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(
        BaselineCorrectionParameters.dataFiles).getValue();

    for (final RawDataFile dataFile : dataFiles) {

      Task newTask = new BaselineCorrectionTask(dataFile, parameters);
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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.removeRawDataFile(file);
  }
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    super(MZmineCore.getConfiguration().getRTFormat());

    setAutoButton = new JButton("Auto range");
    setAutoButton.addActionListener(this);
    RawDataFile currentFiles[] = MZmineCore.getCurrentProject()
        .getDataFiles();
    setAutoButton.setEnabled(currentFiles.length > 0);
    add(setAutoButton, 3, 0, 1, 1, 1, 0, GridBagConstraints.NONE);
  }
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    Object src = event.getSource();

    if (src == setAutoButton) {
      Range rtRange = null;
      RawDataFile currentFiles[] = MZmineCore.getCurrentProject()
          .getDataFiles();
      for (RawDataFile file : currentFiles) {
        Range fileRange = file.getDataRTRange();
        if (rtRange == null)
          rtRange = fileRange;
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    if (command.equals("REMOVE_ALL_MASSLISTS")) {
      MassList selectedMassLists[] = tree
          .getSelectedObjects(MassList.class);
      for (MassList massList : selectedMassLists) {
        String massListName = massList.getName();
        RawDataFile dataFiles[] = MZmineCore.getCurrentProject()
            .getDataFiles();
        for (RawDataFile dataFile : dataFiles) {
          int scanNumbers[] = dataFile.getScanNumbers();
          for (int scanNum : scanNumbers) {
            Scan scan = dataFile.getScan(scanNum);
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  ChromatographicPeak[] getPeaks(int row, int column) {
    return getPeaks(xValues[column], selectedRows[row]);
  }

  ChromatographicPeak[] getPeaks(Comparable<?> xValue, PeakListRow row) {
    RawDataFile files[] = getFiles(xValue);
    ChromatographicPeak[] peaks = new ChromatographicPeak[files.length];
    for (int i = 0; i < files.length; i++) {
      peaks[i] = row.getPeak(files[i]);
    }
    return peaks;
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    DefaultMutableTreeNode node = (DefaultMutableTreeNode) clickedPath
        .getLastPathComponent();
    Object clickedObject = node.getUserObject();

    if (clickedObject instanceof RawDataFile) {
      RawDataFile clickedFile = (RawDataFile) clickedObject;
      TICVisualizerModule.setupNewTICVisualizer(clickedFile);
    }

    if (clickedObject instanceof PeakList) {
      PeakList clickedPeakList = (PeakList) clickedObject;
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    return getFiles(xValues[column]);
  }

  RawDataFile[] getFiles(Comparable<?> xValue) {
    if (xAxisValueSource instanceof String) {
      RawDataFile columnFile = selectedFiles[getColumnIndex(xValue)];
      return new RawDataFile[]{columnFile};
    }
    if (xAxisValueSource instanceof ParameterWrapper) {
      HashSet<RawDataFile> files = new HashSet<RawDataFile>();
      UserParameter xAxisParameter = ((ParameterWrapper) xAxisValueSource)
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          "Cannot create a peak list with no data files"));
    }
    this.name = name;
    this.dataFiles = new RawDataFile[dataFiles.length];

    RawDataFile dataFile;
    for (int i = 0; i < dataFiles.length; i++) {
      dataFile = dataFiles[i];
      this.dataFiles[i] = dataFile;
    }
    peakListRows = new ArrayList<PeakListRow>();
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    Object src = e.getSource();

    if (src == lookupButton) {
      ArrayList<String> currentNames = new ArrayList<String>();
      RawDataFile dataFiles[] = MZmineCore.getCurrentProject()
          .getDataFiles();
      for (RawDataFile dataFile : dataFiles) {
        int scanNums[] = dataFile.getScanNumbers();
        for (int scanNum : scanNums) {
          Scan scan = dataFile.getScan(scanNum);
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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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