Package com.compomics.util.preferences

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

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

                                        peptideShakerGUI.updateAnnotationMenus(currentPeptideAssumption.getIdentificationCharge().value, peptide.getModificationMatches());

                                        // update the spectrum title
                                        String modifiedSequence = peptide.getTaggedModifiedSequence(modificationProfile, false, false, true);
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                                        // add de novo sequencing
                                        tempSpectrumPanel.addAutomaticDeNovoSequencing(tagAssumption.getTag(), annotations,
                                                forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                                                annotationPreferences.showForwardIonDeNovoTags(),
                                                annotationPreferences.showRewindIonDeNovoTags());

                                        // get the modifications for the tag
                                        ArrayList<ModificationMatch> modificationMatches = new ArrayList<ModificationMatch>();

                                        for (TagComponent tagComponent : tagAssumption.getTag().getContent()) {
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                // add de novo sequencing
                spectrum.addAutomaticDeNovoSequencing(peptide, annotations,
                        forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                        annotationPreferences.showForwardIonDeNovoTags(),
                        annotationPreferences.showRewindIonDeNovoTags());

                spectrumChartJPanel.add(spectrum);
                peptideShakerGUI.updateAnnotationMenus(identificationCharge, peptide.getModificationMatches());

                ((TitledBorder) spectrumAndFragmentIonPanel.getBorder()).setTitle(
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                            // add de novo sequencing
                            spectrumPanel.addAutomaticDeNovoSequencing(currentPeptide, annotations,
                                    forwardIon, rewindIon, annotationPreferences.getDeNovoCharge(),
                                    annotationPreferences.showForwardIonDeNovoTags(),
                                    annotationPreferences.showRewindIonDeNovoTags());

                            // add the spectrum panel to the frame
                            spectrumJPanel.removeAll();
                            spectrumJPanel.add(spectrumPanel);
                            spectrumJPanel.revalidate();
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