MS1LabeledRatioQuantifier.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
 
#include <map>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class MS1LabeledRatioQuantifier : public DefaultParamHandler
  {
  public:
    struct ChannelRatio
    {
      unsigned fraction_group = 0;
      unsigned channel = 0;
      double ratio = 0.0;
      double normalized_ratio = 0.0;
      Size count = 0;
    };
 
    MS1LabeledRatioQuantifier();
 
    void run(ConsensusMap& consensus, const ExperimentalDesign& design, ProteinIdentification& proteins);
 
    const std::map<AASequence, std::vector<ChannelRatio>>& getPeptideRatios() const;
 
    const std::map<std::string, std::vector<ChannelRatio>>& getProteinGroupRatios() const;
 
  protected:
    static double median_(std::vector<double>& values);
 
    std::map<AASequence, std::vector<ChannelRatio>> peptide_ratios_;
    std::map<std::string, std::vector<ChannelRatio>> protein_group_ratios_;
  };
} // namespace OpenMS