/*
* ome.xml.model.Channel
*
*-----------------------------------------------------------------------------
*
* 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 Channel extends AbstractOMEModelObject
{
// Base: -- Name: Channel -- Type: Channel -- 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(Channel.class);
// -- Instance variables --
// Property
private Double pinholeSize;
// Property
private String name;
// Property
private AcquisitionMode acquisitionMode;
// Property
private Integer color;
// Property
private ContrastMethod contrastMethod;
// Property
private PositiveInteger excitationWavelength;
// Property
private IlluminationType illuminationType;
// Property
private String fluor;
// Property
private Integer pockelCellSetting;
// Property
private PositiveInteger emissionWavelength;
// Property
private Double ndfilter;
// Property
private String id;
// Property
private PositiveInteger samplesPerPixel;
// Property
private LightSourceSettings lightSourceSettings;
// Property
private OTF otf;
// Property
private DetectorSettings detectorSettings;
// Property
private FilterSet filterSet;
// Reference AnnotationRef
private List<Annotation> annotationList = new ArrayList<Annotation>();
// Property
private LightPath lightPath;
// -- Constructors --
/** Default constructor. */
public Channel()
{
super();
}
/**
* Constructs Channel 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 Channel(Element element, OMEModel model)
throws EnumerationException
{
update(element, model);
}
// -- Custom content from Channel specific template --
// -- OMEModelObject API methods --
/**
* Updates Channel 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 (!"Channel".equals(tagName))
{
LOGGER.debug("Expecting node name of Channel got {}", tagName);
}
if (element.hasAttribute("PinholeSize"))
{
// Attribute property PinholeSize
setPinholeSize(Double.valueOf(
element.getAttribute("PinholeSize")));
}
if (element.hasAttribute("Name"))
{
// Attribute property Name
setName(String.valueOf(
element.getAttribute("Name")));
}
if (element.hasAttribute("AcquisitionMode"))
{
// Attribute property which is an enumeration AcquisitionMode
setAcquisitionMode(AcquisitionMode.fromString(
element.getAttribute("AcquisitionMode")));
}
if (element.hasAttribute("Color"))
{
// Attribute property Color
setColor(Integer.valueOf(
element.getAttribute("Color")));
}
if (element.hasAttribute("ContrastMethod"))
{
// Attribute property which is an enumeration ContrastMethod
setContrastMethod(ContrastMethod.fromString(
element.getAttribute("ContrastMethod")));
}
if (element.hasAttribute("ExcitationWavelength"))
{
// Attribute property ExcitationWavelength
setExcitationWavelength(PositiveInteger.valueOf(
element.getAttribute("ExcitationWavelength")));
}
if (element.hasAttribute("IlluminationType"))
{
// Attribute property which is an enumeration IlluminationType
setIlluminationType(IlluminationType.fromString(
element.getAttribute("IlluminationType")));
}
if (element.hasAttribute("Fluor"))
{
// Attribute property Fluor
setFluor(String.valueOf(
element.getAttribute("Fluor")));
}
if (element.hasAttribute("PockelCellSetting"))
{
// Attribute property PockelCellSetting
setPockelCellSetting(Integer.valueOf(
element.getAttribute("PockelCellSetting")));
}
if (element.hasAttribute("EmissionWavelength"))
{
// Attribute property EmissionWavelength
setEmissionWavelength(PositiveInteger.valueOf(
element.getAttribute("EmissionWavelength")));
}
if (element.hasAttribute("NDFilter"))
{
// Attribute property NDFilter
setNDFilter(Double.valueOf(
element.getAttribute("NDFilter")));
}
if (!element.hasAttribute("ID") && getID() == null)
{
// TODO: Should be its own exception
throw new RuntimeException(String.format(
"Channel 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("SamplesPerPixel"))
{
// Attribute property SamplesPerPixel
setSamplesPerPixel(PositiveInteger.valueOf(
element.getAttribute("SamplesPerPixel")));
}
List<Element> LightSourceSettings_nodeList =
getChildrenByTagName(element, "LightSourceSettings");
if (LightSourceSettings_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"LightSourceSettings node list size %d != 1",
LightSourceSettings_nodeList.size()));
}
else if (LightSourceSettings_nodeList.size() != 0)
{
// Element property LightSourceSettings which is complex (has
// sub-elements)
setLightSourceSettings(new LightSourceSettings(
(Element) LightSourceSettings_nodeList.get(0), model));
}
// Element reference OTFRef
List<Element> OTFRef_nodeList =
getChildrenByTagName(element, "OTFRef");
for (Element OTFRef_element : OTFRef_nodeList)
{
OTFRef otf_reference = new OTFRef();
otf_reference.setID(OTFRef_element.getAttribute("ID"));
model.addReference(this, otf_reference);
}
List<Element> DetectorSettings_nodeList =
getChildrenByTagName(element, "DetectorSettings");
if (DetectorSettings_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"DetectorSettings node list size %d != 1",
DetectorSettings_nodeList.size()));
}
else if (DetectorSettings_nodeList.size() != 0)
{
// Element property DetectorSettings which is complex (has
// sub-elements)
setDetectorSettings(new DetectorSettings(
(Element) DetectorSettings_nodeList.get(0), model));
}
// Element reference FilterSetRef
List<Element> FilterSetRef_nodeList =
getChildrenByTagName(element, "FilterSetRef");
for (Element FilterSetRef_element : FilterSetRef_nodeList)
{
FilterSetRef filterSet_reference = new FilterSetRef();
filterSet_reference.setID(FilterSetRef_element.getAttribute("ID"));
model.addReference(this, filterSet_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);
}
List<Element> LightPath_nodeList =
getChildrenByTagName(element, "LightPath");
if (LightPath_nodeList.size() > 1)
{
// TODO: Should be its own Exception
throw new RuntimeException(String.format(
"LightPath node list size %d != 1",
LightPath_nodeList.size()));
}
else if (LightPath_nodeList.size() != 0)
{
// Element property LightPath which is complex (has
// sub-elements)
setLightPath(new LightPath(
(Element) LightPath_nodeList.get(0), model));
}
}
// -- Channel API methods --
public boolean link(Reference reference, OMEModelObject o)
{
boolean wasHandledBySuperClass = super.link(reference, o);
if (wasHandledBySuperClass)
{
return true;
}
if (reference instanceof OTFRef)
{
OTF o_casted = (OTF) o;
o_casted.linkChannel(this);
otf = o_casted;
return true;
}
if (reference instanceof FilterSetRef)
{
FilterSet o_casted = (FilterSet) o;
o_casted.linkChannel(this);
filterSet = o_casted;
return true;
}
if (reference instanceof AnnotationRef)
{
Annotation o_casted = (Annotation) o;
o_casted.linkChannel(this);
annotationList.add(o_casted);
return true;
}
LOGGER.debug("Unable to handle reference of type: {}", reference.getClass());
return false;
}
// Property
public Double getPinholeSize()
{
return pinholeSize;
}
public void setPinholeSize(Double pinholeSize)
{
this.pinholeSize = pinholeSize;
}
// Property
public String getName()
{
return name;
}
public void setName(String name)
{
this.name = name;
}
// Property
public AcquisitionMode getAcquisitionMode()
{
return acquisitionMode;
}
public void setAcquisitionMode(AcquisitionMode acquisitionMode)
{
this.acquisitionMode = acquisitionMode;
}
// Property
public Integer getColor()
{
return color;
}
public void setColor(Integer color)
{
this.color = color;
}
// Property
public ContrastMethod getContrastMethod()
{
return contrastMethod;
}
public void setContrastMethod(ContrastMethod contrastMethod)
{
this.contrastMethod = contrastMethod;
}
// Property
public PositiveInteger getExcitationWavelength()
{
return excitationWavelength;
}
public void setExcitationWavelength(PositiveInteger excitationWavelength)
{
this.excitationWavelength = excitationWavelength;
}
// Property
public IlluminationType getIlluminationType()
{
return illuminationType;
}
public void setIlluminationType(IlluminationType illuminationType)
{
this.illuminationType = illuminationType;
}
// Property
public String getFluor()
{
return fluor;
}
public void setFluor(String fluor)
{
this.fluor = fluor;
}
// Property
public Integer getPockelCellSetting()
{
return pockelCellSetting;
}
public void setPockelCellSetting(Integer pockelCellSetting)
{
this.pockelCellSetting = pockelCellSetting;
}
// Property
public PositiveInteger getEmissionWavelength()
{
return emissionWavelength;
}
public void setEmissionWavelength(PositiveInteger emissionWavelength)
{
this.emissionWavelength = emissionWavelength;
}
// Property
public Double getNDFilter()
{
return ndfilter;
}
public void setNDFilter(Double ndfilter)
{
this.ndfilter = ndfilter;
}
// Property
public String getID()
{
return id;
}
public void setID(String id)
{
this.id = id;
}
// Property
public PositiveInteger getSamplesPerPixel()
{
return samplesPerPixel;
}
public void setSamplesPerPixel(PositiveInteger samplesPerPixel)
{
this.samplesPerPixel = samplesPerPixel;
}
// Property
public LightSourceSettings getLightSourceSettings()
{
return lightSourceSettings;
}
public void setLightSourceSettings(LightSourceSettings lightSourceSettings)
{
this.lightSourceSettings = lightSourceSettings;
}
// Reference
public OTF getLinkedOTF()
{
return otf;
}
public void linkOTF(OTF o)
{
otf = o;
}
public void unlinkOTF(OTF o)
{
if (otf == o)
{
otf = null;
}
}
// Property
public DetectorSettings getDetectorSettings()
{
return detectorSettings;
}
public void setDetectorSettings(DetectorSettings detectorSettings)
{
this.detectorSettings = detectorSettings;
}
// Reference
public FilterSet getLinkedFilterSet()
{
return filterSet;
}
public void linkFilterSet(FilterSet o)
{
filterSet = o;
}
public void unlinkFilterSet(FilterSet o)
{
if (filterSet == o)
{
filterSet = null;
}
}
// 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.linkChannel(this);
return annotationList.add(o);
}
public boolean unlinkAnnotation(Annotation o)
{
o.unlinkChannel(this);
return annotationList.remove(o);
}
// Property
public LightPath getLightPath()
{
return lightPath;
}
public void setLightPath(LightPath lightPath)
{
this.lightPath = lightPath;
}
public Element asXMLElement(Document document)
{
return asXMLElement(document, null);
}
protected Element asXMLElement(Document document, Element Channel_element)
{
// Creating XML block for Channel
if (Channel_element == null)
{
Channel_element =
document.createElementNS(NAMESPACE, "Channel");
}
if (pinholeSize != null)
{
// Attribute property PinholeSize
Channel_element.setAttribute("PinholeSize", pinholeSize.toString());
}
if (name != null)
{
// Attribute property Name
Channel_element.setAttribute("Name", name.toString());
}
if (acquisitionMode != null)
{
// Attribute property AcquisitionMode
Channel_element.setAttribute("AcquisitionMode", acquisitionMode.toString());
}
if (color != null)
{
// Attribute property Color
Channel_element.setAttribute("Color", color.toString());
}
if (contrastMethod != null)
{
// Attribute property ContrastMethod
Channel_element.setAttribute("ContrastMethod", contrastMethod.toString());
}
if (excitationWavelength != null)
{
// Attribute property ExcitationWavelength
Channel_element.setAttribute("ExcitationWavelength", excitationWavelength.toString());
}
if (illuminationType != null)
{
// Attribute property IlluminationType
Channel_element.setAttribute("IlluminationType", illuminationType.toString());
}
if (fluor != null)
{
// Attribute property Fluor
Channel_element.setAttribute("Fluor", fluor.toString());
}
if (pockelCellSetting != null)
{
// Attribute property PockelCellSetting
Channel_element.setAttribute("PockelCellSetting", pockelCellSetting.toString());
}
if (emissionWavelength != null)
{
// Attribute property EmissionWavelength
Channel_element.setAttribute("EmissionWavelength", emissionWavelength.toString());
}
if (ndfilter != null)
{
// Attribute property NDFilter
Channel_element.setAttribute("NDFilter", ndfilter.toString());
}
if (id != null)
{
// Attribute property ID
Channel_element.setAttribute("ID", id.toString());
}
if (samplesPerPixel != null)
{
// Attribute property SamplesPerPixel
Channel_element.setAttribute("SamplesPerPixel", samplesPerPixel.toString());
}
if (lightSourceSettings != null)
{
// Element property LightSourceSettings which is complex (has
// sub-elements)
Channel_element.appendChild(lightSourceSettings.asXMLElement(document));
}
if (otf != null)
{
// Reference property OTFRef
OTFRef o = new OTFRef();
o.setID(otf.getID());
Channel_element.appendChild(o.asXMLElement(document));
}
if (detectorSettings != null)
{
// Element property DetectorSettings which is complex (has
// sub-elements)
Channel_element.appendChild(detectorSettings.asXMLElement(document));
}
if (filterSet != null)
{
// Reference property FilterSetRef
FilterSetRef o = new FilterSetRef();
o.setID(filterSet.getID());
Channel_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());
Channel_element.appendChild(o.asXMLElement(document));
}
}
if (lightPath != null)
{
// Element property LightPath which is complex (has
// sub-elements)
Channel_element.appendChild(lightPath.asXMLElement(document));
}
return super.asXMLElement(document, Channel_element);
}
}