return peptideAssumption.getIsotopeNumber(precursor.getMz()) + "";
case mz:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
return precursor.getMz() + "";
case total_spectrum_intensity:
Spectrum spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
return spectrum.getTotalIntensity() + "";
case max_intensity:
spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
return spectrum.getMaxIntensity() + "";
case intensity_coverage:
spectrum = SpectrumFactory.getInstance().getSpectrum(spectrumKey);
double coveredIntensity = 0;
Peptide peptide = peptideAssumption.getPeptide();
ArrayList<IonMatch> matches = peptideSpectrumAnnotator.getSpectrumAnnotation(
annotationPreferences.getIonTypes(), annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
peptideAssumption.getIdentificationCharge().value,
(MSnSpectrum) spectrum, peptide, 0, searchParameters.getFragmentIonAccuracy(), false, true);
for (IonMatch ionMatch : matches) {
coveredIntensity += ionMatch.peak.intensity;
}
double coverage = 100 * coveredIntensity / spectrum.getTotalIntensity();
return coverage + "";
case mz_error:
precursor = SpectrumFactory.getInstance().getPrecursor(spectrumKey);
return peptideAssumption.getDeltaMass(precursor.getMz(), true) + "";
case rt: