Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

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    // Get scan numbers from original file.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;

    // Determine MZ range.
    final Range mzRange = origDataFile.getDataMZRange();

    // Create chromatograms.
    final double[][] chromatograms = new double[numBins][numScans];

    for (int scanIndex = 0; !isCanceled() && scanIndex < numScans; scanIndex++) {

      // Get original scan.
      final Scan scan = origDataFile.getScan(scanNumbers[scanIndex]);

      // Process data points.
      for (final DataPoint dataPoint : scan.getDataPoints()) {

        final int bin = mzRange.binNumber(numBins, dataPoint.getMZ());
        final double value = chromatograms[bin][scanIndex];
        chromatograms[bin][scanIndex] = Math.max(value,
            dataPoint.getIntensity());
      }
      progress++;
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    // Get scan numbers from original file.
    final int[] scanNumbers = origDataFile.getScanNumbers(level);
    final int numScans = scanNumbers.length;

    // Determine MZ range.
    final Range mzRange = origDataFile.getDataMZRange();

    // Create chromatograms.
    final double[][] chromatograms = new double[numBins][numScans];

    for (int scanIndex = 0; !isCanceled() && scanIndex < numScans; scanIndex++) {

      // Get original scan.
      final Scan scan = origDataFile.getScan(scanNumbers[scanIndex]);

      // Process data points.
      for (final DataPoint dataPoint : scan.getDataPoints()) {

        chromatograms[mzRange.binNumber(numBins, dataPoint.getMZ())][scanIndex] += dataPoint
            .getIntensity();
      }
      progress++;
    }
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    // Create an ArrayList for new data points.
    final DataPoint[] newDataPoints = new DataPoint[dataPoints.length];

    // Determine MZ range.
    final Range mzRange = origDataFile.getDataMZRange();

    // Loop through all original data points.
    int i = 0;
    for (final DataPoint dp : dataPoints) {

      // Subtract baseline.
      final double mz = dp.getMZ();
      final int bin = mzRange.binNumber(numBins, mz);
      final double baselineIntenstity = baselines[bin][scanIndex];
      newDataPoints[i++] = baselineIntenstity <= 0.0
          ? new SimpleDataPoint(dp)
          : new SimpleDataPoint(mz, Math.max(0.0, dp.getIntensity()
              - baselineIntenstity));
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    // Create an ArrayList for new data points.
    final DataPoint[] newDataPoints = new DataPoint[dataPoints.length];

    // Determine MZ range.
    final Range mzRange = origDataFile.getDataMZRange();

    // Loop through all original data points.
    int i = 0;
    for (final DataPoint dp : dataPoints) {

      // Subtract baseline.
      final double mz = dp.getMZ();
      final int bin = mzRange.binNumber(numBins, mz);
      final double baselineIntenstity = baselines[bin][scanIndex];
      newDataPoints[i++] = baselineIntenstity <= 0.0
          ? new SimpleDataPoint(dp)
          : new SimpleDataPoint(mz, Math.max(0.0, dp.getIntensity()
              * (1.0 - baselineIntenstity)));
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  public PeakListRow[] getRows() {
    return peakListRows.toArray(new PeakListRow[0]);
  }

  public PeakListRow[] getRowsInsideMZRange(Range mzRange) {
    return getRowsInsideScanAndMZRange(new Range(Double.MIN_VALUE,
        Double.MAX_VALUE), mzRange);
  }
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    return getRowsInsideScanAndMZRange(new Range(Double.MIN_VALUE,
        Double.MAX_VALUE), mzRange);
  }

  public PeakListRow[] getRowsInsideScanRange(Range rtRange) {
    return getRowsInsideScanAndMZRange(rtRange, new Range(Double.MIN_VALUE,
        Double.MAX_VALUE));
  }
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    if (row.getDataPointMaxIntensity() > maxDataPointIntensity) {
      maxDataPointIntensity = row.getDataPointMaxIntensity();
    }

    if (mzRange == null) {
      mzRange = new Range(row.getAverageMZ());
      rtRange = new Range(row.getAverageRT());
    } else {
      mzRange.extendRange(row.getAverageMZ());
      rtRange.extendRange(row.getAverageRT());
    }
  }
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   *            End of the retention time range
   * @return
   */
  public ChromatographicPeak[] getPeaksInsideScanRange(RawDataFile file,
      Range rtRange) {
    return getPeaksInsideScanAndMZRange(file, rtRange, new Range(
        Double.MIN_VALUE, Double.MAX_VALUE));
  }
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  /**
   * @see net.sf.mzmine.data.PeakList#getPeaksInsideMZRange(double, double)
   */
  public ChromatographicPeak[] getPeaksInsideMZRange(RawDataFile file,
      Range mzRange) {
    return getPeaksInsideScanAndMZRange(file, new Range(Double.MIN_VALUE,
        Double.MAX_VALUE), mzRange);
  }
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    for (PeakListRow peakListRow : peakListRows) {
      if (peakListRow.getDataPointMaxIntensity() > maxDataPointIntensity)
        maxDataPointIntensity = peakListRow.getDataPointMaxIntensity();

      if (mzRange == null) {
        mzRange = new Range(peakListRow.getAverageMZ());
        rtRange = new Range(peakListRow.getAverageRT());
      } else {
        mzRange.extendRange(peakListRow.getAverageMZ());
        rtRange.extendRange(peakListRow.getAverageRT());
      }
    }
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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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