spectrumPanel.addMirroredSpectrum(allSpectra.get(i).getMzValuesAsArray(), allSpectra.get(i).getIntensityValuesNormalizedAsArray(),
500, "2", "", false, peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor(),
peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
spectrumPanel.setAnnotateHighestPeak(!annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)));
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();

int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
</BUG>
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),

spectrumPanel.addMirroredSpectrum(allSpectra.get(i).getMzValuesAsArray(), allSpectra.get(i).getIntensityValuesNormalizedAsArray(),
500, "2", "", false, peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor(),
peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
spectrumPanel.setAnnotateHighestPeak(!annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)));
Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),
