Examples with PeakIdentity net.sf.mzmine.datamodel.PeakIdentity used on opensource projects

Example 26 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity in project mzmine2 by mzmine.

the class NistMsSearchTask method readSearchResults.

/**
 * Reads the search results file for a given feature list row.
 *
 * @param row the row.
 * @return a list of identities corresponding to the search results, or null if none is found.
 * @throws IOException if and i/o problem occurs.
 */
private List<PeakIdentity> readSearchResults(final PeakListRow row) throws IOException {
    // Search results.
    List<PeakIdentity> hitList = null;
    // Read the results file.
    final BufferedReader reader = new BufferedReader(new FileReader(new File(nistMsSearchDir, SEARCH_RESULTS_FILE_NAME)));
    try {
        // Read results.
        int lineCount = 1;
        String line = reader.readLine();
        while (line != null) {
            // Match the line.
            final Matcher scanMatcher = SEARCH_REGEX.matcher(line);
            final Matcher hitMatcher = HIT_REGEX.matcher(line);
            // Is this the start of a result block?
            if (scanMatcher.matches()) {
                // Is the row ID correct?
                final int rowID = row.getID();
                final int hitID = Integer.parseInt(scanMatcher.group(1));
                if (rowID == hitID) {
                    // Create a new list for the hits.
                    hitList = new ArrayList<PeakIdentity>(1);
                } else {
                    // Search results are for the wrong peak.
                    throw new IllegalArgumentException("Search results are for a different peak.  Expected peak: " + rowID + " but found: " + hitID);
                }
            } else if (hitMatcher.matches()) {
                if (hitList != null) {
                    // Do hit match factors exceed thresholds?
                    final String matchFactor = hitMatcher.group(3);
                    final String reverseMatchFactor = hitMatcher.group(4);
                    if (Integer.parseInt(matchFactor) >= minMatchFactor && Integer.parseInt(reverseMatchFactor) >= minReverseMatchFactor) {
                        // Extract identity from hit information.
                        final SimplePeakIdentity id = new SimplePeakIdentity(hitMatcher.group(1), hitMatcher.group(2), SEARCH_METHOD, hitMatcher.group(7), null);
                        id.setPropertyValue(MATCH_FACTOR_PROPERTY, matchFactor);
                        id.setPropertyValue(REVERSE_MATCH_FACTOR_PROPERTY, reverseMatchFactor);
                        id.setPropertyValue(CAS_PROPERTY, hitMatcher.group(5));
                        id.setPropertyValue(MOLECULAR_WEIGHT_PROPERTY, hitMatcher.group(6));
                        hitList.add(id);
                    }
                } else {
                    throw new IOException("Didn't find start of results block before listing hits at line " + lineCount);
                }
            } else {
                throw new IOException("Unrecognised results file text at line " + lineCount);
            }
            // Read the next line.
            line = reader.readLine();
            lineCount++;
        }
    } finally {
        reader.close();
    }
    return hitList;
}

Example 27 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity in project mzmine2 by mzmine.

the class NistMsSearchTask method writeSpectraFile.

/**
 * Writes a search spectrum file for the given row and its neighbours.
 *
 * @param peakRow the row.
 * @param neighbourRows its neighbouring rows.
 * @return the file.
 * @throws IOException if an i/o problem occurs.
 */
private File writeSpectraFile(final PeakListRow peakRow, final Collection<PeakListRow> neighbourRows) throws IOException {
    final File spectraFile = File.createTempFile(SPECTRA_FILE_PREFIX, SPECTRA_FILE_SUFFIX);
    spectraFile.deleteOnExit();
    final BufferedWriter writer = new BufferedWriter(new FileWriter(spectraFile));
    try {
        LOG.finest("Writing spectra to file " + spectraFile);
        // Write header.
        final PeakIdentity identity = peakRow.getPreferredPeakIdentity();
        final String name = SPECTRUM_NAME_PREFIX + peakRow.getID() + (identity == null ? "" : " (" + identity + ')') + " of " + peakList.getName();
        writer.write("Name: " + name.substring(0, Math.min(SPECTRUM_NAME_MAX_LENGTH, name.length())));
        writer.newLine();
        writer.write("Num Peaks: " + neighbourRows.size());
        writer.newLine();
        for (final PeakListRow row : neighbourRows) {
            final Feature peak = row.getBestPeak();
            final int charge = peak.getCharge();
            final double mass = (peak.getMZ() - ionType.getAddedMass()) * (charge == 0 ? 1.0 : (double) charge);
            writer.write(mass + "\t" + peak.getHeight());
            writer.newLine();
        }
    } finally {
        // Close the open file.
        writer.close();
    }
    return spectraFile;
}

Example 28 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity in project mzmine2 by mzmine.

the class NistMsSearchTask method nistSearch.

/**
 * Run the NIST search.
 *
 * @throws IOException if there are i/o problems.
 */
private void nistSearch() throws IOException {
    // Waiting to get the SEMAPHORE: only one instance of NIST MS Search can
    // run at a time.
    setStatus(TaskStatus.WAITING);
    synchronized (SEMAPHORE) {
        File locatorFile2 = null;
        try {
            if (!isCanceled()) {
                setStatus(TaskStatus.PROCESSING);
                // Configure locator files.
                final File locatorFile1 = new File(nistMsSearchDir, PRIMARY_LOCATOR_FILE_NAME);
                locatorFile2 = getSecondLocatorFile(locatorFile1);
                if (locatorFile2 == null) {
                    throw new IOException("Primary locator file " + locatorFile1 + " doesn't contain the name of a valid file.");
                }
                // Is MS Search already running?
                if (locatorFile2.exists()) {
                    throw new IllegalStateException("NIST MS Search appears to be busy - please wait until it finishes its current task and then try again.  Alternatively, try manually deleting the file " + locatorFile2);
                }
            }
            // Single or multiple row search?
            final PeakListRow[] peakListRows;
            final Map<PeakListRow, Set<PeakListRow>> rowHoods;
            if (peakListRow == null) {
                peakListRows = peakList.getRows();
                rowHoods = groupPeakRows();
            } else {
                peakListRows = new PeakListRow[] { peakListRow };
                rowHoods = new HashMap<PeakListRow, Set<PeakListRow>>(1);
                rowHoods.put(peakListRow, findPeakRowGroup());
            }
            // Reduce neighbourhoods to maximum number of peaks.
            trimNeighbours(rowHoods);
            // Store search results for each neighbourhood - to avoid repeat
            // searches.
            final int numRows = peakListRows.length;
            final Map<Set<PeakListRow>, List<PeakIdentity>> rowIdentities = new HashMap<Set<PeakListRow>, List<PeakIdentity>>(numRows);
            // Search command string.
            final String command = nistMsSearchExe.getAbsolutePath() + ' ' + COMMAND_LINE_ARGS;
            // Perform searches for each feature list row..
            progress = 0;
            progressMax = numRows;
            for (final PeakListRow row : peakListRows) {
                // Get the row's neighbours.
                final Set<PeakListRow> neighbours = rowHoods.get(row);
                // Has this neighbourhood's search been run already?
                if (!rowIdentities.containsKey(neighbours)) {
                    if (!isCanceled()) {
                        // Write spectra file.
                        final File spectraFile = writeSpectraFile(row, neighbours);
                        // Write locator file.
                        writeSecondaryLocatorFile(locatorFile2, spectraFile);
                        // Run the search.
                        runNistMsSearch(command);
                        // Read the search results file and store the
                        // results.
                        rowIdentities.put(neighbours, readSearchResults(row));
                    }
                }
                // Get the search results.
                final List<PeakIdentity> identities = rowIdentities.get(neighbours);
                if (identities != null) {
                    // Add (copy of) identities to peak row.
                    int maxMatchFactor = -1;
                    for (final PeakIdentity identity : identities) {
                        // Copy the identity.
                        final PeakIdentity id = new SimplePeakIdentity((Hashtable<String, String>) identity.getAllProperties());
                        // Best match factor?
                        final boolean isPreferred;
                        final int matchFactor = Integer.parseInt(id.getPropertyValue(MATCH_FACTOR_PROPERTY));
                        if (matchFactor > maxMatchFactor) {
                            maxMatchFactor = matchFactor;
                            isPreferred = true;
                        } else {
                            isPreferred = false;
                        }
                        // Add peak identity.
                        row.addPeakIdentity(id, isPreferred);
                    }
                    // Notify the GUI about the change in the project
                    MZmineCore.getProjectManager().getCurrentProject().notifyObjectChanged(row, false);
                }
                progress++;
            }
        } finally {
            // Clean up.
            if (locatorFile2 != null) {
                locatorFile2.delete();
            }
        }
    }
}

Example 29 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity 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();
    }
}

Example 30 with PeakIdentity

use of net.sf.mzmine.datamodel.PeakIdentity in project mzmine2 by mzmine.

the class PeakListTable method getCellEditor.

public TableCellEditor getCellEditor(int row, int column) {
    CommonColumnType commonColumn = pkTableModel.getCommonColumn(column);
    if (commonColumn == CommonColumnType.IDENTITY) {
        row = this.convertRowIndexToModel(row);
        peakListRow = peakList.getRow(row);
        PeakIdentity[] identities = peakListRow.getPeakIdentities();
        PeakIdentity preferredIdentity = peakListRow.getPreferredPeakIdentity();
        JComboBox<Object> combo;
        if ((identities != null) && (identities.length > 0)) {
            combo = new JComboBox<Object>(identities);
            combo.addItem("-------------------------");
            combo.addItem(REMOVE_IDENTITY);
            combo.addItem(EDIT_IDENTITY);
        } else {
            combo = new JComboBox<Object>();
        }
        combo.setFont(comboFont);
        combo.addItem(NEW_IDENTITY);
        if (preferredIdentity != null) {
            combo.setSelectedItem(preferredIdentity);
        }
        combo.addActionListener(new ActionListener() {

            public void actionPerformed(ActionEvent e) {
                JComboBox<?> combo = (JComboBox<?>) e.getSource();
                Object item = combo.getSelectedItem();
                if (item != null) {
                    if (item.toString() == NEW_IDENTITY) {
                        PeakIdentitySetupDialog dialog = new PeakIdentitySetupDialog(window, peakListRow);
                        dialog.setVisible(true);
                        return;
                    }
                    if (item.toString() == EDIT_IDENTITY) {
                        PeakIdentitySetupDialog dialog = new PeakIdentitySetupDialog(window, peakListRow, peakListRow.getPreferredPeakIdentity());
                        dialog.setVisible(true);
                        return;
                    }
                    if (item.toString() == REMOVE_IDENTITY) {
                        PeakIdentity identity = peakListRow.getPreferredPeakIdentity();
                        if (identity != null) {
                            peakListRow.removePeakIdentity(identity);
                            DefaultComboBoxModel<?> comboModel = (DefaultComboBoxModel<?>) combo.getModel();
                            comboModel.removeElement(identity);
                        }
                        return;
                    }
                    if (item instanceof PeakIdentity) {
                        peakListRow.setPreferredPeakIdentity((PeakIdentity) item);
                        return;
                    }
                }
            }
        });
        // Keep the reference to the editor
        currentEditor = new DefaultCellEditor(combo);
        return currentEditor;
    }
    return super.getCellEditor(row, column);
}