MassFeatureTrace.h

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//--------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FILTERING/DATAREDUCTION/MassTraceDetection.h>

#include <iostream>
#include <iomanip>

namespace OpenMS
{
  class OPENMS_DLLAPI MassFeatureTrace :
      public DefaultParamHandler
  {
  public:
    typedef FLASHDeconvHelperStructs::PrecalculatedAveragine PrecalculatedAveragine;
    typedef FLASHDeconvHelperStructs::LogMzPeak LogMzPeak;

    MassFeatureTrace();

    ~MassFeatureTrace() override = default;

    MassFeatureTrace(const MassFeatureTrace& ) = default;

    MassFeatureTrace(MassFeatureTrace&& other) = default;

    MassFeatureTrace& operator=(const MassFeatureTrace& fd) = default;
    MassFeatureTrace& operator=(MassFeatureTrace&& fd) = default;

    void storeInformationFromDeconvolvedSpectrum(DeconvolvedSpectrum& deconvolved_spectrum);

    std::vector<FLASHDeconvHelperStructs::MassFeature> findFeatures(const PrecalculatedAveragine& averagine);

  protected:
    void updateMembers_() override;

  private:
    double min_isotope_cosine_;
    std::map<double, std::map<double, PeakGroup>> peak_group_map_; // rt , mono mass, peakgroup

  };
}