IntensityBalanceFilter.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.
//
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
 
#include <map>
#include <utility>
 
namespace OpenMS
{
  class OPENMS_DLLAPI IntensityBalanceFilter :
    public FilterFunctor
  {
 
public:
 
    // @name Constructors and Destructors
    // @{
    IntensityBalanceFilter();
 
    IntensityBalanceFilter(const IntensityBalanceFilter & source);
 
    ~IntensityBalanceFilter() override;
    // @}
 
    // @name Operators
    // @{
    IntensityBalanceFilter & operator=(const IntensityBalanceFilter & source);
    // @}
 
    // @name Accessors
    // @{
    static FilterFunctor * create() { return new IntensityBalanceFilter(); }
 
    template <typename SpectrumType>
    double apply(SpectrumType & spectrum)
    {
      double bands = 10;
      std::multimap<double, Size> band_intensity;
      double parentmass = 0.0;
      if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
      Size j = 0;
      for (Size i = 0; i < bands; ++i)
      {
        double intensity = 0;
 
        //bern 2004 says to only check between 300 and size
        //but that seems inappropriate for small peptides (smallest is ca 450)
        while (j < spectrum.size() && spectrum[j].getPosition()[0] < (parentmass - 300) / bands * (i + 1) + 300)
        {
          intensity += spectrum[j++].getIntensity();
        }
        band_intensity.insert(std::make_pair(intensity, i));
      }
      j = 0;
      double total_intensity = 0;
      double twobiggest = 0;
      double sevensmallest = 0;
      for (std::multimap<double, Size>::reverse_iterator mmrit = band_intensity.rbegin(); mmrit != band_intensity.rend(); ++mmrit, ++j)
      {
        total_intensity += mmrit->first;
        //take the two biggest
        if (j < 2)
        {
          twobiggest += mmrit->first;
        }
        //take the seven smallest
        if (j > 2)
        {
          sevensmallest += mmrit->first;
        }
      }
 
      return (twobiggest - sevensmallest) / total_intensity;
    }
 
    static const String getProductName()
    {
      return "IntensityBalanceFilter";
    }
 
    // @}
 
  };
}