MassFeatureTrace.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong, Jihyung Kim $
// $Authors: Kyowon Jeong, Jihyung Kim $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHHelperClasses.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/FEATUREFINDER/MassTraceDetection.h>
#include <iomanip>
#include <iostream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI MassFeatureTrace : public DefaultParamHandler
  {
  public:
    typedef FLASHHelperClasses::PrecalculatedAveragine PrecalculatedAveragine;
    typedef FLASHHelperClasses::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;
 
    std::vector<FLASHHelperClasses::MassFeature> findFeaturesAndUpdateQscore2D(const PrecalculatedAveragine& averagine, std::vector<DeconvolvedSpectrum>& deconvolved_spectra, int ms_level = 1,
                                                                                     bool is_decoy = false);
 
  protected:
    void updateMembers_() override;
 
  private:
    std::map<double, std::map<double, PeakGroup>> peak_group_map_; // rt , mono mass, peakgroup
  };
} // namespace OpenMS