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

net.sf.mzmine.data.impl.SimpleDataPoint
This class represents one data point of a spectrum (m/z and intensity pair). Data point is immutable once created, to make things simple.

    StringTokenizer tokenizer = new StringTokenizer(ions, ",");
    while (tokenizer.hasMoreTokens()) {
      tokens = tokenizer.nextToken().split(":");
      mass = Double.parseDouble(tokens[0]);
      intensity = Double.parseDouble(tokens[1]);
      dataPoints.add(new SimpleDataPoint(mass, intensity));
    }


    scan.setDataPoints(dataPoints.toArray(new SimpleDataPoint[0]));


    return scan;

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      // Replace the MzPeak instance with an instance of SimpleDataPoint,
      // to reduce the memory usage. After we finish this extended peak,
      // we
      // don't need the additional data provided by the MzPeak
      SimpleDataPoint newDataPoint = new SimpleDataPoint(mzPeak);
      dataPointsMap.put(allScanNumbers[i], newDataPoint);


      if (i == 0) {
        rawDataPointsIntensityRange = new Range(mzPeak.getIntensity());
        rawDataPointsMZRange = new Range(mzPeak.getMZ());

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      if (basePeak != null) {
        if (basePeak.getIntensity() > 0)
          dataPointFound = true;
        newPeak.addDatapoint(scan.getScanNumber(), basePeak);
      } else {
        DataPoint fakeDataPoint = new SimpleDataPoint(
            mzRangeWithTol.getAverage(), 0);
        newPeak.addDatapoint(scan.getScanNumber(), fakeDataPoint);
      }


    }

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    for (int i = 0; i < allRetentionTimes.length; i++) {


      shapeHeight = calculateEMGIntensity(H, M, Dp, Ap, C,
          allRetentionTimes[i]);
      if (shapeHeight > height * 0.01d) {
        SimpleDataPoint mzPeak = new SimpleDataPoint(mz, shapeHeight);
        dataPointsMap.put(allScanNumbers[i], mzPeak);
        rawDataPointsRTRange.extendRange(allRetentionTimes[i]);
      }


      currentRT = allRetentionTimes[i] * 60d;

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      }
      intensity /= sqrtScaleLevel;
      // Eliminate the negative part of the wavelet map
      if (intensity < 0)
        intensity = 0;
      cwtDataPoints[dx] = new SimpleDataPoint(dataPoints[dx].getMZ(),
          (double) intensity);
    }


    return cwtDataPoints;
  }

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      }


      rawDataPoints.add(originalDataPoints[ind]);


      if (originalDataPoints[peakMaxInd].getIntensity() > noiseLevel) {
        SimpleDataPoint peakDataPoint = new SimpleDataPoint(
            originalDataPoints[peakMaxInd].getMZ(),
            calcAproxIntensity(rawDataPoints));


        mzPeaks.add(peakDataPoint);

View Full Code Here


    for (int i = 0; i < dataPoints.length; i++) {
      try {
        double mz = peakStream.readDouble();
        double intensity = peakStream.readDouble();
        dataPoints[i] = new SimpleDataPoint(mz, intensity);
      } catch (IOException e) {
        e.printStackTrace();
      }
    }

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    for (int i = 0; i < retentionTimes.length; i++) {


      currentRT = retentionTimes[i] * 60d;


      shapeHeight = calculateIntensity(currentRT);
      SimpleDataPoint mzPeak = new SimpleDataPoint(mz, shapeHeight);
      dataPointsMap.put(scanNumbers[i], mzPeak);


      area += (currentRT - previousRT) * (shapeHeight + previousHeight)
          / 2;
      previousRT = currentRT;

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   */
  public DataPoint getDataPoint(int scanNumber) {
    int index = Arrays.binarySearch(scanNumbers, scanNumber);
    if (index < 0)
      return null;
    SimpleDataPoint dp = new SimpleDataPoint(dataPointMZValues[index],
        dataPointIntensityValues[index]);
    return dp;
  }

View Full Code Here

    for (int i = 0; i < allRetentionTimes.length; i++) {


      currentRT = allRetentionTimes[i] * 60d;
      shapeHeight = calculateIntensity(currentRT);
      if (shapeHeight > height * 0.01d) {
        SimpleDataPoint mzPeak = new SimpleDataPoint(mz, shapeHeight);
        dataPointsMap.put(allScanNumbers[i], mzPeak);
        rawDataPointsRTRange.extendRange(currentRT);
        area += ((currentRT - previousRT) * (shapeHeight + previousHeight)) / 2;
      }

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net.sf.mzmine.data.DataPoint

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net.sf.mzmine.modules.peaklistmethods.gapfilling.peakfinder.Gap

net.sf.mzmine.modules.peaklistmethods.gapfilling.samerange.SameRangeTask

net.sf.mzmine.modules.peaklistmethods.identification.camera.CameraSearchTask

net.sf.mzmine.modules.peaklistmethods.isotopes.deisotoper.IsotopeGrouperTask

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net.sf.mzmine.modules.peaklistmethods.isotopes.isotopeprediction.IsotopePatternCalculator

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