/*
* ome.xml.model.Image
*
*-----------------------------------------------------------------------------
*
* 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 Image extends AbstractOMEModelObject
{
// Base: -- Name: Image -- Type: Image -- 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(Image.class);
// -- Instance variables --
// Property
private String id;
// Property
private String name;
// Property
private String acquiredDate;
// Property
private Experimenter experimenter;
// Property
private String description;
// Property
private Experiment experiment;
// Property
private Group group;
// Reference DatasetRef
private List<Dataset> datasetList = new ArrayList<Dataset>();
// Property
private Instrument instrument;
// Property
private ObjectiveSettings objectiveSettings;
// Property
private ImagingEnvironment imagingEnvironment;
// Property
private StageLabel stageLabel;
// Property
private Pixels pixels;
// Reference ROIRef
private List<ROI> roiList = new ArrayList<ROI>();
// Reference MicrobeamManipulationRef
private List<MicrobeamManipulation> microbeamManipulationList = new ArrayList<MicrobeamManipulation>();
// Reference AnnotationRef
private List<Annotation> annotationList = new ArrayList<Annotation>();
// Back reference WellSample_BackReference
private List<WellSample> wellSample_BackReferenceList = new ArrayList<WellSample>();
// -- Constructors --
/** Default constructor. */
public Image()
{
super();
}
/**
* Constructs Image 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 Image(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
// -- Custom content from Image specific template --
// -- OMEModelObject API methods --
/**
* Updates Image 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 (!"Image".equals(tagName))
{
LOGGER.debug("Expecting node name of Image got {}", tagName);
}
if (!element.hasAttribute("ID") && getID() == null)
{
// TODO: Should be its own exception
throw new RuntimeException(String.format(
"Image 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("Name"))
{
// Attribute property Name
setName(String.valueOf(
element.getAttribute("Name")));
}
List<Element> AcquiredDate_nodeList =
getChildrenByTagName(element, "AcquiredDate");
if (AcquiredDate_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"AcquiredDate node list size %d != 1",
AcquiredDate_nodeList.size()));
}
else if (AcquiredDate_nodeList.size() != 0)
{
// Element property AcquiredDate which is not complex (has no
// sub-elements)
setAcquiredDate(
String.valueOf(AcquiredDate_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);
}
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 ExperimentRef
List<Element> ExperimentRef_nodeList =
getChildrenByTagName(element, "ExperimentRef");
for (Element ExperimentRef_element : ExperimentRef_nodeList)
{
ExperimentRef experiment_reference = new ExperimentRef();
experiment_reference.setID(ExperimentRef_element.getAttribute("ID"));
model.addReference(this, experiment_reference);
}
// Element reference GroupRef
List<Element> GroupRef_nodeList =
getChildrenByTagName(element, "GroupRef");
for (Element GroupRef_element : GroupRef_nodeList)
{
GroupRef group_reference = new GroupRef();
group_reference.setID(GroupRef_element.getAttribute("ID"));
model.addReference(this, group_reference);
}
// Element reference DatasetRef
List<Element> DatasetRef_nodeList =
getChildrenByTagName(element, "DatasetRef");
for (Element DatasetRef_element : DatasetRef_nodeList)
{
DatasetRef datasetList_reference = new DatasetRef();
datasetList_reference.setID(DatasetRef_element.getAttribute("ID"));
model.addReference(this, datasetList_reference);
}
// Element reference InstrumentRef
List<Element> InstrumentRef_nodeList =
getChildrenByTagName(element, "InstrumentRef");
for (Element InstrumentRef_element : InstrumentRef_nodeList)
{
InstrumentRef instrument_reference = new InstrumentRef();
instrument_reference.setID(InstrumentRef_element.getAttribute("ID"));
model.addReference(this, instrument_reference);
}
List<Element> ObjectiveSettings_nodeList =
getChildrenByTagName(element, "ObjectiveSettings");
if (ObjectiveSettings_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"ObjectiveSettings node list size %d != 1",
ObjectiveSettings_nodeList.size()));
}
else if (ObjectiveSettings_nodeList.size() != 0)
{
// Element property ObjectiveSettings which is complex (has
// sub-elements)
setObjectiveSettings(new ObjectiveSettings(
(Element) ObjectiveSettings_nodeList.get(0), model));
}
List<Element> ImagingEnvironment_nodeList =
getChildrenByTagName(element, "ImagingEnvironment");
if (ImagingEnvironment_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"ImagingEnvironment node list size %d != 1",
ImagingEnvironment_nodeList.size()));
}
else if (ImagingEnvironment_nodeList.size() != 0)
{
// Element property ImagingEnvironment which is complex (has
// sub-elements)
setImagingEnvironment(new ImagingEnvironment(
(Element) ImagingEnvironment_nodeList.get(0), model));
}
List<Element> StageLabel_nodeList =
getChildrenByTagName(element, "StageLabel");
if (StageLabel_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"StageLabel node list size %d != 1",
StageLabel_nodeList.size()));
}
else if (StageLabel_nodeList.size() != 0)
{
// Element property StageLabel which is complex (has
// sub-elements)
setStageLabel(new StageLabel(
(Element) StageLabel_nodeList.get(0), model));
}
List<Element> Pixels_nodeList =
getChildrenByTagName(element, "Pixels");
if (Pixels_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"Pixels node list size %d != 1",
Pixels_nodeList.size()));
}
else if (Pixels_nodeList.size() != 0)
{
// Element property Pixels which is complex (has
// sub-elements)
setPixels(new Pixels(
(Element) Pixels_nodeList.get(0), model));
}
// Element reference ROIRef
List<Element> ROIRef_nodeList =
getChildrenByTagName(element, "ROIRef");
for (Element ROIRef_element : ROIRef_nodeList)
{
ROIRef roiList_reference = new ROIRef();
roiList_reference.setID(ROIRef_element.getAttribute("ID"));
model.addReference(this, roiList_reference);
}
// Element reference MicrobeamManipulationRef
List<Element> MicrobeamManipulationRef_nodeList =
getChildrenByTagName(element, "MicrobeamManipulationRef");
for (Element MicrobeamManipulationRef_element : MicrobeamManipulationRef_nodeList)
{
MicrobeamManipulationRef microbeamManipulationList_reference = new MicrobeamManipulationRef();
microbeamManipulationList_reference.setID(MicrobeamManipulationRef_element.getAttribute("ID"));
model.addReference(this, microbeamManipulationList_reference);
}
// Element reference AnnotationRef
List<Element> AnnotationRef_nodeList =
getChildrenByTagName(element, "AnnotationRef");
for (Element AnnotationRef_element : AnnotationRef_nodeList)
{
AnnotationRef annotationList_reference = new AnnotationRef();
annotationList_reference.setID(AnnotationRef_element.getAttribute("ID"));
model.addReference(this, annotationList_reference);
}
// *** IGNORING *** Skipped back reference WellSample_BackReference
}
// -- Image 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.linkImage(this);
experimenter = o_casted;
return true;
}
if (reference instanceof ExperimentRef)
{
Experiment o_casted = (Experiment) o;
o_casted.linkImage(this);
experiment = o_casted;
return true;
}
if (reference instanceof GroupRef)
{
Group o_casted = (Group) o;
o_casted.linkImage(this);
group = o_casted;
return true;
}
if (reference instanceof DatasetRef)
{
Dataset o_casted = (Dataset) o;
o_casted.linkImage(this);
datasetList.add(o_casted);
return true;
}
if (reference instanceof InstrumentRef)
{
Instrument o_casted = (Instrument) o;
o_casted.linkImage(this);
instrument = o_casted;
return true;
}
if (reference instanceof ROIRef)
{
ROI o_casted = (ROI) o;
o_casted.linkImage(this);
roiList.add(o_casted);
return true;
}
if (reference instanceof MicrobeamManipulationRef)
{
MicrobeamManipulation o_casted = (MicrobeamManipulation) o;
o_casted.linkImage(this);
microbeamManipulationList.add(o_casted);
return true;
}
if (reference instanceof AnnotationRef)
{
Annotation o_casted = (Annotation) o;
o_casted.linkImage(this);
annotationList.add(o_casted);
return true;
}
LOGGER.debug("Unable to handle reference of type: {}", reference.getClass());
return false;
}
// Property
public String getID()
{
return id;
}
public void setID(String id)
{
this.id = id;
}
// Property
public String getName()
{
return name;
}
public void setName(String name)
{
this.name = name;
}
// Property
public String getAcquiredDate()
{
return acquiredDate;
}
public void setAcquiredDate(String acquiredDate)
{
this.acquiredDate = acquiredDate;
}
// Reference
public Experimenter getLinkedExperimenter()
{
return experimenter;
}
public void linkExperimenter(Experimenter o)
{
experimenter = o;
}
public void unlinkExperimenter(Experimenter o)
{
if (experimenter == o)
{
experimenter = null;
}
}
// Property
public String getDescription()
{
return description;
}
public void setDescription(String description)
{
this.description = description;
}
// Reference
public Experiment getLinkedExperiment()
{
return experiment;
}
public void linkExperiment(Experiment o)
{
experiment = o;
}
public void unlinkExperiment(Experiment o)
{
if (experiment == o)
{
experiment = null;
}
}
// Reference
public Group getLinkedGroup()
{
return group;
}
public void linkGroup(Group o)
{
group = o;
}
public void unlinkGroup(Group o)
{
if (group == o)
{
group = null;
}
}
// Reference which occurs more than once
public int sizeOfLinkedDatasetList()
{
return datasetList.size();
}
public List<Dataset> copyLinkedDatasetList()
{
return new ArrayList<Dataset>(datasetList);
}
public Dataset getLinkedDataset(int index)
{
return datasetList.get(index);
}
public Dataset setLinkedDataset(int index, Dataset o)
{
return datasetList.set(index, o);
}
public boolean linkDataset(Dataset o)
{
o.linkImage(this);
return datasetList.add(o);
}
public boolean unlinkDataset(Dataset o)
{
o.unlinkImage(this);
return datasetList.remove(o);
}
// Reference
public Instrument getLinkedInstrument()
{
return instrument;
}
public void linkInstrument(Instrument o)
{
instrument = o;
}
public void unlinkInstrument(Instrument o)
{
if (instrument == o)
{
instrument = null;
}
}
// Property
public ObjectiveSettings getObjectiveSettings()
{
return objectiveSettings;
}
public void setObjectiveSettings(ObjectiveSettings objectiveSettings)
{
this.objectiveSettings = objectiveSettings;
}
// Property
public ImagingEnvironment getImagingEnvironment()
{
return imagingEnvironment;
}
public void setImagingEnvironment(ImagingEnvironment imagingEnvironment)
{
this.imagingEnvironment = imagingEnvironment;
}
// Property
public StageLabel getStageLabel()
{
return stageLabel;
}
public void setStageLabel(StageLabel stageLabel)
{
this.stageLabel = stageLabel;
}
// Property
public Pixels getPixels()
{
return pixels;
}
public void setPixels(Pixels pixels)
{
this.pixels = pixels;
}
// Reference which occurs more than once
public int sizeOfLinkedROIList()
{
return roiList.size();
}
public List<ROI> copyLinkedROIList()
{
return new ArrayList<ROI>(roiList);
}
public ROI getLinkedROI(int index)
{
return roiList.get(index);
}
public ROI setLinkedROI(int index, ROI o)
{
return roiList.set(index, o);
}
public boolean linkROI(ROI o)
{
o.linkImage(this);
return roiList.add(o);
}
public boolean unlinkROI(ROI o)
{
o.unlinkImage(this);
return roiList.remove(o);
}
// Reference which occurs more than once
public int sizeOfLinkedMicrobeamManipulationList()
{
return microbeamManipulationList.size();
}
public List<MicrobeamManipulation> copyLinkedMicrobeamManipulationList()
{
return new ArrayList<MicrobeamManipulation>(microbeamManipulationList);
}
public MicrobeamManipulation getLinkedMicrobeamManipulation(int index)
{
return microbeamManipulationList.get(index);
}
public MicrobeamManipulation setLinkedMicrobeamManipulation(int index, MicrobeamManipulation o)
{
return microbeamManipulationList.set(index, o);
}
public boolean linkMicrobeamManipulation(MicrobeamManipulation o)
{
o.linkImage(this);
return microbeamManipulationList.add(o);
}
public boolean unlinkMicrobeamManipulation(MicrobeamManipulation o)
{
o.unlinkImage(this);
return microbeamManipulationList.remove(o);
}
// Reference which occurs more than once
public int sizeOfLinkedAnnotationList()
{
return annotationList.size();
}
public List<Annotation> copyLinkedAnnotationList()
{
return new ArrayList<Annotation>(annotationList);
}
public Annotation getLinkedAnnotation(int index)
{
return annotationList.get(index);
}
public Annotation setLinkedAnnotation(int index, Annotation o)
{
return annotationList.set(index, o);
}
public boolean linkAnnotation(Annotation o)
{
o.linkImage(this);
return annotationList.add(o);
}
public boolean unlinkAnnotation(Annotation o)
{
o.unlinkImage(this);
return annotationList.remove(o);
}
// Reference which occurs more than once
public int sizeOfLinkedWellSampleList()
{
return wellSample_BackReferenceList.size();
}
public List<WellSample> copyLinkedWellSampleList()
{
return new ArrayList<WellSample>(wellSample_BackReferenceList);
}
public WellSample getLinkedWellSample(int index)
{
return wellSample_BackReferenceList.get(index);
}
public WellSample setLinkedWellSample(int index, WellSample o)
{
return wellSample_BackReferenceList.set(index, o);
}
public boolean linkWellSample(WellSample o)
{
return wellSample_BackReferenceList.add(o);
}
public boolean unlinkWellSample(WellSample o)
{
return wellSample_BackReferenceList.remove(o);
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
protected Element asXMLElement(Document document, Element Image_element)
{
// Creating XML block for Image
if (Image_element == null)
{
Image_element =
document.createElementNS(NAMESPACE, "Image");
}
if (id != null)
{
// Attribute property ID
Image_element.setAttribute("ID", id.toString());
}
if (name != null)
{
// Attribute property Name
Image_element.setAttribute("Name", name.toString());
}
if (acquiredDate != null)
{
// Element property AcquiredDate which is not complex (has no
// sub-elements)
Element acquiredDate_element =
document.createElementNS(NAMESPACE, "AcquiredDate");
acquiredDate_element.setTextContent(acquiredDate.toString());
Image_element.appendChild(acquiredDate_element);
}
if (experimenter != null)
{
// Reference property ExperimenterRef
ExperimenterRef o = new ExperimenterRef();
o.setID(experimenter.getID());
Image_element.appendChild(o.asXMLElement(document));
}
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());
Image_element.appendChild(description_element);
}
if (experiment != null)
{
// Reference property ExperimentRef
ExperimentRef o = new ExperimentRef();
o.setID(experiment.getID());
Image_element.appendChild(o.asXMLElement(document));
}
if (group != null)
{
// Reference property GroupRef
GroupRef o = new GroupRef();
o.setID(group.getID());
Image_element.appendChild(o.asXMLElement(document));
}
if (datasetList != null)
{
// Reference property DatasetRef which occurs more than once
for (Dataset datasetList_value : datasetList)
{
DatasetRef o = new DatasetRef();
o.setID(datasetList_value.getID());
Image_element.appendChild(o.asXMLElement(document));
}
}
if (instrument != null)
{
// Reference property InstrumentRef
InstrumentRef o = new InstrumentRef();
o.setID(instrument.getID());
Image_element.appendChild(o.asXMLElement(document));
}
if (objectiveSettings != null)
{
// Element property ObjectiveSettings which is complex (has
// sub-elements)
Image_element.appendChild(objectiveSettings.asXMLElement(document));
}
if (imagingEnvironment != null)
{
// Element property ImagingEnvironment which is complex (has
// sub-elements)
Image_element.appendChild(imagingEnvironment.asXMLElement(document));
}
if (stageLabel != null)
{
// Element property StageLabel which is complex (has
// sub-elements)
Image_element.appendChild(stageLabel.asXMLElement(document));
}
if (pixels != null)
{
// Element property Pixels which is complex (has
// sub-elements)
Image_element.appendChild(pixels.asXMLElement(document));
}
if (roiList != null)
{
// Reference property ROIRef which occurs more than once
for (ROI roiList_value : roiList)
{
ROIRef o = new ROIRef();
o.setID(roiList_value.getID());
Image_element.appendChild(o.asXMLElement(document));
}
}
if (microbeamManipulationList != null)
{
// Reference property MicrobeamManipulationRef which occurs more than once
for (MicrobeamManipulation microbeamManipulationList_value : microbeamManipulationList)
{
MicrobeamManipulationRef o = new MicrobeamManipulationRef();
o.setID(microbeamManipulationList_value.getID());
Image_element.appendChild(o.asXMLElement(document));
}
}
if (annotationList != null)
{
// Reference property AnnotationRef which occurs more than once
for (Annotation annotationList_value : annotationList)
{
AnnotationRef o = new AnnotationRef();
o.setID(annotationList_value.getID());
Image_element.appendChild(o.asXMLElement(document));
}
}
if (wellSample_BackReferenceList != null)
{
// *** IGNORING *** Skipped back reference WellSample_BackReference
}
return super.asXMLElement(document, Image_element);
}
}