Package net.sf.mzmine.data

Examples of net.sf.mzmine.data.Scan

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        .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
        .getAverageMZ());

    DataPoint fragmentDataPoints[] = fragmentScan
        .getDataPointsByMass(ms2mzRange);

    // If there is a MS/MS peak of required height, we have a hit
    for (DataPoint dp : fragmentDataPoints) {
      if (dp.getIntensity() > minMS2peakHeight)
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      // Cancel?
      if (status == TaskStatus.CANCELED)
        return;

      Scan scan = rawDataFile.getScan(scanNumbers[index]);
      DataPoint scanBasePeak = scan.getBasePeak();
      retentionTimes[index] = scan.getRetentionTime();
      basePeaks[index] = (scanBasePeak == null ? 0 : scanBasePeak
          .getIntensity());
      DataPoint scanDataPoints[] = scan.getDataPoints();
      dataPointMatrix[index] = new SoftReference<DataPoint[]>(
          scanDataPoints);
      processedScans++;
    }
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  private double getMaxIntensity(int dataPointMatrixIndex, Range mzRange,
      PlotMode plotMode) {
    DataPoint dataPoints[] = dataPointMatrix[dataPointMatrixIndex].get();
    if (dataPoints == null) {
      Scan scan = rawDataFile.getScan(scanNumbers[dataPointMatrixIndex]);
      dataPoints = scan.getDataPoints();
      dataPointMatrix[dataPointMatrixIndex] = new SoftReference<DataPoint[]>(
          dataPoints);
    }
    return getMaxIntensity(dataPoints, mzRange, plotMode);
  }
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    for (int i = 0; i < totalScans; i++) {

      if (isCanceled())
        return;

      Scan scan = dataFile.getScan(scanNumbers[i]);

      MassList massList = scan.getMassList(massListName);
      if (massList == null) {
        setStatus(TaskStatus.ERROR);
        this.errorMessage = "Scan " + dataFile + " #" + scanNumbers[i]
            + " does not have a mass list " + massListName;
        return;
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    // Update fragment scan
    fragmentScan = ScanUtils.findBestFragmentScan(dataFile,
        dataFile.getDataRTRange(1), rawDataPointsMZRange);

    if (fragmentScan > 0) {
      Scan fragmentScanObject = dataFile.getScan(fragmentScan);
      int precursorCharge = fragmentScanObject.getPrecursorCharge();
      if (precursorCharge > 0)
        this.charge = precursorCharge;
    }

    // Discard the fields we don't need anymore
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    for (int scanNumber : scanNumbers) {
      if (isCanceled())
        return;

      // Get next MS/MS scan
      Scan scan = dataFile.getScan(scanNumber);

      // no parents scan for this msms scan
      if (scan.getParentScanNumber() <= 0) {
        continue;
      }

      // Get the MS Scan
      Scan bestScan = null;
      Range rtWindow = new Range(scan.getRetentionTime()
          - (binTime / 2.0f), scan.getRetentionTime()
          + (binTime / 2.0f));
      Range mzWindow = new Range(
          scan.getPrecursorMZ() - (binSize / 2.0f),
          scan.getPrecursorMZ() + (binSize / 2.0f));
      DataPoint point;
      DataPoint maxPoint = null;
      int[] regionScanNumbers = dataFile.getScanNumbers(1, rtWindow);
      for (int regionScanNumber : regionScanNumbers) {
        Scan regionScan = dataFile.getScan(regionScanNumber);
        point = ScanUtils.findBasePeak(regionScan, mzWindow);
        // no datapoint found
        if (point == null) {
          continue;
        }
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    ArrayList<Integer> eligibleScanNumbers = new ArrayList<Integer>();

    Enumeration<StorableScan> scansEnum = scans.elements();
    while (scansEnum.hasMoreElements()) {
      Scan scan = scansEnum.nextElement();

      if ((scan.getMSLevel() == msLevel)
          && (rtRange.contains(scan.getRetentionTime())))
        eligibleScanNumbers.add(scan.getScanNumber());
    }

    int[] numbersArray = CollectionUtils.toIntArray(eligibleScanNumbers);
    Arrays.sort(numbersArray);
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    Set<Integer> msLevelsSet = new HashSet<Integer>();

    Enumeration<StorableScan> scansEnum = scans.elements();
    while (scansEnum.hasMoreElements()) {
      Scan scan = scansEnum.nextElement();
      msLevelsSet.add(scan.getMSLevel());
    }

    int[] msLevels = CollectionUtils.toIntArray(msLevelsSet);
    Arrays.sort(msLevels);
    return msLevels;
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      return maxBasePeak;

    // find the value
    Enumeration<StorableScan> scansEnum = scans.elements();
    while (scansEnum.hasMoreElements()) {
      Scan scan = scansEnum.nextElement();

      // ignore scans of other ms levels
      if (scan.getMSLevel() != msLevel)
        continue;

      DataPoint scanBasePeak = scan.getBasePeak();
      if (scanBasePeak == null)
        continue;

      if ((maxBasePeak == null)
          || (scanBasePeak.getIntensity() > maxBasePeak))
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      return maxTIC.doubleValue();

    // find the value
    Enumeration<StorableScan> scansEnum = scans.elements();
    while (scansEnum.hasMoreElements()) {
      Scan scan = scansEnum.nextElement();

      // ignore scans of other ms levels
      if (scan.getMSLevel() != msLevel)
        continue;

      if ((maxTIC == null) || (scan.getTIC() > maxTIC))
        maxTIC = scan.getTIC();

    }

    // return -1 if no scan at this MS level
    if (maxTIC == null)
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