Examples with ScanSelection net.sf.mzmine.parameters.parametertypes.selectors.ScanSelection used on opensource projects

Example 11 with ScanSelection

use of net.sf.mzmine.parameters.parametertypes.selectors.ScanSelection in project mzmine2 by mzmine.

the class TICVisualizerModule method runModule.

@Override
@Nonnull
public ExitCode runModule(@Nonnull MZmineProject project, @Nonnull ParameterSet parameters, @Nonnull Collection<Task> tasks) {
    final RawDataFile[] dataFiles = parameters.getParameter(TICVisualizerParameters.DATA_FILES).getValue().getMatchingRawDataFiles();
    final Range<Double> mzRange = parameters.getParameter(TICVisualizerParameters.MZ_RANGE).getValue();
    final ScanSelection scanSelection = parameters.getParameter(TICVisualizerParameters.scanSelection).getValue();
    final TICPlotType plotType = parameters.getParameter(TICVisualizerParameters.PLOT_TYPE).getValue();
    final Feature[] selectionPeaks = parameters.getParameter(TICVisualizerParameters.PEAKS).getValue();
    // Add the window to the desktop only if we actually have any raw
    // data to show.
    boolean weHaveData = false;
    for (RawDataFile dataFile : dataFiles) {
        Scan[] selectedScans = scanSelection.getMatchingScans(dataFile);
        if (selectedScans.length > 0)
            weHaveData = true;
    }
    if (weHaveData) {
        TICVisualizerWindow window = new TICVisualizerWindow(dataFiles, plotType, scanSelection, mzRange, selectionPeaks, ((TICVisualizerParameters) parameters).getPeakLabelMap());
        window.setVisible(true);
    } else {
        MZmineCore.getDesktop().displayErrorMessage(MZmineCore.getDesktop().getMainWindow(), "No scans found");
    }
    return ExitCode.OK;
}

Example 12 with ScanSelection

use of net.sf.mzmine.parameters.parametertypes.selectors.ScanSelection in project mzmine2 by mzmine.

the class PeakSummaryComponent method actionPerformed.

public void actionPerformed(ActionEvent e) {
    String command = e.getActionCommand();
    if (command.equals("SHOW")) {
        String visualizerType = (String) comboShow.getSelectedItem();
        int[] indexesRow = peaksInfoList.getSelectedRows();
        Feature[] selectedPeaks = new Feature[indexesRow.length];
        RawDataFile[] dataFiles = new RawDataFile[indexesRow.length];
        Range<Double> rtRange = null, mzRange = null;
        for (int i = 0; i < indexesRow.length; i++) {
            selectedPeaks[i] = listElementModel.getElementAt(indexesRow[i]);
            dataFiles[i] = selectedPeaks[i].getDataFile();
            if ((rtRange == null) || (mzRange == null)) {
                rtRange = dataFiles[i].getDataRTRange(1);
                mzRange = selectedPeaks[i].getRawDataPointsMZRange();
            } else {
                rtRange = rtRange.span(dataFiles[i].getDataRTRange(1));
                mzRange = mzRange.span(selectedPeaks[i].getRawDataPointsMZRange());
            }
        }
        if (dataFiles.length == 0) {
            return;
        }
        if (visualizerType.equals("Chromatogram")) {
            // Label best peak with preferred identity.
            final Feature bestPeak = row.getBestPeak();
            final PeakIdentity peakIdentity = row.getPreferredPeakIdentity();
            final Map<Feature, String> labelMap = new HashMap<Feature, String>(1);
            if (bestPeak != null && peakIdentity != null) {
                labelMap.put(bestPeak, peakIdentity.getName());
            }
            ScanSelection scanSelection = new ScanSelection(rtRange, 1);
            TICVisualizerModule.showNewTICVisualizerWindow(dataFiles, selectedPeaks, labelMap, scanSelection, TICPlotType.BASEPEAK, mzRange);
            return;
        } else if (visualizerType.equals("Mass spectrum")) {
            for (int i = 0; i < selectedPeaks.length; ++i) {
                final Feature peak = selectedPeaks[i];
                final IsotopePattern ip = peak.getIsotopePattern();
                if (ip != null) {
                    // ------------------------------
                    // Multiply isotope pattern by -1
                    // ------------------------------
                    DataPoint[] newDataPoints = Arrays.stream(ip.getDataPoints()).map(p -> new SimpleDataPoint(p.getMZ(), -p.getIntensity())).toArray(DataPoint[]::new);
                    // ---------------------------
                    // Construct identity spectrum
                    // ---------------------------
                    List<DataPoint> identityDataPoints = new ArrayList<>();
                    PeakIdentity identity = row.getPreferredPeakIdentity();
                    if (identity != null) {
                        String spectrum = identity.getPropertyValue(PeakIdentity.PROPERTY_SPECTRUM);
                        if (spectrum != null && spectrum.length() > 2) {
                            spectrum = spectrum.substring(1, spectrum.length() - 1);
                            for (String strPair : spectrum.split(",")) {
                                String[] pair = strPair.split("=", 2);
                                if (pair.length == 2)
                                    identityDataPoints.add(new SimpleDataPoint(Double.parseDouble(pair[0]), Double.parseDouble(pair[1])));
                            }
                        }
                    }
                    if (// Plot raw spectrum and isotope pattern
                    identityDataPoints.isEmpty())
                        SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber(), null, null, null, new SimpleIsotopePattern(newDataPoints, ip.getStatus(), ip.getDescription()));
                    else
                        // Plot raw spectrum, isotope pattern, and identity spectrum
                        SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber(), null, new SimpleIsotopePattern(identityDataPoints.toArray(new DataPoint[identityDataPoints.size()]), IsotopePatternStatus.DETECTED, identity.getPropertyValue(PeakIdentity.PROPERTY_FORMULA)), null, new SimpleIsotopePattern(newDataPoints, ip.getStatus(), ip.getDescription()));
                } else
                    // Plot raw spectrum without isotope pattern
                    SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], peak.getRepresentativeScanNumber());
            }
        } else if (visualizerType.equals("Peak in 2D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen), peakRTRange.upperEndpoint() + rtLen);
                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen), peakMZRange.upperEndpoint() + mzLen);
                TwoDVisualizerModule.show2DVisualizerSetupDialog(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("Peak in 3D")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                Range<Double> peakRTRange = selectedPeaks[i].getRawDataPointsRTRange();
                Range<Double> peakMZRange = selectedPeaks[i].getRawDataPointsMZRange();
                final double rtLen = peakRTRange.upperEndpoint() - peakRTRange.lowerEndpoint();
                Range<Double> localRTRange = Range.closed(Math.max(0, peakRTRange.lowerEndpoint() - rtLen), peakRTRange.upperEndpoint() + rtLen);
                final double mzLen = peakMZRange.upperEndpoint() - peakMZRange.lowerEndpoint();
                Range<Double> localMZRange = Range.closed(Math.max(0, peakMZRange.lowerEndpoint() - mzLen), peakMZRange.upperEndpoint() + mzLen);
                Fx3DVisualizerModule.setupNew3DVisualizer(dataFiles[i], localMZRange, localRTRange);
            }
        } else if (visualizerType.equals("MS/MS")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                int scanNumber = selectedPeaks[i].getMostIntenseFragmentScanNumber();
                if (scanNumber > 0) {
                    SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], scanNumber);
                } else {
                    JFrame frame = (JFrame) SwingUtilities.getAncestorOfClass(JFrame.class, this);
                    MZmineCore.getDesktop().displayMessage(frame, "There is no fragment for the mass " + MZmineCore.getConfiguration().getMZFormat().format(selectedPeaks[i].getMZ()) + "m/z in the current raw data.");
                    return;
                }
            }
        } else if (visualizerType.equals("Isotope pattern")) {
            for (int i = 0; i < selectedPeaks.length; i++) {
                IsotopePattern ip = selectedPeaks[i].getIsotopePattern();
                if (ip == null) {
                    return;
                }
                SpectraVisualizerModule.showNewSpectrumWindow(dataFiles[i], selectedPeaks[i].getMostIntenseFragmentScanNumber(), ip);
            }
        }
        return;
    }
    if (command.equals("CHANGE")) {
        int indexRow = peaksInfoList.getSelectedRow();
        if (indexRow == -1) {
            return;
        }
        Feature selectedPeak = listElementModel.getElementAt(indexRow);
        ManualPeakPickerModule.runManualDetection(selectedPeak.getDataFile(), row, null, null);
        return;
    }
}

Example 13 with ScanSelection

use of net.sf.mzmine.parameters.parametertypes.selectors.ScanSelection in project mzmine2 by mzmine.

the class FeatureOverviewWindow method addTicPlot.

private JSplitPane addTicPlot(PeakListRow row) {
    JSplitPane pane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT);
    // labels for TIC visualizer
    Map<Feature, String> labelsMap = new HashMap<Feature, String>(0);
    // scan selection
    ScanSelection scanSelection = new ScanSelection(rawFiles[0].getDataRTRange(1), 1);
    // mz range
    Range<Double> mzRange = null;
    mzRange = feature.getRawDataPointsMZRange();
    // optimize output by extending the range
    double upper = mzRange.upperEndpoint();
    double lower = mzRange.lowerEndpoint();
    double fiveppm = (upper * 5E-6);
    mzRange = Range.closed(lower - fiveppm, upper + fiveppm);
    // labels
    labelsMap.put(feature, feature.toString());
    TICVisualizerWindow window = new // raw
    TICVisualizerWindow(// raw
    rawFiles, // plot type
    TICPlotType.BASEPEAK, // scan selection
    scanSelection, // mz range
    mzRange, // selected features
    row.getPeaks(), // labels
    labelsMap);
    pane.add(window.getTICPlot());
    pane.add(window.getToolBar());
    pane.setResizeWeight(1);
    pane.setDividerSize(1);
    pane.setBorder(BorderFactory.createLineBorder(Color.black));
    return pane;
}

Example 14 with ScanSelection

use of net.sf.mzmine.parameters.parametertypes.selectors.ScanSelection in project mzmine2 by mzmine.

the class PeakListTablePopupMenu method actionPerformed.

@Override
public void actionPerformed(final ActionEvent e) {
    final Object src = e.getSource();
    if (deleteRowsItem.equals(src)) {
        final int[] rowsToDelete = table.getSelectedRows();
        final int[] unsortedIndexes = new int[rowsToDelete.length];
        for (int i = rowsToDelete.length - 1; i >= 0; i--) {
            unsortedIndexes[i] = table.convertRowIndexToModel(rowsToDelete[i]);
        }
        // sort row indexes and start removing from the last
        Arrays.sort(unsortedIndexes);
        // delete the rows starting from last
        for (int i = unsortedIndexes.length - 1; i >= 0; i--) {
            peakList.removeRow(unsortedIndexes[i]);
        }
        // Notify the GUI that peaklist contents have changed
        updateTableGUI();
    }
    if (plotRowsItem.equals(src)) {
        final int[] selectedTableRows = table.getSelectedRows();
        final PeakListRow[] selectedRows = new PeakListRow[selectedTableRows.length];
        for (int i = 0; i < selectedTableRows.length; i++) {
            selectedRows[i] = getPeakListRow(table.convertRowIndexToModel(selectedTableRows[i]));
        }
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                IntensityPlotModule.showIntensityPlot(MZmineCore.getProjectManager().getCurrentProject(), peakList, selectedRows);
            }
        });
    }
    if (showXICItem.equals(src) && allClickedPeakListRows.length != 0) {
        // Map peaks to their identity labels.
        final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);
        final RawDataFile selectedDataFile = clickedDataFile == null ? allClickedPeakListRows[0].getBestPeak().getDataFile() : clickedDataFile;
        Range<Double> mzRange = null;
        final List<Feature> selectedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        for (final PeakListRow row : allClickedPeakListRows) {
            for (final Feature peak : row.getPeaks()) {
                if (mzRange == null) {
                    mzRange = peak.getRawDataPointsMZRange();
                    double upper = mzRange.upperEndpoint();
                    double lower = mzRange.lowerEndpoint();
                    if ((upper - lower) < 0.000001) {
                        // Workaround to make ultra narrow mzRanges (e.g. from imported mzTab peaklist),
                        // a more reasonable default for a HRAM instrument (~5ppm)
                        double fiveppm = (upper * 5E-6);
                        mzRange = Range.closed(lower - fiveppm, upper + fiveppm);
                    }
                } else {
                    mzRange = mzRange.span(peak.getRawDataPointsMZRange());
                }
            }
            final Feature filePeak = row.getPeak(selectedDataFile);
            if (filePeak != null) {
                selectedPeaks.add(filePeak);
                // Label the peak with the row's preferred identity.
                final PeakIdentity identity = row.getPreferredPeakIdentity();
                if (identity != null) {
                    labelsMap.put(filePeak, identity.getName());
                }
            }
        }
        ScanSelection scanSelection = new ScanSelection(selectedDataFile.getDataRTRange(1), 1);
        TICVisualizerModule.showNewTICVisualizerWindow(new RawDataFile[] { selectedDataFile }, selectedPeaks.toArray(new Feature[selectedPeaks.size()]), labelsMap, scanSelection, TICPlotType.BASEPEAK, mzRange);
    }
    if (showXICSetupItem.equals(src) && allClickedPeakListRows.length != 0) {
        // Map peaks to their identity labels.
        final Map<Feature, String> labelsMap = new HashMap<Feature, String>(allClickedPeakListRows.length);
        final RawDataFile[] selectedDataFiles = clickedDataFile == null ? peakList.getRawDataFiles() : new RawDataFile[] { clickedDataFile };
        Range<Double> mzRange = null;
        final ArrayList<Feature> allClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        final ArrayList<Feature> selectedClickedPeaks = new ArrayList<Feature>(allClickedPeakListRows.length);
        for (final PeakListRow row : allClickedPeakListRows) {
            // Label the peak with the row's preferred identity.
            final PeakIdentity identity = row.getPreferredPeakIdentity();
            for (final Feature peak : row.getPeaks()) {
                allClickedPeaks.add(peak);
                if (peak.getDataFile() == clickedDataFile) {
                    selectedClickedPeaks.add(peak);
                }
                if (mzRange == null) {
                    mzRange = peak.getRawDataPointsMZRange();
                } else {
                    mzRange = mzRange.span(peak.getRawDataPointsMZRange());
                }
                if (identity != null) {
                    labelsMap.put(peak, identity.getName());
                }
            }
        }
        ScanSelection scanSelection = new ScanSelection(selectedDataFiles[0].getDataRTRange(1), 1);
        TICVisualizerModule.setupNewTICVisualizer(MZmineCore.getProjectManager().getCurrentProject().getDataFiles(), selectedDataFiles, allClickedPeaks.toArray(new Feature[allClickedPeaks.size()]), selectedClickedPeaks.toArray(new Feature[selectedClickedPeaks.size()]), labelsMap, scanSelection, mzRange);
    }
    if (show2DItem.equals(src)) {
        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {
            TwoDVisualizerModule.show2DVisualizerSetupDialog(showPeak.getDataFile(), getPeakMZRange(showPeak), getPeakRTRange(showPeak));
        }
    }
    if (show3DItem.equals(src)) {
        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {
            Fx3DVisualizerModule.setupNew3DVisualizer(showPeak.getDataFile(), getPeakMZRange(showPeak), getPeakRTRange(showPeak), showPeak);
        }
    }
    if (manuallyDefineItem.equals(src)) {
        // ManualPeakPickerModule.runManualDetection(clickedDataFile, clickedPeakListRow, peakList,
        // table);
        XICManualPickerModule.runManualDetection(clickedDataFile, clickedPeakListRow, peakList, table);
    }
    if (showSpectrumItem.equals(src)) {
        final Feature showPeak = getSelectedPeak();
        if (showPeak != null) {
            SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), showPeak.getRepresentativeScanNumber(), showPeak);
        }
    }
    if (openCompoundIdUrl.equals(src)) {
        if (clickedPeakListRow != null && clickedPeakListRow.getPreferredPeakIdentity() != null) {
            String url = clickedPeakListRow.getPreferredPeakIdentity().getPropertyValue(PeakIdentity.PROPERTY_URL);
            if (url != null && !url.isEmpty() && Desktop.isDesktopSupported()) {
                try {
                    Desktop.getDesktop().browse(new URI(url));
                } catch (IOException | URISyntaxException e1) {
                }
            }
        }
    }
    if (showMSMSItem.equals(src)) {
        if (allClickedPeakListRows != null && allClickedPeakListRows.length > 1) {
            // show multi msms window of multiple rows
            MultiMSMSWindow multi = new MultiMSMSWindow();
            multi.setData(allClickedPeakListRows, peakList.getRawDataFiles(), clickedDataFile, true, SortingProperty.MZ, SortingDirection.Ascending);
            multi.setVisible(true);
        } else {
            Feature showPeak = getSelectedPeakForMSMS();
            if (showPeak != null) {
                final int scanNumber = showPeak.getMostIntenseFragmentScanNumber();
                if (scanNumber > 0) {
                    SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), scanNumber);
                } else {
                    MZmineCore.getDesktop().displayMessage(window, "There is no fragment for " + MZmineCore.getConfiguration().getMZFormat().format(showPeak.getMZ()) + " m/z in the current raw data.");
                }
            }
        }
    }
    // mirror of the two best fragment scans
    if (showMSMSMirrorItem.equals(src)) {
        if (allClickedPeakListRows != null && allClickedPeakListRows.length == 2) {
            PeakListRow a = allClickedPeakListRows[0];
            PeakListRow b = allClickedPeakListRows[1];
            Scan scan = a.getBestFragmentation();
            Scan mirror = b.getBestFragmentation();
            if (scan != null && mirror != null) {
                // show mirror msms window of two rows
                MirrorScanWindow mirrorWindow = new MirrorScanWindow();
                mirrorWindow.setScans(scan, mirror);
                mirrorWindow.setVisible(true);
            }
        }
    }
    // show spectral db matches
    if (showSpectralDBResults.equals(src)) {
        List<SpectralDBPeakIdentity> spectralID = Arrays.stream(clickedPeakListRow.getPeakIdentities()).filter(pi -> pi instanceof SpectralDBPeakIdentity).map(pi -> ((SpectralDBPeakIdentity) pi)).collect(Collectors.toList());
        if (!spectralID.isEmpty()) {
            SpectraIdentificationResultsWindow window = new SpectraIdentificationResultsWindow();
            window.addMatches(spectralID);
            window.setTitle("Matched " + spectralID.size() + " compounds for feature list row" + clickedPeakListRow.getID());
            window.setVisible(true);
        }
    }
    if (showAllMSMSItem.equals(src)) {
        final Feature showPeak = getSelectedPeakForMSMS();
        RawDataFile raw = clickedPeakListRow.getBestFragmentation().getDataFile();
        if (showPeak != null && showPeak.getMostIntenseFragmentScanNumber() != 0)
            raw = showPeak.getDataFile();
        if (clickedPeakListRow.getBestFragmentation() != null) {
            MultiSpectraVisualizerWindow multiSpectraWindow = new MultiSpectraVisualizerWindow(clickedPeakListRow, raw);
            multiSpectraWindow.setVisible(true);
        } else {
            MZmineCore.getDesktop().displayMessage(window, "There is no fragment for " + MZmineCore.getConfiguration().getMZFormat().format(showPeak.getMZ()) + " m/z in the current raw data.");
        }
    }
    if (showIsotopePatternItem.equals(src)) {
        final Feature showPeak = getSelectedPeak();
        if (showPeak != null && showPeak.getIsotopePattern() != null) {
            SwingUtilities.invokeLater(new Runnable() {

                @Override
                public void run() {
                    SpectraVisualizerModule.showNewSpectrumWindow(showPeak.getDataFile(), showPeak.getRepresentativeScanNumber(), showPeak.getIsotopePattern());
                }
            });
        }
    }
    if (formulaItem != null && formulaItem.equals(src)) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                FormulaPredictionModule.showSingleRowIdentificationDialog(clickedPeakListRow);
            }
        });
    }
    // peak.
    if (siriusItem != null && siriusItem.equals(src)) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                SiriusProcessingModule.showSingleRowIdentificationDialog(clickedPeakListRow);
            }
        });
    }
    if (onlineDbSearchItem != null && onlineDbSearchItem.equals(src)) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                OnlineDBSearchModule.showSingleRowIdentificationDialog(clickedPeakListRow);
            }
        });
    }
    if (spectralDbSearchItem != null && spectralDbSearchItem.equals(src)) {
        SwingUtilities.invokeLater(new Runnable() {

            @Override
            public void run() {
                LocalSpectralDBSearchModule.showSelectedRowsIdentificationDialog(allClickedPeakListRows, table);
            }
        });
    }
    if (nistSearchItem != null && nistSearchItem.equals(src)) {
        NistMsSearchModule.singleRowSearch(peakList, clickedPeakListRow);
    }
    if (addNewRowItem.equals(src)) {
        // find maximum ID and add 1
        int newID = 1;
        for (final PeakListRow row : peakList.getRows()) {
            if (row.getID() >= newID) {
                newID = row.getID() + 1;
            }
        }
        // create a new row
        final PeakListRow newRow = new SimplePeakListRow(newID);
        ManualPeakPickerModule.runManualDetection(peakList.getRawDataFiles(), newRow, peakList, table);
    }
    if (showPeakRowSummaryItem.equals(src)) {
        PeakSummaryVisualizerModule.showNewPeakSummaryWindow(clickedPeakListRow);
    }
    if (exportIsotopesItem.equals(src)) {
        IsotopePatternExportModule.exportIsotopePattern(clickedPeakListRow);
    }
    if (exportToSirius.equals(src)) {
        // export all selected rows
        SiriusExportModule.exportSingleRows(allClickedPeakListRows);
    }
    if (exportMSMSLibrary.equals(src)) {
        // open window with all selected rows
        MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
        libraryWindow.setData(allClickedPeakListRows, SortingProperty.MZ, SortingDirection.Ascending, true);
        libraryWindow.setVisible(true);
    }
    if (exportMS1Library.equals(src)) {
        // open window with all selected rows
        MSMSLibrarySubmissionWindow libraryWindow = new MSMSLibrarySubmissionWindow();
        libraryWindow.setData(allClickedPeakListRows, SortingProperty.MZ, SortingDirection.Ascending, false);
        libraryWindow.setVisible(true);
    }
    if (exportMSMSItem.equals(src)) {
        MSMSExportModule.exportMSMS(clickedPeakListRow);
    }
    if (clearIdsItem.equals(src)) {
        // Delete identities of selected rows.
        for (final PeakListRow row : allClickedPeakListRows) {
            // Selected row index.
            for (final PeakIdentity id : row.getPeakIdentities()) {
                // Remove id.
                row.removePeakIdentity(id);
            }
        }
        // Update table GUI.
        updateTableGUI();
    }
    if (copyIdsItem.equals(src) && allClickedPeakListRows.length > 0) {
        final PeakIdentity id = allClickedPeakListRows[0].getPreferredPeakIdentity();
        if (id != null) {
            copiedId = (PeakIdentity) id.clone();
        }
    }
    if (pasteIdsItem.equals(src) && copiedId != null) {
        // Paste identity into selected rows.
        for (final PeakListRow row : allClickedPeakListRows) {
            row.setPreferredPeakIdentity((PeakIdentity) copiedId.clone());
        }
        // Update table GUI.
        updateTableGUI();
    }
}