Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.PeakList

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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

    PeakList peakLists[] = parameters.getParameter(
        MascotParameters.peakLists).getValue();

    for (PeakList peakList : peakLists) {
      Task newTask = new MascotSearchTask(parameters, peakList);
      tasks.add(newTask);
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  }

  @Override
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {
    PeakList peakLists[] = parameters.getParameter(
        FormulaPredictionPeakListParameters.PEAK_LISTS).getValue();

    for (PeakList peakList : peakLists) {
      Task newTask = new FormulaPredictionPeakListTask(peakList,
          parameters);
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  private JFreeChart chart;

  public IntensityPlotFrame(ParameterSet parameters) {
    super("", true, true, true, true);

    PeakList peakList = parameters.getParameter(
        IntensityPlotParameters.peakList).getValue()[0];

    String title = "Intensity plot [" + peakList + "]";
    String xAxisLabel = parameters
        .getParameter(IntensityPlotParameters.xAxisValueSource)
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    super.actionPerformed(event);

    Object src = event.getSource();

    if (src == comboPeakList) {
      PeakList selectedPeakList = (PeakList) comboPeakList
          .getSelectedItem();
      PeakListRow rows[] = selectedPeakList.getRows();
      comboPeak.removeActionListener(this);
      comboPeak.removeAllItems();
      for (PeakListRow row : rows) {
        comboPeak.addItem(row);
      }
      comboPeak.addActionListener(this);
      comboPeak.setSelectedIndex(0);
      return;
    }

    if (src == preview) {
      if (preview.isSelected()) {
        // Set the height of the preview to 200 cells, so it will span
        // the whole vertical length of the dialog (buttons are at row
        // no
        // 100). Also, we set the weight to 10, so the preview component
        // will consume most of the extra available space.
        mainPanel.add(pnlPlotXY, 3, 0, 1, 200, 10, 10);
        pnlVisible.add(pnlLabelsFields, BorderLayout.CENTER);
        updateMinimumSize();
        pack();
        PeakList selected[] = MZmineCore.getDesktop()
            .getSelectedPeakLists();
        if (selected.length > 0)
          comboPeakList.setSelectedItem(selected[0]);
        else
          comboPeakList.setSelectedIndex(0);
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   * original ParameterSetupDialog.
   *
   */
  private void addComponents() {

    PeakList peakLists[] = MZmineCore.getCurrentProject().getPeakLists();

    // Elements of pnlpreview
    JPanel pnlpreview = new JPanel(new BorderLayout());

    preview = new JCheckBox(" Show preview of peak building ");
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      label.setIcon(peakListIcon);
      label.setFont(smallFont);
    }

    if (embeddedObject instanceof PeakList) {
      PeakList p = (PeakList) embeddedObject;
      if (p.getNumberOfRawDataFiles() > 1) {
        label.setFont(smallerFont.deriveFont(Font.BOLD));
        label.setIcon(alignedPeaklistIcon);
      } else {
        label.setFont(smallerFont);
        label.setIcon(peakListIcon);
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  }

  @Override
  public ExitCode showSetupDialog() {

    PeakList selectedPeakLists[] = getParameter(peakList).getValue();

    if (selectedPeakLists.length != 1) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

    PeakList peakLists[] = parameters.getParameter(
        GPLipidSearchParameters.peakLists).getValue();

    for (PeakList peakList : peakLists) {
      Task newTask = new GPLipidSearchTask(parameters, peakList);
      tasks.add(newTask);
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   * @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;
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      processedRows++;
    }

    // Create the new peak list.
    final PeakList newPeakList = new SimplePeakList(origPeakList + " "
        + suffix, origPeakList.getRawDataFiles());

    // Add all remaining rows to a new peak list.
    for (int i = 0; !isCanceled() && i < rowCount; i++) {

      final PeakListRow row = peakListRows[i];

      if (row != null) {

        // Copy the peak list row.
        final PeakListRow newRow = new SimplePeakListRow(row.getID());
        PeakUtils.copyPeakListRowProperties(row, newRow);

        // Copy the peaks.
        for (final ChromatographicPeak peak : row.getPeaks()) {

          final ChromatographicPeak newPeak = new SimpleChromatographicPeak(
              peak);
          PeakUtils.copyPeakProperties(peak, newPeak);
          newRow.addPeak(peak.getDataFile(), newPeak);
        }

        newPeakList.addRow(newRow);
      }
    }

    if (!isCanceled()) {

      // Load previous applied methods.
      for (final PeakListAppliedMethod method : origPeakList
          .getAppliedMethods()) {

        newPeakList.addDescriptionOfAppliedTask(method);
      }

      // Add task description to peakList
      newPeakList
          .addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod(
              "Duplicate peak list rows filter", parameters));
    }

    return newPeakList;
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Related Classes of net.sf.mzmine.data.PeakList

  • net.sf.mzmine.desktop.impl.MainMenu
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeRenderer
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentVisualizationTask
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassDetectionTest
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherModule
  • net.sf.mzmine.modules.peaklistmethods.alignment.path.functions.ScoreAligner
  • net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerSetupDialog
  • net.sf.mzmine.modules.peaklistmethods.dataanalysis.clustering.ClusteringParameters
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