Examples of eu.isas.peptideshaker.utils.DisplayFeaturesGenerator

eu.isas.peptideshaker.utils.DisplayFeaturesGenerator
This class creates the display features needed for the GUI. @author Marc Vaudel @author Harald Barsnes

                            return null;
                        }
                    case 7:
                        if (identification.matchExists(spectrumKey)) {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                return displayFeaturesGenerator.getTaggedPeptideSequence(spectrumMatch, true, true, true);
                            } else if (spectrumMatch.getBestTagAssumption() != null) {
                                //TODO: include fixed ptms
                                return spectrumMatch.getBestTagAssumption().getTag().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), true, true, true, false, false);
                            }
                        }
                        return null;
                    case 8:
                        if (identification.matchExists(spectrumKey)) {
                            SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                            DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                            if (spectrumMatch.getBestPeptideAssumption() != null) {
                                return displayFeaturesGenerator.addDatabaseLinks(spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(
                                        peptideShakerGUI.getSequenceMatchingPreferences()));
                            }
                        }
                        return null;
                    case 9:

View Full Code Here

                String spectrumKey = Spectrum.getSpectrumKey(fileSelected, spectrumFactory.getSpectrumTitles(fileSelected).get(spectrumTable.convertRowIndexToModel(row)));


                // check if we ought to show a tooltip with mod details
                if (identification.matchExists(spectrumKey)) {
                    try {
                        DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                        SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumKey);
                        if (spectrumMatch.getBestPeptideAssumption() != null) {
                            String tooltip = displayFeaturesGenerator.getPeptideModificationTooltipAsHtml(spectrumMatch);
                            spectrumTable.setToolTipText(tooltip);
                        } else if (spectrumMatch.getBestTagAssumption() != null) {
                            TagAssumption tagAssumption = spectrumMatch.getBestTagAssumption();
                            spectrumTable.setToolTipText(peptideShakerGUI.getDisplayFeaturesGenerator().getTagModificationTooltipAsHtml(tagAssumption.getTag()));
                        } else {

View Full Code Here

                    SpectrumMatch spectrumMatch = identification.getSpectrumMatch(key);
                    PSParameter probabilities = new PSParameter();
                    probabilities = (PSParameter) identification.getSpectrumMatchParameter(key, probabilities);


                    // fill peptide shaker table
                    DisplayFeaturesGenerator displayFeaturesGenerator = peptideShakerGUI.getDisplayFeaturesGenerator();
                    String proteins = "";
                    String sequence;
                    if (spectrumMatch.getBestPeptideAssumption() != null) {
                        proteins = displayFeaturesGenerator.addDatabaseLinks(spectrumMatch.getBestPeptideAssumption().getPeptide().getParentProteins(peptideShakerGUI.getSequenceMatchingPreferences()));
                        sequence = displayFeaturesGenerator.getTaggedPeptideSequence(spectrumMatch, true, true, true);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getPeptideModificationTooltipAsHtml(spectrumMatch);
                    } else if (spectrumMatch.getBestTagAssumption() != null) {
                        sequence = spectrumMatch.getBestTagAssumption().getTag().getTaggedModifiedSequence(peptideShakerGUI.getSearchParameters().getModificationProfile(), true, true, true, false, false);
                        peptideShakerJTablePeptideTooltip = displayFeaturesGenerator.getTagModificationTooltipAsHtml(spectrumMatch.getBestTagAssumption().getTag());
                    } else {
                        throw new IllegalArgumentException("No best hit found for spectrum " + spectrumMatch.getKey());
                    }
                    ((DefaultTableModel) peptideShakerJTable.getModel()).addRow(new Object[]{
                        1,

View Full Code Here


    /**
     * Resets the display features generator.
     */
    public void resetDisplayFeaturesGenerator() {
        displayFeaturesGenerator = new DisplayFeaturesGenerator(getSearchParameters().getModificationProfile(), exceptionHandler);
        displayFeaturesGenerator.setDisplayedPTMs(getDisplayPreferences().getDisplayedPtms());
    }

View Full Code Here

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