Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.RawDataFile

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    if (isForSamples) {
      rawData = new double[selectedRawDataFiles.length][selectedRows.length];
      for (int rowIndex = 0; rowIndex < selectedRows.length; rowIndex++) {
        PeakListRow peakListRow = selectedRows[rowIndex];
        for (int fileIndex = 0; fileIndex < selectedRawDataFiles.length; fileIndex++) {
          RawDataFile rawDataFile = selectedRawDataFiles[fileIndex];
          ChromatographicPeak p = peakListRow.getPeak(rawDataFile);
          if (p != null) {
            if (useArea) {
              rawData[fileIndex][rowIndex] = p.getArea();
            } else {
              rawData[fileIndex][rowIndex] = p.getHeight();
            }
          }
        }
      }
    } else {
      rawData = new double[selectedRows.length][selectedRawDataFiles.length];
      for (int rowIndex = 0; rowIndex < selectedRows.length; rowIndex++) {
        PeakListRow peakListRow = selectedRows[rowIndex];
        for (int fileIndex = 0; fileIndex < selectedRawDataFiles.length; fileIndex++) {
          RawDataFile rawDataFile = selectedRawDataFiles[fileIndex];
          ChromatographicPeak p = peakListRow.getPeak(rawDataFile);
          if (p != null) {
            if (useArea) {
              rawData[rowIndex][fileIndex] = p.getArea();
            } else {
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      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
    }

    RawDataFile plDataFiles[] = selectedPeakLists[0].getRawDataFiles();

    getParameter(groupOneFiles).setChoices(plDataFiles);
    getParameter(groupTwoFiles).setChoices(plDataFiles);

    return super.showSetupDialog();
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  @Override
  public ExitCode showSetupDialog() {

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

    RawDataFile dataFileChoices[];
    if (selectedPeakList.length == 1) {
      dataFileChoices = selectedPeakList[0].getRawDataFiles();
    } else {
      dataFileChoices = new RawDataFile[0];
    }
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  public PeakXICComponent(ChromatographicPeak peak, double maxIntensity) {

    this.peak = peak;

    // find data boundaries
    RawDataFile dataFile = peak.getDataFile();
    this.rtRange = dataFile.getDataRTRange(1);
    this.maxIntensity = maxIntensity;

    this.setBorder(componentBorder);

    // add tooltip
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    // get canvas size
    Dimension size = getSize();

    // get scan numbers, one data point per each scan
    RawDataFile dataFile = peak.getDataFile();
    int scanNumbers[] = peak.getScanNumbers();

    // If we have no data, just return
    if (scanNumbers.length == 0)
      return;

    // for each datapoint, find [X:Y] coordinates of its point in painted
    // image
    int xValues[] = new int[scanNumbers.length];
    int yValues[] = new int[scanNumbers.length];

    // find one datapoint with maximum intensity in each scan
    for (int i = 0; i < scanNumbers.length; i++) {

      double dataPointIntensity = 0;
      DataPoint dataPoint = peak.getDataPoint(scanNumbers[i]);

      if (dataPoint != null)
        dataPointIntensity = dataPoint.getIntensity();

      // get retention time (X value)
      double retentionTime = dataFile.getScan(scanNumbers[i])
          .getRetentionTime();

      // calculate [X:Y] coordinates
      xValues[i] = (int) Math.floor((retentionTime - rtRange.getMin())
          / rtRange.getSize() * (size.width - 1));
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  public CVDataset(PeakList alignedPeakList, ParameterSet parameters) {

    int numOfRows = alignedPeakList.getNumberOfRows();

    RawDataFile selectedFiles[] = parameters.getParameter(
        CVParameters.dataFiles).getValue();
    PeakMeasurementType measurementType = parameters.getParameter(
        CVParameters.measurementType).getValue();

    // Generate title for the dataset
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      MZmineCore.getDesktop().displayErrorMessage(
          "Please select a single peak list");
      return ExitCode.CANCEL;
    }

    RawDataFile plDataFiles[] = selectedPeakLists[0].getRawDataFiles();

    getParameter(dataFiles).setChoices(plDataFiles);

    return super.showSetupDialog();
  }
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    dataFiles = MZmineCore.getCurrentProject().getDataFiles();

    if (dataFiles.length == 0)
      return;

    RawDataFile selectedFiles[] = MZmineCore.getDesktop()
        .getSelectedDataFiles();

    if (selectedFiles.length > 0)
      previewDataFile = selectedFiles[0];
    else
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    }

    // <VALUE>
    if (qName.equals(UserParameterElementName_2_5_FiehnlabFork.VALUE
        .getElementName())) {
      RawDataFile currentDataFile = dataFilesIDMap.get(currentDataFileID);
      String valueString = getTextOfElement();
      Object value;
      if (currentParameter instanceof DoubleParameter) {
        value = new Double(valueString);
      } else
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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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