NeutralLossDiffFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
 
#include <map>
#include <cmath>
 
namespace OpenMS
{
  class OPENMS_DLLAPI NeutralLossDiffFilter :
    public FilterFunctor
  {
public:
 
    // @name Constructors and Destructors
    // @{
    NeutralLossDiffFilter();
 
    NeutralLossDiffFilter(const NeutralLossDiffFilter & source);
 
    ~NeutralLossDiffFilter() override;
    // @}
 
    // @name Operators
    // @{
    NeutralLossDiffFilter & operator=(const NeutralLossDiffFilter & source);
    // @}
 
    // @name Accessors
    // @{
    static FilterFunctor * create() { return new NeutralLossDiffFilter(); }
 
    template <typename SpectrumType>
    double apply(SpectrumType & spectrum)
    {
      double tolerance = (double)param_.getValue("tolerance");
      double isodiff = 0;
      //iterate over all peaks
      for (int i = 0; i < (int)spectrum.size(); ++i)
      {
        for (int j = 1; i - j >= 0; ++j)
        {
          double pos_diff = std::fabs(spectrum[i - j].getPosition()[0] - spectrum[i].getPosition()[0]);
          if (std::fabs(pos_diff - 18) < tolerance || std::fabs(pos_diff - 17) < tolerance)   // water and ammonium
          {
            isodiff += spectrum[i - j].getIntensity() + spectrum[i].getIntensity();
          }
          else
          {
            if (pos_diff > 18 + tolerance)
            {
              break;
            }
          }
        }
      }
 
      return isodiff;
    }
 
    static const String getProductName()
    {
      return "NeutralLossDiffFilter";
    }
 
    // @}
 
  };
}