spectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakColor());
spectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakWidth());
spectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakWidth());
spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();

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

spectrumPanel.setPeakWaterMarkColor(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakColor());
spectrumPanel.setPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedPeakWidth());
spectrumPanel.setBackgroundPeakWidth(peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumBackgroundPeakWidth());
spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),
