IsotopeDiffFilter.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
#include <cmath>
 
namespace OpenMS
{
  class OPENMS_DLLAPI IsotopeDiffFilter :
    public FilterFunctor
  {
 
public:
 
    // @name Constructors and Destructors
    // @{
    IsotopeDiffFilter();
 
    IsotopeDiffFilter(const IsotopeDiffFilter & source);
 
    ~IsotopeDiffFilter() override;
    // @}
 
    // @name Operators
    // @{
    IsotopeDiffFilter & operator=(const IsotopeDiffFilter & source);
    // @}
 
    // @name Accessors
    // @{
 
    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;
    }
 
    // @}
 
private:
  };
}