IsobaricNormalizer.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifierStatistics.h>
 
#include <map>
 
namespace OpenMS
{
  class IsobaricQuantitationMethod;
  class ConsensusMap;
 
  class OPENMS_DLLAPI IsobaricNormalizer
  {
public:
    explicit IsobaricNormalizer(const IsobaricQuantitationMethod* const quant_method);
 
    IsobaricNormalizer(const IsobaricNormalizer& other);
 
    IsobaricNormalizer& operator=(const IsobaricNormalizer& rhs);
 
    void normalize(ConsensusMap& consensus_map);
 
private:
    const IsobaricQuantitationMethod* quant_meth_;
 
    String reference_channel_name_;
 
    ConsensusFeature::HandleSetType::iterator findReferenceChannel_(ConsensusFeature& cf, const ConsensusMap& consensus_map) const;
 
    void buildVectorIndex_(const ConsensusMap& consensus_map);
 
    void collectRatios_(const ConsensusFeature& cf,
                        const Peak2D::IntensityType& ref_intensity);
 
    void computeNormalizationFactors_(std::vector<Peak2D::IntensityType>& normalization_factors);
 
    std::map<Size, Size> map_to_vec_index_;
 
    Size ref_map_id_;
 
    std::vector<std::vector<Peak2D::IntensityType> > peptide_ratios_;
 
    std::vector<std::vector<Peak2D::IntensityType> > peptide_intensities_;
 
  };
} // namespace