Package net.sf.mzmine.modules.visualization.spectra.datasets

Examples of net.sf.mzmine.modules.visualization.spectra.datasets.ScanDataSet

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    }
  }

  protected void loadPreview(SpectraPlot spectrumPlot, Scan previewScan) {

    ScanDataSet spectraDataSet = new ScanDataSet(previewScan);

    // Set plot mode only if it hasn't been set before
    // if the scan is centroided, switch to centroid mode
    if (previewScan.isCentroided()) {
      spectrumPlot.setPlotMode(PlotMode.CENTROID);
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  public void loadRawData(Scan scan) {

    logger.finest("Loading scan #" + scan.getScanNumber() + " from "
        + dataFile + " for spectra visualizer");

    spectrumDataSet = new ScanDataSet(scan);

    this.currentScan = scan;

    // If the plot mode has not been set yet, set it accordingly
    if (spectrumPlot.getPlotMode() == null) {
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    // We need to find a normalization factor for the new isotope
    // pattern, to show meaningful intensity range
    double mz = newPattern.getHighestIsotope().getMZ();
    Range searchMZRange = new Range(mz - 0.5, mz + 0.5);
    ScanDataSet scanDataSet = spectrumPlot.getMainScanDataSet();
    double normalizationFactor = scanDataSet
        .getHighestIntensity(searchMZRange);

    // If normalization factor is 0, it means there were no data points
    // in given m/z range. In such case we use the max intensity of
    // whole scan as normalization factor.
    if (normalizationFactor == 0) {
      searchMZRange = new Range(0, Double.MAX_VALUE);
      normalizationFactor = scanDataSet
          .getHighestIntensity(searchMZRange);
    }

    IsotopePattern normalizedPattern = IsotopePatternCalculator
        .normalizeIsotopePattern(newPattern, normalizationFactor);
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   */
  protected void loadPreview(SpectraPlot spectrumPlot, Scan previewScan) {

    Scan newScan = rawDataFilter.filterScan(previewScan, filterParameters);

    ScanDataSet spectraDataSet = new ScanDataSet("Filtered scan", newScan);
    ScanDataSet spectraOriginalDataSet = new ScanDataSet("Original scan",
        previewScan);

    spectrumPlot.removeAllDataSets();

    spectrumPlot.addDataSet(spectraOriginalDataSet,
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      boolean transparency) {

    XYItemRenderer newRenderer;

    if (dataSet instanceof ScanDataSet) {
      ScanDataSet scanDataSet = (ScanDataSet) dataSet;
      Scan scan = scanDataSet.getScan();
      if (scan.isCentroided())
        newRenderer = new PeakRenderer(color, transparency);
      else {
        newRenderer = new ContinuousRenderer(color, transparency);
        ((ContinuousRenderer) newRenderer)
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    // Remove previous data sets
    spectrumPlot.removeAllDataSets();

    // Add scan data set
    ScanDataSet scanDataSet = new ScanDataSet(previewScan);
    spectrumPlot.addDataSet(scanDataSet, SpectraVisualizerWindow.scanColor,
        false);

    // If the scan is centroided, switch to centroid mode
    if (previewScan.isCentroided()) {
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Related Classes of net.sf.mzmine.modules.visualization.spectra.datasets.ScanDataSet

  • net.sf.mzmine.data.DataPoint
  • net.sf.mzmine.modules.masslistmethods.shoulderpeaksfilter.ShoulderPeaksFilterSetupDialog
  • net.sf.mzmine.modules.rawdatamethods.filtering.scanfilters.ScanFilterSetupDialog
  • net.sf.mzmine.modules.rawdatamethods.peakpicking.massdetection.MassDetectorSetupDialog
  • net.sf.mzmine.modules.visualization.spectra.SpectraPlot
  • net.sf.mzmine.modules.visualization.spectra.SpectraVisualizerWindow
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