.id = id;
}
// Property
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 microbeamManipulationList.size();
}
public List<MicrobeamManipulation> copyMicrobeamManipulationList()
{
return new ArrayList<MicrobeamManipulation>(microbeamManipulationList);
}
public MicrobeamManipulation getMicrobeamManipulation(int index)
{
return microbeamManipulationList.get(index);
}
public MicrobeamManipulation setMicrobeamManipulation(int index, MicrobeamManipulation microbeamManipulation)
{
return microbeamManipulationList.set(index, microbeamManipulation);
}
public void addMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
{
microbeamManipulationList.add(microbeamManipulation);
}
public void removeMicrobeamManipulation(MicrobeamManipulation microbeamManipulation)
{
microbeamManipulationList.remove(microbeamManipulation);
}
// Reference which occurs more than once
public int sizeOfLinkedImageList()
{
return image_BackReferenceList.size();
}
public List<Image> copyLinkedImageList()
{
return new ArrayList<Image>(image_BackReferenceList);
}
public Image getLinkedImage(int index)
{
return image_BackReferenceList.get(index);
}
public Image setLinkedImage(int index, Image o)
{
return image_BackReferenceList.set(index, o);
}
public boolean linkImage(Image o)
{
return image_BackReferenceList.add(o);
}
public boolean unlinkImage(Image o)
{
return image_BackReferenceList.remove(o);
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
protected Element asXMLElement(Document document, Element Experiment_element)
{
// Creating XML block for Experiment
if (Experiment_element == null)
{
Experiment_element =
document.createElementNS(NAMESPACE, "Experiment");
}
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());
Experiment_element.appendChild(o.asXMLElement(document));
}
if (microbeamManipulationList != null)
{
// Element property MicrobeamManipulation which is complex (has
// sub-elements) and occurs more than once
for (MicrobeamManipulation microbeamManipulationList_value : microbeamManipulationList)
{
Experiment_element.appendChild(microbeamManipulationList_value.asXMLElement(document));
}
}
if (image_BackReferenceList != null)
{
// *** IGNORING *** Skipped back reference Image_BackReference
}
return super.asXMLElement(document, Experiment_element);
}
}