3b15cb8269b0d8375d98db031cf30ea490acc0d3,src/main/java/eu/isas/peptideshaker/gui/tabpanels/OverviewPanel.java,OverviewPanel,updateSpectrum,#number#boolean#,4695

Before Change


                            spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

                            int forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched1();
                            int rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getIonSearched2();

                            // add de novo sequencing
                            spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations,

After Change


                            spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

                            Integer forwardIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getForwardIons().get(0);
                            Integer rewindIon = peptideShakerGUI.getIdentificationParameters().getSearchParameters().getRewindIons().get(0);

                            // add de novo sequencing
                            spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations,