IsotopeMarker.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/FILTERING/TRANSFORMERS/PeakMarker.h>
#include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
 
#include <map>
#include <vector>
#include <cmath>
#include <utility>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI IsotopeMarker :
    public PeakMarker
  {
public:
 
    // @name Constructors and Destructors
    // @{
    IsotopeMarker();
 
    IsotopeMarker(const IsotopeMarker & source);
 
    ~IsotopeMarker() override;
    // @}
 
    // @name Operators
    // @{
    IsotopeMarker & operator=(const IsotopeMarker & source);
    // @}
 
    // @name Accessors
    // @{
    static PeakMarker * create() { return new IsotopeMarker(); }
 
    template <typename SpectrumType>
    void apply(std::map<double, bool> & marked, SpectrumType & spectrum)
    {
      double mzvariation = (double)param_.getValue("mz_variation");
      double invariation = (double)param_.getValue("in_variation");
      Size marks = param_.getValue("marks");
 
      spectrum.sortByPosition();
 
      std::map<double, Size> isotopemarks;        // possible isotopes
 
      for (Size i = 0; i < spectrum.size(); ++i)
      {
        double mz = spectrum[i].getPosition()[0];
        double intensity = spectrum[i].getIntensity();
        Size j = i + 1;
 
        //std::vector<std::pair<double, double> > isotopes = SpectrumGenerator::instance()->isotopepeaks(mz, intensity);
        CoarseIsotopePatternGenerator solver;
        auto id = solver.estimateFromPeptideWeight(mz);
 
        while (j < spectrum.size() && spectrum[j].getPosition()[0] <= mz + 3 + mzvariation)
        {
          double curmz = spectrum[j].getPosition()[0];
          double curIntensity = spectrum[j].getIntensity();
          UInt iso = (UInt)(curmz - mz + 0.499999);
          if (iso > 0 && curmz - mz - iso > mzvariation)
          {
            ++j;
            continue;
          }
          if (std::fabs(id.begin()->getIntensity() * intensity - curIntensity) < invariation * id.begin()->getIntensity() * intensity)
          {
            isotopemarks[mz]++;
            isotopemarks[curmz]++;
          }
          ++j;
        }
      }
 
      for (std::map<double, Size>::const_iterator cmit = isotopemarks.begin(); cmit != isotopemarks.end(); ++cmit)
      {
        if (cmit->second >= marks)
        {
          marked.insert(std::pair<double, bool>(cmit->first, true));
        }
      }
      return;
    }
 
    static const String getProductName()
    {
      return "IsotopeMarker";
    }
 
    // @}
 
  };
 
}