public boolean linkAnnotation(Annotation o) {
o.linkScreen(this);
if (!annotationLinks.contains(o)) {
return annotationLinks.add(o);
}
return false;
}
public boolean link(Reference reference, OMEModelObject o) {
boolean wasHandledBySuperClass = super.link(reference, o);
if (wasHandledBySuperClass) {
return true;
}
if (reference instanceof PlateRef) {
Plate o_casted = (Plate) o;
o_casted.linkScreen(this);
if (!plateLinks.contains(o_casted)) {
plateLinks.add(o_casted);
}
return true;
}
if (reference instanceof AnnotationRef) {
Annotation o_casted = (Annotation) o;
o_casted.linkScreen(this);
if (!annotationLinks.contains(o_casted)) {
annotationLinks.add(o_casted);
}
return true;
}
LOGGER.debug("Unable to handle reference of type: {}", reference.getClass());
return false;
}
/**
* Updates DoubleAnnotation 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 (!"DoubleAnnotation".equals(tagName)) {
LOGGER.debug("Expecting node name of DoubleAnnotation got {}", tagName);
}
List<Element> Value_nodeList = getChildrenByTagName(element, "Value");
if (Value_nodeList.size() > 1) {
// TODO: Should be its own Exception
throw new RuntimeException(
String.format("Value node list size %d != 1", Value_nodeList.size()));
} else if (Value_nodeList.size() != 0) {
// Element property Value which is not complex (has no
// sub-elements)
setValue(Double.valueOf(Value_nodeList.get(0).getTextContent()));
}
}
protected Element asXMLElement(Document document, Element Screen_element) {
// Creating XML block for Screen
if (Screen_element == null) {
Screen_element = document.createElementNS(NAMESPACE, "Screen");
}
if (name != null) {
// Attribute property Name
Screen_element.setAttribute("Name", name.toString());
}
if (protocolDescription != null) {
// Attribute property ProtocolDescription
Screen_element.setAttribute("ProtocolDescription", protocolDescription.toString());
}
if (protocolIdentifier != null) {
// Attribute property ProtocolIdentifier
Screen_element.setAttribute("ProtocolIdentifier", protocolIdentifier.toString());
}
if (reagentSetDescription != null) {
// Attribute property ReagentSetDescription
Screen_element.setAttribute("ReagentSetDescription", reagentSetDescription.toString());
}
if (type != null) {
// Attribute property Type
Screen_element.setAttribute("Type", type.toString());
}
if (id != null) {
// Attribute property ID
Screen_element.setAttribute("ID", id.toString());
}
if (reagentSetIdentifier != null) {
// Attribute property ReagentSetIdentifier
Screen_element.setAttribute("ReagentSetIdentifier", reagentSetIdentifier.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());
Screen_element.appendChild(description_element);
}
if (reagents != null) {
// Element property Reagent which is complex (has
// sub-elements) and occurs more than once
for (Reagent reagents_value : reagents) {
Screen_element.appendChild(reagents_value.asXMLElement(document));
}
}
if (plateLinks != null) {
// Reference property PlateRef which occurs more than once
for (Plate plateLinks_value : plateLinks) {
PlateRef o = new PlateRef();
o.setID(plateLinks_value.getID());
Screen_element.appendChild(o.asXMLElement(document));
}
}
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());
Screen_element.appendChild(o.asXMLElement(document));
}
}
return super.asXMLElement(document, Screen_element);
}
public boolean unlinkAnnotation(Annotation o) {
o.unlinkScreen(this);
return annotationLinks.remove(o);
}
