Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.RawDataFile

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

    RawDataFile dataFiles[] = parameters.getParameter(
        NeutralLossParameters.dataFiles).getValue();

    NeutralLossVisualizerWindow newWindow = new NeutralLossVisualizerWindow(
        dataFiles[0], parameters);
    MZmineCore.getDesktop().addInternalFrame(newWindow);
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    // Do an additional check for centroid/continuous data and show a
    // warning if there is a potential problem
    boolean centroidData = false;
    int selectedMSLevel = getParameter(msLevel).getValue();
    RawDataFile selectedFiles[] = getParameter(dataFiles).getValue();

    // If no file selected (e.g. in batch mode setup), just return
    if (selectedFiles == null)
      return exitCode;
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    if (project == currentProject)
      return;

    // Close previous data files
    if (currentProject != null) {
      RawDataFile prevDataFiles[] = currentProject.getDataFiles();
      for (RawDataFile prevDataFile : prevDataFiles) {
        prevDataFile.close();
      }
    }
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  /**
   * @see java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
   */
  public void actionPerformed(ActionEvent event) {
    Object src = event.getSource();
    RawDataFile file = menuItemFiles.get(src);
    if (file != null)
      visualizer.addRawDataFile(file);
  }
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    peak = p;
    name = id;

    final int[] scanNumbers = peak.getScanNumbers();
    final RawDataFile dataFile = peak.getDataFile();
    final int peakScanNumber = peak.getRepresentativeScanNumber();

    // Copy peak data.
    final int scanCount = scanNumbers.length;
    retentionTimes = new double[scanCount];
    intensities = new double[scanCount];
    mzValues = new double[scanCount];
    int peakIndex = -1;
    for (int i = 0; i < scanCount; i++) {

      // Representative scan number?
      final int scanNumber = scanNumbers[i];
      if (peakIndex < 0 && scanNumber == peakScanNumber) {

        peakIndex = i;
      }

      // Copy RT and m/z.
      retentionTimes[i] = dataFile.getScan(scanNumber).getRetentionTime();
      final DataPoint dataPoint = peak.getDataPoint(scanNumber);
      if (dataPoint == null) {

        mzValues[i] = 0.0;
        intensities[i] = 0.0;
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    Object src = e.getSource();

    MZmineProcessingModule module = moduleMenuItems.get(src);
    if (module != null) {
      RawDataFile selectedFiles[] = MZmineCore.getDesktop()
          .getSelectedDataFiles();
      PeakList selectedPeakLists[] = MZmineCore.getDesktop()
          .getSelectedPeakLists();

      ParameterSet moduleParameters = MZmineCore.getConfiguration()
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    if (object instanceof RawDataFile) {

      int childCount = getChildCount(dataFilesNode);
      insertNodeInto(newNode, dataFilesNode, childCount);
      RawDataFile dataFile = (RawDataFile) object;
      int scanNumbers[] = dataFile.getScanNumbers();
      for (int i = 0; i < scanNumbers.length; i++) {
        Scan scan = dataFile.getScan(scanNumbers[i]);
        DefaultMutableTreeNode scanNode = new DefaultMutableTreeNode(
            scan);
        treeObjects.put(scan, scanNode);
        insertNodeInto(scanNode, newNode, i);
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    return result;
  }

  public synchronized RawDataFile[] getDataFiles() {
    int childrenCount = getChildCount(dataFilesNode);
    RawDataFile result[] = new RawDataFile[childrenCount];
    for (int j = 0; j < childrenCount; j++) {
      DefaultMutableTreeNode child = (DefaultMutableTreeNode) getChild(
          dataFilesNode, j);
      result[j] = (RawDataFile) child.getUserObject();
    }
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    DefaultMutableTreeNode node = (DefaultMutableTreeNode) path
        .getLastPathComponent();
    Object object = node.getUserObject();
    String newName = (String) value;
    if (object instanceof RawDataFile) {
      RawDataFile df = (RawDataFile) object;
      df.setName(newName);
    }
    if (object instanceof PeakList) {
      PeakList pl = (PeakList) object;
      pl.setName(newName);
    }
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {
    RawDataFile dataFiles[] = parameters.getParameter(
        SpectraVisualizerParameters.dataFiles).getValue();

    if ((dataFiles == null) || (dataFiles.length == 0)) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Please select raw data file");
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Related Classes of net.sf.mzmine.data.RawDataFile

  • net.sf.mzmine.data.impl.SimplePeakList
  • net.sf.mzmine.desktop.impl.MainMenu
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeModel
  • net.sf.mzmine.desktop.impl.projecttree.ProjectTreeMouseHandler
  • net.sf.mzmine.main.ShutDownHook
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.table.ResultsListTableColumnModel
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.table.MassListTable
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.table.MassListTableColumnModel
  • net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest
  • net.sf.mzmine.modules.peaklistmethods.alignment.ransac.RansacAlignerSetupDialog
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