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(
        CustomDBSearchParameters.peakLists).getValue();

    for (PeakList peakList : peakLists) {
      Task newTask = new CustomDBSearchTask(peakList, parameters);
      tasks.add(newTask);
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  /**
   * Returns selected peak list
   */
  PeakList getSelectedPeakList() {
    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    return selectedPeakList;
  }
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   */
  void rebuildPeakListSelector() {

    logger.finest("Rebuilding the peak list selector");

    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    PeakList currentPeakLists[] = MZmineCore.getCurrentProject()
        .getPeakLists(dataFile);
    peakListSelector.setEnabled(false);
    peakListSelector.removeActionListener(masterFrame);
    peakListSelector.removeAllItems();

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      propertiesDialog.setVisible(true);
    }

    if ("PEAKLIST_CHANGE".equals(command)) {

      final PeakList selectedPeakList = bottomPanel.getSelectedPeakList();
      if (selectedPeakList != null) {

        LOG.finest("Loading a peak list " + selectedPeakList
            + " to a 3D view of " + dataFile);

        try {
          display.setPeaks(selectedPeakList, selectedPeakList
              .getPeaksInsideScanAndMZRange(dataFile, rtRange,
                  mzRange), bottomPanel
              .showCompoundNameSelected());
        } catch (RemoteException ex) {
          LOG.log(Level.WARNING, "Unable to set peaks", ex);
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      // If no scan is loaded yet, ignore
      if (currentScan == null)
        return;

      PeakList selectedPeakList = bottomPanel.getSelectedPeakList();
      loadPeaks(selectedPeakList);

    }

    if (command.equals("PREVIOUS_SCAN")) {
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  /**
   * Returns selected peak list
   */
  PeakList getSelectedPeakList() {
    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    return selectedPeakList;
  }
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   */
  void rebuildPeakListSelector() {

    logger.finest("Rebuilding the peak list selector");

    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    PeakList currentPeakLists[] = MZmineCore.getCurrentProject()
        .getPeakLists(dataFile);
    peakListSelector.removeAllItems();
    for (int i = currentPeakLists.length - 1; i >= 0; i--) {
      peakListSelector.addItem(currentPeakLists[i]);
    }
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    MZmineProcessingModule module = moduleMenuItems.get(src);
    if (module != null) {
      RawDataFile selectedFiles[] = MZmineCore.getDesktop()
          .getSelectedDataFiles();
      PeakList selectedPeakLists[] = MZmineCore.getDesktop()
          .getSelectedPeakLists();

      ParameterSet moduleParameters = MZmineCore.getConfiguration()
          .getModuleParameters(module.getClass());
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      PeakListDataSet peakListDataSet = (PeakListDataSet) dataset;

      ChromatographicPeak peak = peakListDataSet.getPeak(series, item);

      PeakList peakList = peakListDataSet.getPeakList();
      PeakListRow row = peakList.getPeakRow(peak);

      String tooltip = "Peak: " + peak + "\nStatus: "
          + peak.getPeakStatus() + "\nPeak list row: " + row
          + "\nData point m/z: " + mzFormat.format(mzValue)
          + "\nData point intensity: "
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    treeObjects.put(object, newNode);

    if (object instanceof PeakList) {
      int childCount = getChildCount(peakListsNode);
      insertNodeInto(newNode, peakListsNode, childCount);
      final PeakList peakList = (PeakList) object;
      PeakListRow rows[] = peakList.getRows();
      for (int i = 0; i < rows.length; i++) {
        DefaultMutableTreeNode rowNode = new DefaultMutableTreeNode(
            rows[i]);
        treeObjects.put(rows[i], rowNode);
        insertNodeInto(rowNode, newNode, i);
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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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