Package net.sf.mzmine.data.impl

Examples of net.sf.mzmine.data.impl.SimpleIsotopePattern

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          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
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          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
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      for (int i = 0; i < isotopes.length; i++) {
        ChromatographicPeak p = originalPeaks[i];
        isotopes[i] = new SimpleDataPoint(p.getMZ(), p.getHeight());

      }
      SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
          isotopes, IsotopePatternStatus.DETECTED, aPeak.toString());

      // Depending on user's choice, we leave either the most intenst, or
      // the lowest m/z peak
      if (chooseMostIntense) {
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          peakMZRange, peakIntensityRange);

      peak.setCharge(currentPeakCharge);

      if (currentIsotopes.size() > 0) {
        SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
            currentIsotopes.toArray(new DataPoint[0]),
            currentIsotopePatternStatus,
            currentIsotopePatternDescription);
        peak.setIsotopePattern(newPattern);
        currentIsotopes.clear();
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    }

    String formulaString = MolecularFormulaManipulator
        .getString(cdkFormula);

    SimpleIsotopePattern newPattern = new SimpleIsotopePattern(dataPoints,
        IsotopePatternStatus.PREDICTED, formulaString);

    return newPattern;

  }
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          * normalizedValue;

      newDataPoints[i] = new SimpleDataPoint(mz, intensity);
    }

    SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
        newDataPoints, pattern.getStatus(), pattern.getDescription());

    return newPattern;

  }
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    for (DataPoint dp : dataPoints) {
      if (dp != null)
        newDataPoints.add(dp);
    }

    SimpleIsotopePattern newPattern = new SimpleIsotopePattern(
        newDataPoints.toArray(new DataPoint[0]), pattern.getStatus(),
        pattern.getDescription());

    return newPattern;
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Related Classes of net.sf.mzmine.data.impl.SimpleIsotopePattern

  • net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperTask
  • net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_0.PeakListOpenHandler_2_0
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_3.PeakListOpenHandler_2_3
  • net.sf.mzmine.modules.projectmethods.projectload.version_2_5.PeakListOpenHandler_2_5
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