ArrayList<IonMatch> annotations = peptideShakerGUI.getSpectrumAnnotator().getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, peptide);
spectrum.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrum.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrum.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
<BUG>int forwardIon = searchParameters.getIonSearched1();

int rewindIon = searchParameters.getIonSearched2();
</BUG>
spectrum.addAutomaticDeNovoSequencing(peptide, annotations,

ArrayList<IonMatch> annotations = peptideShakerGUI.getSpectrumAnnotator().getSpectrumAnnotation(annotationPreferences, specificAnnotationPreferences, currentSpectrum, peptide);
spectrum.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), !annotationPreferences.isHighResolutionAnnotation());
spectrum.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
spectrum.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
Integer forwardIon = searchParameters.getForwardIons().get(0);
Integer rewindIon = searchParameters.getRewindIons().get(0);
spectrum.addAutomaticDeNovoSequencing(peptide, annotations,
