Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

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    Map<DataPoint, String> msmsAnnotations = new Hashtable<DataPoint, String>();

    msmsCycle : for (DataPoint dp : msmsIons) {

      // Check if this is an isotope
      Range isotopeCheckRange = new Range(dp.getMZ() - 1.4,
          dp.getMZ() - 0.6);
      for (DataPoint dpCheck : msmsIons) {
        // If we have any MS/MS peak with 1 neutron mass smaller m/z
        // and higher intensity, it means the current peak is an
        // isotope and we should ignore it
        if (isotopeCheckRange.contains(dpCheck.getMZ())
            && (dpCheck.getIntensity() > dp.getIntensity())) {
          continue msmsCycle;
        }
      }

      // We don't know the charge of the fragment, so we will simply
      // assume 1
      double neutralLoss = msmsScan.getPrecursorMZ()
          * msmsScan.getPrecursorCharge() - dp.getMZ();

      // Ignore negative neutral losses and parent ion, <5 may be a
      // good threshold
      if (neutralLoss < 5)
        continue;

      Range msmsTargetRange = msmsTolerance
          .getToleranceRange(neutralLoss);

      FormulaGenerator msmsEngine = new FormulaGenerator(msmsTargetRange,
          msmsElementRules);

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    // <PEAK>
    if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {

      DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
      Range peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
      RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);

      if (dataFile == null)
        throw new SAXException("Error in project: data file "
            + peakColumnID + " not found");

      for (int i = 0; i < numOfMZpeaks; i++) {

        Scan sc = dataFile.getScan(scanNumbers[i]);
        double retentionTime = sc.getRetentionTime();

        double mz = masses[i];
        double intensity = intensities[i];

        if ((peakRTRange == null) || (peakIntensityRange == null)) {
          peakRTRange = new Range(retentionTime);
          peakIntensityRange = new Range(intensity);
        } else {
          peakRTRange.extendRange(retentionTime);
          peakIntensityRange.extendRange(intensity);
        }
        if (mz > 0.0) {
          mzPeaks[i] = new SimpleDataPoint(mz, intensity);
          if (peakMZRange == null)
            peakMZRange = new Range(mz);
          else
            peakMZRange.extendRange(mz);
        }
      }
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  public static boolean checkRDBE(double rdbeValue, ParameterSet parameters) {

    boolean mustBeInteger = parameters.getParameter(
        RDBERestrictionParameters.rdbeWholeNum).getValue();
    Range rdbeRange = parameters.getParameter(
        RDBERestrictionParameters.rdbeRange).getValue();

    if ((mustBeInteger) && (Math.floor(rdbeValue) != rdbeValue))
      return false;

    return rdbeRange.contains(rdbeValue);

  }
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   *
   * @return unique mass
   */
  public DataPoint getUniqueMass() {
    if (uniqueMass == null && uniqueMassValue > 0) {
      DataPoint[] p = getDataPointsByMass(new Range(uniqueMassValue,
          uniqueMassValue));
      uniqueMass = (p.length == 1) ? p[0] : null;
    }

    return uniqueMass;
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      // Calculate limits for a row with which the row can be aligned
      MZTolerance mzTolerance = super.parameterSet.getParameter(
          RansacAlignerParameters.MZTolerance).getValue();
      RTTolerance rtTolerance = super.parameterSet.getParameter(
          RansacAlignerParameters.RTToleranceBefore).getValue();
      Range mzRange = mzTolerance.getToleranceRange(row.getAverageMZ());
      Range rtRange = rtTolerance.getToleranceRange(row.getAverageRT());

      // Get all rows of the aligned peaklist within parameter limits
      PeakListRow candidateRows[] = peakListY
          .getRowsInsideScanAndMZRange(rtRange, mzRange);
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      System.out.println(f);

    Scan spectrum = dataFile.getScan(1);

    assert (dataFile.getName().contains("filtered"));
    assert (spectrum.getDataPointsByMass(new Range(146, 149)).length == 1);
    assert (spectrum.getDataPointsByMass(new Range(234, 246)).length == 1);
    assert (spectrum.getDataPointsByMass(new Range(249, 261)).length == 1);
  }
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  }

  @Nonnull
  @Override
  public Range getRawDataPointsRTRange() {
    return new Range(0, 0);
  }
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  }

  @Nonnull
  @Override
  public Range getRawDataPointsMZRange() {
    return new Range(0, 0);
  }
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  }

  @Nonnull
  @Override
  public Range getRawDataPointsIntensityRange() {
    return new Range(0, 0);
  }
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    try {
      rtTolerance = parameters.getParameter(
          PathAlignerParameters.RTTolerance).getValue();
      mzTolerance = parameters.getParameter(
          PathAlignerParameters.MZTolerance).getValue();
      Range rtRange = rtTolerance.getToleranceRange(path.getRT());
      Range mzRange = mzTolerance.getToleranceRange(path.getMZ());

      if (!rtRange.contains(peak.getAverageRT())
          || !mzRange.contains(peak.getAverageMZ())) {
        return WORST_SCORE;
      }

      double mzDiff = Math.abs(path.getMZ() - peak.getAverageMZ());

      double rtDiff = Math.abs(path.getRT() - peak.getAverageRT());

      double score = ((mzDiff / (mzRange.getSize() / 2)))
          + ((rtDiff / (rtRange.getSize() / 2)));

      if (parameters.getParameter(
          PathAlignerParameters.SameChargeRequired).getValue()) {
        if (!PeakUtils.compareChargeState(
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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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