IsobaricChannelExtractor.h

Go to the documentation of this file.

// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $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;
 
  struct ChannelQC
  {
 
    std::vector<double> mz_deltas; 
    int signal_not_unique{0};  
  };
 
  typedef std::map<std::string, ChannelQC> ChannelQCSet;
 
  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);
 
    std::vector<double> extractSingleSpec(Size spec_idx, const MSExperiment& exp, std::vector<std::pair<double, unsigned>>& channel_qc);
 
    void registerChannelsInOutputMap(ConsensusMap& consensus_map, const std::string& filename = "");
 
    void printStats();
    void printStats(ChannelQCSet& stats) const;
 
    void printStatsWithMissing(std::vector<ChannelQC>& stats) const;
 
    void clearStats();
 
    ChannelQCSet& getStats();
 
    static bool scanWindowCoversChannels(const MSSpectrum& spec, const IsobaricQuantitationMethod& method, double tolerance = 0.0);
 
private:
    struct PurityState_
    {
      PeakMap::ConstIterator precursorScan;
      PeakMap::ConstIterator followUpScan;
 
      bool hasFollowUpScan;
      const PeakMap& baseExperiment;
 
      PurityState_(const PeakMap& targetExp);
 
      void advanceFollowUp(const double rt);
 
      bool followUpValid(const double rt) const;
    };
 
    const IsobaricQuantitationMethod* quant_method_;
 
    std::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_;
 
    static constexpr double qc_dist_mz = 0.5; // fixed! Do not change!
 
    ChannelQCSet channel_mz_delta;
 
    bool isValidPrecursor_(const Precursor& precursor) const;
 
    bool hasLowIntensityReporter_(const ConsensusFeature& cf) const;
 
    double computePrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PurityState_& precursor) const;
 
    double computeSingleScanPrecursorPurity_(const PeakMap::ConstIterator& ms2_spec, const PeakMap::SpectrumType& precursor_spec) const;
 
    std::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[static_cast<size_t>(*(it->getActivationMethods().begin()))];
      }
      return "";
    }
 
 
protected:
    void setDefaultParams_();
 
    void updateMembers_() override;
  };
} // namespace