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

Example 81 with PeakList

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

the class ProjectSavingTask method savePeakLists.

/**
 * Save the feature lists
 *
 * @throws SAXException
 * @throws TransformerConfigurationException
 */
private void savePeakLists(ZipOutputStream zipStream) throws IOException, TransformerConfigurationException, SAXException {
    PeakList[] peakLists = savedProject.getPeakLists();
    for (int i = 0; i < peakLists.length; i++) {
        if (isCanceled())
            return;
        logger.info("Saving feature list: " + peakLists[i].getName());
        String peakListSavedName = "Peak list #" + (i + 1) + " " + peakLists[i].getName();
        zipStream.putNextEntry(new ZipEntry(peakListSavedName + ".xml"));
        peakListSaveHandler = new PeakListSaveHandler(zipStream, dataFilesIDMap);
        currentSavedObjectName = peakLists[i].getName();
        peakListSaveHandler.savePeakList(peakLists[i]);
        finishedSaveItems++;
    }
}

Example 82 with PeakList

use of net.sf.mzmine.datamodel.PeakList 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 83 with PeakList

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

the class IntensityPlotParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    PeakList[] selectedPeakLists = getParameter(peakList).getValue().getMatchingPeakLists();
    if (selectedPeakLists.length > 0) {
        RawDataFile[] plDataFiles = selectedPeakLists[0].getRawDataFiles();
        PeakListRow[] plRows = selectedPeakLists[0].getRows();
        Arrays.sort(plRows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
        getParameter(dataFiles).setChoices(plDataFiles);
        getParameter(dataFiles).setValue(plDataFiles);
    }
    return super.showSetupDialog(parent, valueCheckRequired);
}

Example 84 with PeakList

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

the class KendrickMassPlotParameters method showSetupDialog.

@Override
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
    PeakList[] selectedPeakLists = getParameter(peakList).getValue().getMatchingPeakLists();
    if (selectedPeakLists.length > 0) {
        PeakListRow[] plRows = selectedPeakLists[0].getRows();
        Arrays.sort(plRows, new PeakListRowSorter(SortingProperty.MZ, SortingDirection.Ascending));
    }
    return super.showSetupDialog(parent, valueCheckRequired);
}

Example 85 with PeakList

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

the class SpectraToolTipGenerator method generateToolTip.

/**
 * @see org.jfree.chart.labels.XYToolTipGenerator#generateToolTip(org.jfree.data.xy.XYDataset,
 *      int, int)
 */
public String generateToolTip(XYDataset dataset, int series, int item) {
    double intValue = dataset.getYValue(series, item);
    double mzValue = dataset.getXValue(series, item);
    if (dataset instanceof PeakListDataSet) {
        PeakListDataSet peakListDataSet = (PeakListDataSet) dataset;
        Feature peak = peakListDataSet.getPeak(series, item);
        PeakList peakList = peakListDataSet.getPeakList();
        PeakListRow row = peakList.getPeakRow(peak);
        String tooltip = "Peak: " + peak + "\nStatus: " + peak.getFeatureStatus() + "\nFeature list row: " + row + "\nData point m/z: " + mzFormat.format(mzValue) + "\nData point intensity: " + intensityFormat.format(intValue);
        return tooltip;
    }
    if (dataset instanceof IsotopesDataSet) {
        IsotopesDataSet isotopeDataSet = (IsotopesDataSet) dataset;
        IsotopePattern pattern = isotopeDataSet.getIsotopePattern();
        double relativeIntensity = intValue / pattern.getHighestDataPoint().getIntensity() * 100;
        String tooltip = "Isotope pattern: " + pattern.getDescription() + "\nStatus: " + pattern.getStatus() + "\nData point m/z: " + mzFormat.format(mzValue) + "\nData point intensity: " + intensityFormat.format(intValue) + "\nRelative intensity: " + percentFormat.format(relativeIntensity) + "%";
        return tooltip;
    }
    if (dataset instanceof ExtendedIsotopePatternDataSet) {
        return "Isotope pattern: " + ((ExtendedIsotopePatternDataSet) dataset).getIsotopePattern().getDescription() + "\nm/z: " + mzFormat.format(mzValue) + "\nIdentity: " + ((ExtendedIsotopePatternDataSet) dataset).getItemDescription(series, item) + "\nRelative intensity: " + percentFormat.format((dataset.getY(series, item).doubleValue() * 100)) + "%";
    }
    String tooltip = "m/z: " + mzFormat.format(mzValue) + "\nIntensity: " + intensityFormat.format(intValue);
    return tooltip;
}