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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 Objective extends ManufacturerSpec
{
// Base: ManufacturerSpec -- Name: Objective -- Type: Objective -- modelBaseType: ManufacturerSpec -- 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(Objective.class);
// -- Instance variables --
// ID property
private String id;
// Correction property
private Correction correction;
// Immersion property
private Immersion immersion;
// LensNA property
private Double lensNA;
// NominalMagnification property
private Double nominalMagnification;
// CalibratedMagnification property
private Double calibratedMagnification;
// WorkingDistance property
private Length workingDistance;
// Iris property
private Boolean iris;
// AnnotationRef reference (occurs more than once)
private List annotationLinks = new ReferenceList();
// Instrument_BackReference back reference
private Instrument instrument;
// -- Constructors --
/** Default constructor. */
public Objective()
{
super();
}
/**
* Constructs Objective 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 Objective(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
/** Copy constructor. */
public Objective(Objective orig)
{
super(orig);
id = orig.id;
correction = orig.correction;
immersion = orig.immersion;
lensNA = orig.lensNA;
nominalMagnification = orig.nominalMagnification;
calibratedMagnification = orig.calibratedMagnification;
workingDistance = orig.workingDistance;
iris = orig.iris;
annotationLinks = orig.annotationLinks;
instrument = orig.instrument;
}
// -- Custom content from Objective specific template --
// -- OMEModelObject API methods --
/**
* Updates Objective 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(
"Objective 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("Correction"))
{
// Attribute property which is an enumeration Correction
setCorrection(Correction.fromString(
element.getAttribute("Correction")));
}
if (element.hasAttribute("Immersion"))
{
// Attribute property which is an enumeration Immersion
setImmersion(Immersion.fromString(
element.getAttribute("Immersion")));
}
if (element.hasAttribute("LensNA"))
{
// Attribute property LensNA
setLensNA(Double.valueOf(
element.getAttribute("LensNA")));
}
if (element.hasAttribute("NominalMagnification"))
{
// Attribute property NominalMagnification
setNominalMagnification(Double.valueOf(
element.getAttribute("NominalMagnification")));
}
if (element.hasAttribute("CalibratedMagnification"))
{
// Attribute property CalibratedMagnification
setCalibratedMagnification(Double.valueOf(
element.getAttribute("CalibratedMagnification")));
}
if (element.hasAttribute("WorkingDistance"))
{
// Attribute property WorkingDistance with unit companion WorkingDistanceUnit
String unitSymbol = element.getAttribute("WorkingDistanceUnit");
if ((unitSymbol == null) || (unitSymbol.isEmpty()))
{
// Use default value specified in the xsd model
unitSymbol = getWorkingDistanceUnitXsdDefault();
}
UnitsLength modelUnit =
UnitsLength.fromString(unitSymbol);
Double baseValue = Double.valueOf(
element.getAttribute("WorkingDistance"));
if (baseValue != null)
{
setWorkingDistance(UnitsLengthEnumHandler.getQuantity(baseValue, modelUnit));
}
}
if (element.hasAttribute("Iris"))
{
// Attribute property Iris
setIris(Boolean.valueOf(
element.getAttribute("Iris")));
}
// Element reference AnnotationRef
List AnnotationRef_nodeList =
getChildrenByTagName(element, "AnnotationRef");
for (Element AnnotationRef_element : AnnotationRef_nodeList)
{
AnnotationRef annotationLinks_reference = new AnnotationRef();
annotationLinks_reference.setID(AnnotationRef_element.getAttribute("ID"));
model.addReference(this, annotationLinks_reference);
}
}
// -- Objective API methods --
public boolean link(Reference reference, OMEModelObject o)
{
if (reference instanceof AnnotationRef)
{
Annotation o_casted = (Annotation) o;
o_casted.linkObjective(this);
annotationLinks.add(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 Correction
public Correction getCorrection()
{
return correction;
}
public void setCorrection(Correction correction)
{
this.correction = correction;
}
// Property Immersion
public Immersion getImmersion()
{
return immersion;
}
public void setImmersion(Immersion immersion)
{
this.immersion = immersion;
}
// Property LensNA
public Double getLensNA()
{
return lensNA;
}
public void setLensNA(Double lensNA)
{
this.lensNA = lensNA;
}
// Property NominalMagnification
public Double getNominalMagnification()
{
return nominalMagnification;
}
public void setNominalMagnification(Double nominalMagnification)
{
this.nominalMagnification = nominalMagnification;
}
// Property CalibratedMagnification
public Double getCalibratedMagnification()
{
return calibratedMagnification;
}
public void setCalibratedMagnification(Double calibratedMagnification)
{
this.calibratedMagnification = calibratedMagnification;
}
// Property WorkingDistance with unit companion WorkingDistanceUnit
public Length getWorkingDistance()
{
return workingDistance;
}
public void setWorkingDistance(Length workingDistance)
{
this.workingDistance = workingDistance;
}
// Property WorkingDistanceUnit is a unit companion
public static String getWorkingDistanceUnitXsdDefault()
{
return "µm";
}
// Property Iris
public Boolean getIris()
{
return iris;
}
public void setIris(Boolean iris)
{
this.iris = iris;
}
// Reference which occurs more than once
public int sizeOfLinkedAnnotationList()
{
return annotationLinks.size();
}
public List copyLinkedAnnotationList()
{
return new ArrayList(annotationLinks);
}
public Annotation getLinkedAnnotation(int index)
{
return annotationLinks.get(index);
}
public Annotation setLinkedAnnotation(int index, Annotation o)
{
return annotationLinks.set(index, o);
}
public boolean linkAnnotation(Annotation o)
{
o.linkObjective(this);
return annotationLinks.add(o);
}
public boolean unlinkAnnotation(Annotation o)
{
o.unlinkObjective(this);
return annotationLinks.remove(o);
}
// Property Instrument_BackReference
public Instrument getInstrument()
{
return instrument;
}
public void setInstrument(Instrument instrument_BackReference)
{
this.instrument = instrument_BackReference;
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
public Element asXMLElement(Document document, Element Objective_element)
{
// Creating XML block for Objective
if (Objective_element == null)
{
Objective_element =
document.createElementNS(NAMESPACE, "Objective");
}
// Ensure any base annotations add their Elements first
super.asXMLElement(document, Objective_element);
if (id != null)
{
// Attribute property ID
Objective_element.setAttribute("ID", id.toString());
}
if (correction != null)
{
// Attribute property Correction
Objective_element.setAttribute("Correction", correction.toString());
}
if (immersion != null)
{
// Attribute property Immersion
Objective_element.setAttribute("Immersion", immersion.toString());
}
if (lensNA != null)
{
// Attribute property LensNA
Objective_element.setAttribute("LensNA", lensNA.toString());
}
if (nominalMagnification != null)
{
// Attribute property NominalMagnification
Objective_element.setAttribute("NominalMagnification", nominalMagnification.toString());
}
if (calibratedMagnification != null)
{
// Attribute property CalibratedMagnification
Objective_element.setAttribute("CalibratedMagnification", calibratedMagnification.toString());
}
if (workingDistance != null)
{
// Attribute property WorkingDistance with units companion prop.unitsCompanion.name
if (workingDistance.value() != null)
{
Objective_element.setAttribute("WorkingDistance", workingDistance.value().toString());
}
if (workingDistance.unit() != null)
{
try
{
UnitsLength enumUnits = UnitsLength.fromString(workingDistance.unit().getSymbol());
Objective_element.setAttribute("WorkingDistanceUnit", enumUnits.toString());
} catch (EnumerationException e)
{
LOGGER.debug("Unable to create xml for Objective:WorkingDistanceUnit: {}", e.toString());
}
}
}
if (iris != null)
{
// Attribute property Iris
Objective_element.setAttribute("Iris", iris.toString());
}
if (annotationLinks != null)
{
// Reference property AnnotationRef which occurs more than once
for (Annotation annotationLinks_value : annotationLinks)
{
AnnotationRef o = new AnnotationRef();
o.setID(annotationLinks_value.getID());
Element child =
document.createElementNS(NAMESPACE, "AnnotationRef");
o.asXMLElement(document, child);
Objective_element.appendChild(child);
}
}
if (instrument != null)
{
// *** IGNORING *** Skipped back reference Instrument_BackReference
}
return Objective_element;
}
}
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