Package com.compomics.util.preferences

Examples of com.compomics.util.preferences.AnnotationPreferences.yAxisZoomExcludesBackgroundPeaks()

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                                                annotationPreferences.getFragmentIonAccuracy(), false, annotationPreferences.isHighResolutionAnnotation());

                                        // add the spectrum annotations
                                        tempSpectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                                        tempSpectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                                        tempSpectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

                                        // add de novo sequencing
                                        tempSpectrumPanel.addAutomaticDeNovoSequencing(peptide, annotations,
                                                forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                                                annotationPreferences.showForwardIonDeNovoTags(),
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                                                false, annotationPreferences.isHighResolutionAnnotation());

                                        // add the spectrum annotations
                                        tempSpectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                                        tempSpectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                                        tempSpectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

                                        // add de novo sequencing
                                        tempSpectrumPanel.addAutomaticDeNovoSequencing(tagAssumption.getTag(), annotations,
                                                forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                                                annotationPreferences.showForwardIonDeNovoTags(),
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                currentSpectrumKey = spectrumMatch.getKey();

                // add the spectrum annotations
                spectrum.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations));
                spectrum.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                spectrum.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

                SearchParameters searchParameters = peptideShakerGUI.getSearchParameters();
                int forwardIon = searchParameters.getIonSearched1();
                int rewindIon = searchParameters.getIonSearched2();
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                            currentSpectrumKey = spectrumKey;

                            // show all or just the annotated peaks
                            spectrumPanel.showAnnotatedPeaksOnly(!annotationPreferences.showAllPeaks());
                            spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(annotationPreferences.yAxisZoomExcludesBackgroundPeaks());

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

                            // add de novo sequencing
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