/**
* Overriding clone, used to do deep copy of jaxb elements that implement Copyable. Otherwise,
* just a shallow copy.
*
* @see java.lang.Object#clone()
*/
@Override
@SuppressWarnings("unchecked")
public Object clone() {
GenericDefaultValue<E> o = (GenericDefaultValue<E>) super.clone();
// jaxb copyable
if (value instanceof CopyTo) {
E val;
try {
val = (E) value.getClass().newInstance();
} catch (Exception e) {
log.warn("Could not create new instance of value, doing a shallow copy");
return o;
}
((CopyTo) value).copyTo(val);
// log.debug("Copied value from '"+value+"' to '"+val+"'");// TODO locale
o.setValue(val);
return o;
} else {
return o;
}
}
@SuppressWarnings("unchecked")
@Override
protected void parseFile(String[] argFileString, IMetadataFieldSet argDefaultFields)
throws InvalidDendroFileException {
defaults = (TrimsToTridasDefaults) argDefaultFields;
// TODO run the 'metadata' through the defaults, as
// the user may have specified his own metadata
// Extract 'metadata' ;-)
String userid = argFileString[0].trim();
SafeIntYear startYear = null;
try {
startYear = new SafeIntYear(argFileString[2].trim());
} catch (NumberFormatException e) {
}
// Extract data
ArrayList<TridasValue> ringWidthValues = new ArrayList<TridasValue>();
for (int i = 3; i < argFileString.length; i++) {
TridasValue v = new TridasValue();
if (argFileString[i].startsWith(" ")) {
if (argFileString[i].trim().equals("999")) {
break;
}
v.setValue(argFileString[i].trim());
ringWidthValues.add(v);
log.debug("value = " + String.valueOf(argFileString[i]));
} else {
throw new InvalidDendroFileException(I18n.getText("trims.expectingSpace"), i);
}
}
// Now build up our measurementSeries
TridasMeasurementSeries series = defaults.getMeasurementSeriesWithDefaults();
TridasUnit units = new TridasUnit();
// Set units to 1/100th mm. Is this always the case?
units.setNormalTridas(NormalTridasUnit.HUNDREDTH_MM);
// Build identifier for series
TridasIdentifier seriesId = new ObjectFactory().createTridasIdentifier();
seriesId.setValue(UUID.randomUUID().toString());
seriesId.setDomain(
defaults.getDefaultValue(TridasMandatoryField.IDENTIFIER_DOMAIN).getStringValue());
// Build interpretation group for series
TridasInterpretation interp = new TridasInterpretation();
interp.setFirstYear(startYear.toTridasYear(DatingSuffix.AD));
interp.setLastYear(startYear.add(ringWidthValues.size() - 1).toTridasYear(DatingSuffix.AD));
// Add values to nested value(s) tags
TridasValues valuesGroup = new TridasValues();
valuesGroup.setValues(ringWidthValues);
valuesGroup.setUnit(units);
GenericDefaultValue<TridasVariable> variable =
(GenericDefaultValue<TridasVariable>)
defaults.getDefaultValue(TridasMandatoryField.MEASUREMENTSERIES_VARIABLE);
valuesGroup.setVariable(variable.getValue());
ArrayList<TridasValues> valuesGroupList = new ArrayList<TridasValues>();
valuesGroupList.add(valuesGroup);
// Add all the data to the series
series.setValues(valuesGroupList);
series.setInterpretation(interp);
series.setIdentifier(seriesId);
series.setLastModifiedTimestamp(DateUtils.getTodaysDateTime());
series.setDendrochronologist(userid);
// Add series to our list
mseriesList.add(series);
}