PeakTypeEstimator.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Marcel Schilling $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_PEAKTYPEESTIMATOR_H
#define OPENMS_FORMAT_PEAKTYPEESTIMATOR_H

#include <OpenMS/METADATA/SpectrumSettings.h>

#include <cmath>
#include <numeric>

namespace OpenMS
{
  class OPENMS_DLLAPI PeakTypeEstimator
  {
public:
    template <typename PeakConstIterator>
    SpectrumSettings::SpectrumType estimateType(const PeakConstIterator & begin, const PeakConstIterator & end) const
    {
      const Size MAX_SAMPLED_DISTANCES = 1000;
      const double DISTANCE_VARIANCE_THRESHOLD = 0.5;

      // abort if there are less than 5 peak in the iterator range
      if (end - begin < 5)
      {
        return SpectrumSettings::UNKNOWN;
      }

      double count(0);

      std::vector<double> distances;

      PeakConstIterator peak(begin);

      for (; peak->getIntensity() <= 0 && peak != end - 2; ++peak)  // 1st positive intensity
      {
      }

      double scnd_last_mz(peak->getMZ());

      for (++peak; peak->getIntensity() <= 0 && peak != end - 1; ++peak) // 2nd positive intensity
      {
      }

      double last_mz(peak->getMZ());

      double last_dist(last_mz - scnd_last_mz);

      for (++peak; peak != end && count < MAX_SAMPLED_DISTANCES; ++peak) // max  positive intensity
      {
        if (peak->getIntensity() > 0)
        {
          double mz(peak->getMZ());
          double dist(mz - last_mz);
          distances.push_back(std::min(last_dist, dist)); // min distances
          ++count;
          scnd_last_mz = last_mz;
          last_mz = mz;
          last_dist = dist;
        }
      }

      if (count < 4) // at least 4 distances for non-zero(!) intensity peaks
      {
        return SpectrumSettings::UNKNOWN;
      }

      double mean(std::accumulate(distances.begin(), distances.end(), 0) / count); // sum/size

      // calculate variance
      double variance(0);
      for (std::vector<double>::iterator value = distances.begin(); value != distances.end(); ++value)
      {
        double delta = (*value - mean);
        variance += delta * delta;
      }
      variance /= count - 1;

      // calculate stdev
      double standard_deviation(std::sqrt(variance));

      if (standard_deviation < DISTANCE_VARIANCE_THRESHOLD)
      {
        return SpectrumSettings::RAWDATA;
      }
      else
      {
        return SpectrumSettings::PEAKS;
      }
    }

  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_PEAKTYPEESTIMATOR_H