IsobaricChannelExtractor.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow $
// $Authors: Stephan Aiche, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/Peak2D.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>

namespace OpenMS
{
  class IsobaricQuantitationMethod;
  class ConsensusMap;
  class ConsensusFeature;

  class OPENMS_DLLAPI IsobaricChannelExtractor :
    public DefaultParamHandler
  {
public:
    explicit IsobaricChannelExtractor(const IsobaricQuantitationMethod* const quant_method);

    IsobaricChannelExtractor(const IsobaricChannelExtractor& other);

    IsobaricChannelExtractor& operator=(const IsobaricChannelExtractor& rhs);

    void extractChannels(const PeakMap& ms_exp_data, ConsensusMap& consensus_map);

private:
    struct PuritySate_
    {
      PeakMap::ConstIterator precursorScan;
      PeakMap::ConstIterator followUpScan;

      bool hasFollowUpScan;
      const PeakMap& baseExperiment;

      PuritySate_(const PeakMap& targetExp);

      void advanceFollowUp(const double rt);

      bool followUpValid(const double rt);
    };

    const IsobaricQuantitationMethod* quant_method_;

    String selected_activation_;

    Peak2D::CoordinateType reporter_mass_shift_;

    Peak2D::IntensityType min_precursor_intensity_;

    bool keep_unannotated_precursor_;

    Peak2D::IntensityType min_reporter_intensity_;

    bool remove_low_intensity_quantifications_;

    double min_precursor_purity_;

    double max_precursor_isotope_deviation_;

    bool interpolate_precursor_purity_;

    void registerChannelsInOutputMap_(ConsensusMap& consensus_map);

    bool isValidPrecursor_(const Precursor& precursor) const;

    bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;

    double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PuritySate_& pState) const;

    double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;

    String getActivationMethod_(const PeakMap::SpectrumType& s) const
    {
      for (std::vector<Precursor>::const_iterator it = s.getPrecursors().begin(); it != s.getPrecursors().end(); ++it)
      {
        if (!it->getActivationMethods().empty()) return Precursor::NamesOfActivationMethod[*(it->getActivationMethods().begin())];
      }
      return "";
    }


protected:
    void setDefaultParams_();

    void updateMembers_() override;
  };
} // namespace