Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.RawDataFile

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    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(
        HistogramParameters.dataRange).getType();
    int numOfBins = parameters.getParameter(HistogramParameters.numOfBins)
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  }

  public ExitCode showSetupDialog() {
    PeakList selectedPeaklists[] = getParameter(
        HistogramParameters.peakList).getValue();
    RawDataFile dataFiles[];
    if ((selectedPeaklists == null) || (selectedPeaklists.length != 1)) {
      dataFiles = MZmineCore.getCurrentProject().getDataFiles();
    } else {
      dataFiles = selectedPeaklists[0].getRawDataFiles();
    }
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  @Override
  @Nonnull
  public ExitCode runModule(@Nonnull ParameterSet parameters,
      @Nonnull Collection<Task> tasks) {
    RawDataFile dataFiles[] = parameters.getParameter(
        TwoDParameters.dataFiles).getValue();

    if ((dataFiles == null) || (dataFiles.length == 0)) {
      MZmineCore.getDesktop().displayErrorMessage(
          "Please select raw data file");
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    int fragmentScanNumber = mainPeak.getBestPeak()
        .getMostIntenseFragmentScanNumber();
    if (fragmentScanNumber <= 0)
      return false;

    RawDataFile dataFile = mainPeak.getBestPeak().getDataFile();
    Scan fragmentScan = dataFile.getScan(fragmentScanNumber);
    if (fragmentScan == null)
      return false;

    // Get MS/MS data points in the tolerance range
    Range ms2mzRange = ms2mzTolerance.getToleranceRange(possibleFragment
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    }

    for (int i = 0; i < peakList.getNumberOfRawDataFiles(); i++) {

      RawDataFile dataFile = peakList.getRawDataFile(i);
      ColumnGroup fileGroup = new ColumnGroup(dataFile.getName());
      header.addColumnGroup(fileGroup);

      for (int j = 0; j < visibleDataFileColumns.length; j++) {

        DataFileColumnType dataFileColumn = visibleDataFileColumns[j];
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      }

    } else {

      DataFileColumnType dataFileColumn = getDataFileColumn(col);
      RawDataFile file = getColumnDataFile(col);
      ChromatographicPeak peak = peakListRow.getPeak(file);

      if (peak == null) {
        if (dataFileColumn == DataFileColumnType.STATUS)
          return PeakStatus.UNKNOWN;
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    for (int columnIndex = 0; columnIndex < parameterValues.keySet().size(); columnIndex++) {
      UserParameter parameter = tablemodelParameterValues
          .getParameter(columnIndex + 1);

      for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {
        RawDataFile file = dataFiles[dataFileIndex];

        Object value = tablemodelParameterValues.getValueAt(
            dataFileIndex, columnIndex + 1);
        if (parameter instanceof DoubleParameter) {
          Double doubleValue = null;
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    MZmineProject currentProject = MZmineCore.getCurrentProject();

    for (int dataFileIndex = 0; dataFileIndex < dataFiles.length; dataFileIndex++) {

      RawDataFile file = dataFiles[dataFileIndex];
      UserParameter[] parameters = currentProject.getParameters();

      // Loop through all parameters defined for this file
      for (UserParameter p : parameters) {
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    } catch (Exception e) {
      e.printStackTrace();
    }

    // Close all temporary files
    RawDataFile dataFiles[] = MZmineCore.getCurrentProject().getDataFiles();
    for (RawDataFile dataFile : dataFiles) {
      dataFile.close();
    }

  }
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        ThreeDVisualizerParameters.retentionTimeRange).getValue();

    final Desktop desktop = MZmineCore.getDesktop();

    // Check scan numbers.
    final RawDataFile dataFile = dataFiles[0];
    if (dataFile.getScanNumbers(msLevel, rtRange).length == 0) {

      desktop.displayErrorMessage("No scans found at MS level " + msLevel
          + " within given retention time range.");
      return ExitCode.ERROR;
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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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