GoodDiffFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//

#pragma once

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

#include <map>
#include <string>
#include <cmath>

namespace OpenMS
{
  class OPENMS_DLLAPI GoodDiffFilter :
    public FilterFunctor
  {
public:

    // @name Constructors and Destructors
    // @{
    GoodDiffFilter();

    GoodDiffFilter(const GoodDiffFilter & source);

    ~GoodDiffFilter() override;
    // @}

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

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

    template <typename SpectrumType>
    double apply(SpectrumType & spectrum)
    {
      double tolerance = (double)param_.getValue("tolerance");
      double gooddiff = 0;
      //iterate over all peaks
      double totaldiff = 0;
      for (Size i = 0; i < spectrum.size(); ++i)
      {
        //look for each peakdifference that is in range of aa residuemasses (56/187), if it could be a aa (aamass)
        for (Size j = i; i + j < spectrum.size(); ++j)
        {
          double diff =  spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0];
          if (diff < 56)
          {
            continue;
          }

          if (diff > 187)
          {
            j = spectrum.size();
          }
          else
          {
            totaldiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
            std::map<double, char>::const_iterator aait = aamass_.lower_bound(diff);
            if (aait == aamass_.end())
            {
              continue;
            }
            //look for aamasses that fit diff
            if (fabs(aait->first - diff) <= tolerance)
            {
              gooddiff += spectrum[i + j].getIntensity()  + spectrum[i].getIntensity();
            }
            else
            {
              ++aait;
              if ((aait) != aamass_.end() && fabs((aait)->first - diff) <= tolerance)
              {
                gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
              }
            }
          }
        }
      }

      return gooddiff / totaldiff;
    }

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

    // @}


private:

    std::map<double, char> aamass_;
  };
}