Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

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      Chromatogram bestChromatogram = null;

      for (Chromatogram testChrom : buildingChromatograms) {

        DataPoint lastMzPeak = testChrom.getLastMzPeak();
        Range toleranceRange = mzTolerance.getToleranceRange(lastMzPeak
            .getMZ());
        if (toleranceRange.contains(mzPeak.getMZ())) {
          if ((bestChromatogram == null)
              || (testChrom.getLastMzPeak().getIntensity() > bestChromatogram
                  .getLastMzPeak().getIntensity())) {
            bestChromatogram = testChrom;
          }
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    SimplePeakIdentity newIdentity = new SimplePeakIdentity(lineName,
        lineFormula, dataBaseFile.getName(), lineID, null);

    for (PeakListRow peakRow : peakList.getRows()) {

      Range mzRange = mzTolerance.getToleranceRange(peakRow
          .getAverageMZ());
      Range rtRange = rtTolerance.getToleranceRange(peakRow
          .getAverageRT());

      boolean mzMatches = (lineMZ == 0d) || mzRange.contains(lineMZ);
      boolean rtMatches = (lineRT == 0d) || rtRange.contains(lineRT);

      if (mzMatches && rtMatches) {

        logger.finest("Found compound " + lineName + " (m/z " + lineMZ
            + ", RT " + lineRT + ")");
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    // find m/z range and base peak
    if (dataPoints.length > 0) {

      basePeak = dataPoints[0];
      mzRange = new Range(dataPoints[0].getMZ(), dataPoints[0].getMZ());
      double tic = 0;

      for (DataPoint dp : dataPoints) {

        if (dp.getIntensity() > basePeak.getIntensity())
          basePeak = dp;

        mzRange.extendRange(dp.getMZ());

        tic += dp.getIntensity();

      }

      totalIonCurrent = new Double(tic);

    } else {
      mzRange = new Range(0);
      totalIonCurrent = new Double(0);
    }
  }
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   */
  private Data createPeakBox(final ChromatographicPeak peak)
      throws VisADException {

    // Get the extents.
    final Range rtRange = peak.getRawDataPointsRTRange();
    final Range mzRange = peak.getRawDataPointsMZRange();
    final float rtMin = (float) rtRange.getMin();
    final float rtMax = (float) rtRange.getMax();
    final float mzMin = (float) mzRange.getMin();
    final float mzMax = (float) mzRange.getMax();
    final float heightMin = 1.0F;
    final float heightMax = (float) peak.getRawDataPointsIntensityRange()
        .getMax();

    // Create the box set.
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        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;
        }
        if (maxPoint == null) {
          maxPoint = point;
        }
        int result = Double.compare(maxPoint.getIntensity(),
            point.getIntensity());
        if (result <= 0) {
          maxPoint = point;
          bestScan = regionScan;
        }

      }

      // if no representative dataPoint
      if (bestScan == null) {
        continue;
      }

      assert maxPoint != null;

      SimpleChromatographicPeak c = new SimpleChromatographicPeak(
          dataFile, scan.getPrecursorMZ(),
          bestScan.getRetentionTime(), maxPoint.getIntensity(),
          maxPoint.getIntensity(),
          new int[]{bestScan.getScanNumber()},
          new DataPoint[]{maxPoint}, PeakStatus.DETECTED,
          bestScan.getScanNumber(), scan.getScanNumber(), new Range(
              bestScan.getRetentionTime()), new Range(
              scan.getPrecursorMZ()), new Range(
              maxPoint.getIntensity()));

      PeakListRow entry = new SimplePeakListRow(scan.getScanNumber());
      entry.addPeak(dataFile, c);
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   */
  public @Nonnull
  int[] getScanNumbers(int msLevel) {
    if (scanNumbersCache.containsKey(msLevel))
      return scanNumbersCache.get(msLevel);
    int scanNumbers[] = getScanNumbers(msLevel, new Range(
        Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY));
    scanNumbersCache.put(msLevel, scanNumbers);
    return scanNumbers;
  }
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  public @Nonnull
  Range getDataMZRange(int msLevel) {

    // check if we have this value already cached
    Range mzRange = dataMZRange.get(msLevel);
    if (mzRange != null)
      return mzRange;

    // find the value
    for (Scan scan : scans.values()) {

      // ignore scans of other ms levels
      if ((msLevel != 0) && (scan.getMSLevel() != msLevel))
        continue;

      if (mzRange == null)
        mzRange = scan.getMZRange();
      else
        mzRange.extendRange(scan.getMZRange());

    }

    // cache the value, if we found any
    if (mzRange != null)
      dataMZRange.put(msLevel, mzRange);
    else
      mzRange = new Range(0);

    return mzRange;

  }
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  public @Nonnull
  Range getDataRTRange(int msLevel) {

    // check if we have this value already cached
    Range rtRange = dataRTRange.get(msLevel);
    if (rtRange != null)
      return rtRange;

    // find the value
    for (Scan scan : scans.values()) {

      // ignore scans of other ms levels
      if ((msLevel != 0) && (scan.getMSLevel() != msLevel))
        continue;

      if (rtRange == null)
        rtRange = new Range(scan.getRetentionTime());
      else
        rtRange.extendRange(scan.getRetentionTime());

    }

    // cache the value
    if (rtRange != null)
      dataRTRange.put(msLevel, rtRange);
    else
      rtRange = new Range(0);

    return rtRange;

  }
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    final RawDataFile[] dataFiles = parameters.getParameter(
        ThreeDVisualizerParameters.dataFiles).getValue();
    final int msLevel = parameters.getParameter(
        ThreeDVisualizerParameters.msLevel).getValue();
    final Range rtRange = parameters.getParameter(
        ThreeDVisualizerParameters.retentionTimeRange).getValue();

    final Desktop desktop = MZmineCore.getDesktop();

    // Check scan numbers.
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  public void loadIsotopes(IsotopePattern newPattern) {

    // 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
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Related Classes of net.sf.mzmine.util.Range

  • net.sf.mzmine.data.impl.SimpleChromatographicPeak
  • net.sf.mzmine.data.impl.SimplePeakList
  • net.sf.mzmine.data.impl.SimpleScan
  • net.sf.mzmine.modules.deconvolutedanalysis.CorrectedSpectrum
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameCorrection
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.table.ResultsListTable
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassCandidate
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherComparisonTask
  • net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest
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