/** finish handling and set up the enclosed object Usually called when the end tag is seen */
@Override
public void finishProcessing() {
IMeasuredSpectrum pMeasured = null;
final double pScore = getScore();
final double pHyperScore = getHyperScore();
final double rawScore = getRawScore();
IonTypeScorer scorer = getIonScore();
IProteinPosition[] containedInProteins = m_Positions.toArray(IProteinPosition.EMPTY_ARRAY);
((Polypeptide) m_Peptide).setContainedInProteins(containedInProteins);
SpectralMatch scan =
new SpectralMatch(m_Peptide, pMeasured, pScore, pHyperScore, rawScore, scorer, null);
if (m_Usage != null) scan.getUsage().addTo(m_Usage);
setElementObject(scan);
}
@Override
public void endElement(String elx, String localName, String el) throws SAXException {
if ("IonScore".equals(el)) {
IonScoreHandler handler = (IonScoreHandler) getHandler().popCurrentHandler();
m_IonScore.set(handler.getElementObject());
return;
}
if ("ProteinPosition".equals(el)) {
ProteinPositionHandler handler = (ProteinPositionHandler) getHandler().popCurrentHandler();
m_Positions.add(handler.getElementObject());
return;
}
if ("usage".equals(el)) {
String txt = getIncludedText();
m_Usage = SpectralPeakUsage.deserializeUsage(txt);
return;
}
super.endElement(elx, localName, el);
}