IsotopeDiffFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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// $Maintainer: Andreas Bertsch $
// $Authors: $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_FILTERING_TRANSFORMERS_ISOTOPEDIFFFILTER_H
#define OPENMS_FILTERING_TRANSFORMERS_ISOTOPEDIFFFILTER_H

#include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
#include <cmath>

namespace OpenMS
{
  class OPENMS_DLLAPI IsotopeDiffFilter :
    public FilterFunctor
  {

public:

    // @name Constructors and Destrutors
    // @{
    IsotopeDiffFilter();

    IsotopeDiffFilter(const IsotopeDiffFilter & source);

    virtual ~IsotopeDiffFilter();
    // @}

    // @name Operators
    // @{
    IsotopeDiffFilter & operator=(const IsotopeDiffFilter & source);
    // @}

    // @name Accessors
    // @{
    static FilterFunctor * create() { return new IsotopeDiffFilter(); }

    template <typename SpectrumType>
    double apply(SpectrumType & spectrum)
    {
      double tolerance = (double)param_.getValue("tolerance");
      double isodiff = 0;

      //iterate over all peaks
      for (Size i = 0; i < spectrum.size(); ++i)
      {
        for (Size j = 1; i + j < spectrum.size(); ++j)
        {
          double pos_ij = spectrum[i + j].getPosition()[0];
          double pos_i = spectrum[i].getPosition()[0];
          if (std::fabs(pos_ij - pos_i + 1) < tolerance)
          {
            isodiff += spectrum[i].getIntensity() + spectrum[i + j].getIntensity();
          }
          else
          {
            if (std::fabs(spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0]) > 1 + tolerance)
            {
              break;
            }
          }
        }
      }
      return isodiff;
    }

    static const String getProductName()
    {
      return "IsotopeDiffFilter";
    }

    // @}

private:
  };
}
#endif // OPENMS_FILTERING_TRANSFORMERS_ISOTOPEDIFFFILTER_H