IsobaricNormalizer.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: Timo Sachsenberg $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/ANALYSIS/QUANTITATION/IsobaricQuantifierStatistics.h>

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);

    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