Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.PeakList

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  }

  public synchronized PeakList[] getPeakLists() {
    int childrenCount = getChildCount(peakListsNode);
    PeakList result[] = new PeakList[childrenCount];
    for (int j = 0; j < childrenCount; j++) {
      DefaultMutableTreeNode child = (DefaultMutableTreeNode) getChild(
          peakListsNode, j);
      result[j] = (PeakList) child.getUserObject();
    }
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    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) {

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

    PeakList peakList = peakLists[0];
    if (peakList.getNumberOfRawDataFiles() < 2) {
      MZmineCore
          .getDesktop()
          .displayErrorMessage(
              "There is only one raw data file in the selected "
                  + "peak list, it is necessary at least two for comparison");
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    }

    if (command.equals("REMOVE_FILE")) {
      RawDataFile[] selectedFiles = tree
          .getSelectedObjects(RawDataFile.class);
      PeakList allPeakLists[] = MZmineCore.getCurrentProject()
          .getPeakLists();
      for (RawDataFile file : selectedFiles) {
        for (PeakList peakList : allPeakLists) {
          if (peakList.hasRawDataFile(file)) {
            String msg = "Cannot remove file " + file.getName()
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      RawDataFile clickedFile = (RawDataFile) clickedObject;
      TICVisualizerModule.setupNewTICVisualizer(clickedFile);
    }

    if (clickedObject instanceof PeakList) {
      PeakList clickedPeakList = (PeakList) clickedObject;
      PeakListTableModule
          .showNewPeakListVisualizerWindow(clickedPeakList);
    }

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

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

    for (final PeakList peakList : peakLists) {
      Task newTask = new ShapeModelerTask(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(
        SmoothingParameters.peakLists).getValue();

    for (final PeakList peakList : peakLists) {
      Task newTask = new SmoothingTask(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(
        CameraSearchParameters.PEAK_LISTS).getValue();

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

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

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

  @Override
  public ExitCode showSetupDialog() {

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

    RawDataFile dataFileChoices[];

    if ((selectedPeakList != null) && (selectedPeakList.length == 1)) {
      dataFileChoices = selectedPeakList[0].getRawDataFiles();
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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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