*/
private void insertBarCharts() {
AnnotationPreferences annotationPreferences = peptideShakerGUI.getAnnotationPreferences();
PtmtableContent tempContent, tableContent = new PtmtableContent();
MSnSpectrum spectrum;
SpectrumMatch spectrumMatch;
SpectrumFactory spectrumFactory = SpectrumFactory.getInstance();
PTMFactory ptmFactory = PTMFactory.getInstance();
String ptmName = ptm.getName(), shortName = ptmFactory.getShortName(ptmName);
for (String spectrumKey : spectrumKeys) {
try {
spectrum = (MSnSpectrum) spectrumFactory.getSpectrum(spectrumKey);
spectrumMatch = peptideShakerGUI.getIdentification().getSpectrumMatch(spectrumKey);
tempContent = PtmtableContent.getPTMTableContent(peptide, ptm, nPTM, spectrum, annotationPreferences.getIonTypes(),
annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges(),
spectrumMatch.getBestPeptideAssumption().getIdentificationCharge().value,
annotationPreferences.getFragmentIonAccuracy(), spectrum.getIntensityLimit(annotationPreferences.getAnnotationIntensityLimit()));
tempContent.normalize();
tableContent.addAll(tempContent);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}