Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.PeakList

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    ExitCode exitCode = BatchModeModule.runBatch(batchFile);
    assert (exitCode == ExitCode.OK);

    assert (MZmineCore.getCurrentProject().getPeakLists().length > 0);

    PeakList peakList = MZmineCore.getCurrentProject().getPeakLists()[0];
    assert (peakList.getNumberOfRows() > 0);

    logger.info("Set #3 Mass Candidates: " + peakList.getNumberOfRows());

    for (PeakListRow row : peakList.getRows()) {
      assert (row.getNumberOfPeaks() > 0);
      assert (row.getRawDataFiles().length > 0);
      assert (row.getNumberOfPeaks() > 0);

      for (ChromatographicPeak p : row.getPeaks()) {
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

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

    for (final PeakList peakList : peakLists) {
      Task newTask = new IsotopeGrouperTask(peakList, parameters);
      tasks.add(newTask);
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

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

    for (PeakList pl : peakLists) {

      // Create dataset & paint scale
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  }

  @Override
  public ExitCode showSetupDialog() {

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

    if (selectedPeakLists.length != 1) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
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  }

  @Override
  public ExitCode showSetupDialog() {

    PeakList selectedPeakList[] = getParameter(peakLists).getValue();

    RawDataFile dataFileChoices[];
    if (selectedPeakList.length == 1) {
      dataFileChoices = selectedPeakList[0].getRawDataFiles();
    } else {
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

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

    for (PeakList pl : peakLists) {

      // Create dataset & paint scale
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

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

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

  @Override
  public ExitCode showSetupDialog() {

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

    if (selectedPeakLists.length != 1) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
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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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