Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.PeakList

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  public HistogramWindow(ParameterSet parameters) {

    super(null, true, true, true, true);

    PeakList peakList = parameters.getParameter(
        HistogramParameters.peakList).getValue()[0];

    this.setTitle("Histogram of " + peakList.getName());

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

    HistogramDataType dataType = parameters.getParameter(
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  public HistogramParameters() {
    super(new Parameter[]{peakList, dataFiles, dataRange, numOfBins});
  }

  public ExitCode showSetupDialog() {
    PeakList selectedPeaklists[] = getParameter(
        HistogramParameters.peakList).getValue();
    RawDataFile dataFiles[];
    if ((selectedPeaklists == null) || (selectedPeaklists.length != 1)) {
      dataFiles = MZmineCore.getCurrentProject().getDataFiles();
    } else {
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  public String generateToolTip(XYDataset dataset, int series, int item) {

    PeakDataSet peakDataSet = (PeakDataSet) dataset;
    PeakDataPoint dataPoint = peakDataSet.getDataPoint(series, item);

    PeakList peakList = peakDataSet.getPeakList();
    ChromatographicPeak peak = peakDataSet.getPeak(series);
    PeakListRow row = peakList.getPeakRow(peak);
    double rtValue = dataPoint.getRT();
    double intValue = dataPoint.getIntensity();
    double mzValue = dataPoint.getMZ();
    int scanNumber = dataPoint.getScanNumber();
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {

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

    for (PeakList peakList : peakLists) {
      Task newTask = new FragmentSearchTask(parameters, peakList);
      tasks.add(newTask);
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   * Returns a peak list different peaks depending on the selected option of
   * the "peak Threshold" combo box
   */
  PeakList getPeaksInThreshold() {

    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    PeakThresholdMode mode = (PeakThresholdMode) thresholdCombo
        .getSelectedItem();

    switch (mode) {
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  /**
   * Returns a peak list with the peaks which intensity is above the parameter
   * "intensity"
   */
  PeakList getIntensityThresholdPeakList(double intensity) {
    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    if (selectedPeakList == null)
      return null;
    SimplePeakList newList = new SimplePeakList(selectedPeakList.getName(),
        selectedPeakList.getRawDataFiles());

    for (PeakListRow peakRow : selectedPeakList.getRows()) {
      ChromatographicPeak peak = peakRow.getPeak(dataFile);
      if (peak == null)
        continue;
      if (peak.getRawDataPointsIntensityRange().getMax() > intensity) {
        newList.addRow(peakRow);
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   * Returns a peak list with the top peaks defined by the parameter
   * "threshold"
   */
  PeakList getTopThresholdPeakList(int threshold) {

    PeakList selectedPeakList = (PeakList) peakListSelector
        .getSelectedItem();
    if (selectedPeakList == null)
      return null;
    SimplePeakList newList = new SimplePeakList(selectedPeakList.getName(),
        selectedPeakList.getRawDataFiles());

    Vector<PeakListRow> peakRows = new Vector<PeakListRow>();

    Range mzRange = selectedPeakList.getRowsMZRange();
    Range rtRange = selectedPeakList.getRowsRTRange();

    PeakThresholdMode selectedPeakOption = (PeakThresholdMode) thresholdCombo
        .getSelectedItem();
    if (selectedPeakOption == PeakThresholdMode.TOP_PEAKS_AREA) {
      mzRange = masterFrame.getPlot().getXYPlot().getAxisRange();
      rtRange = masterFrame.getPlot().getXYPlot().getDomainRange();
    }

    for (PeakListRow peakRow : selectedPeakList.getRows()) {
      if (mzRange.contains(peakRow.getAverageMZ())
          && rtRange.contains(peakRow.getAverageRT())) {
        peakRows.add(peakRow);
      }
    }
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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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          thresholdSettings.setTopPeaksThreshold(topPeaks);
          break;
      }
    }

    PeakList selectedPeakList = getPeaksInThreshold();
    if (selectedPeakList != null)
      masterFrame.getPlot().loadPeakList(selectedPeakList);

  }
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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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