ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, currentPeptide);
spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.rescale(lowerMzZoomRange, upperMzZoomRange);
spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
<BUG>int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();

int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
</BUG>
spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations,

ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, currentPeptide);
spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.rescale(lowerMzZoomRange, upperMzZoomRange);
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(currentPeptide, annotations,
