3b15cb8269b0d8375d98db031cf30ea490acc0d3,src/main/java/eu/isas/peptideshaker/gui/tabpanels/OverviewPanel.java,OverviewPanel,updateBubblePlot,#,4018
Before Change
spectrumPanel.setAnnotateHighestPeak(!annotationPreferences.isHighResolutionAnnotation());
spectrumPanel.setAnnotationsMirrored(SpectrumAnnotator.getSpectrumAnnotation(allAnnotations.get(i)));
int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();
int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();
spectrumPanel.addAutomaticDeNovoSequencing(peptides.get(i), allAnnotations.get(i),
forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
After Change
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),
forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),