TopDownIsobaricQuantification.h

Go to the documentation of this file.

// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeon $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantitationMethod.h>
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHHelperClasses.h>
#include <OpenMS/ANALYSIS/TOPDOWN/PeakGroup.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <iomanip>
#include <iostream>
 
namespace OpenMS
{
  class OPENMS_DLLAPI TopDownIsobaricQuantification : public DefaultParamHandler
  {
  public:
 
    TopDownIsobaricQuantification();
 
    ~TopDownIsobaricQuantification() override = default;
 
    TopDownIsobaricQuantification(const TopDownIsobaricQuantification&);
 
    TopDownIsobaricQuantification(TopDownIsobaricQuantification&& other) = default;
 
    TopDownIsobaricQuantification& operator=(const TopDownIsobaricQuantification& other);
 
    void quantify(const MSExperiment& exp, std::vector<DeconvolvedSpectrum>& deconvolved_spectra, const std::vector<FLASHHelperClasses::MassFeature>& mass_features);
 
  protected:
    void updateMembers_() override;
    void setDefaultParams_();
 
  private:
    std::map<String, std::unique_ptr<IsobaricQuantitationMethod>> quant_methods_;
    bool only_fully_quantified_ = false;
    void addMethod_(std::unique_ptr<IsobaricQuantitationMethod> ptr)
    {
      std::string internal_name = ptr->getMethodName();
      quant_methods_[internal_name] = std::move(ptr);
    }
  };
} // namespace OpenMS