IDMapper.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: Chris Bielow $
// $Authors: Marc Sturm, Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
 
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
 
#include <algorithm>
#include <limits>
 
namespace OpenMS
{
  class AnnotatedMSRun;
  class OPENMS_DLLAPI IDMapper :
    public DefaultParamHandler
  {
public:
    enum Measure {MEASURE_PPM = 0, MEASURE_DA};
 
    IDMapper();
 
    IDMapper(const IDMapper& cp);
 
    IDMapper& operator=(const IDMapper& rhs);
 
    void annotate(AnnotatedMSRun& map, const PeptideIdentificationList& peptide_ids, const std::vector<ProteinIdentification>& protein_ids, const bool clear_ids = false, const bool map_ms1 = false);
 
    void annotate(AnnotatedMSRun& map, const FeatureMap& fmap, const bool clear_ids = false, const bool map_ms1 = false);
 
    void annotate(FeatureMap& map, const PeptideIdentificationList& ids, const std::vector<ProteinIdentification>& protein_ids, bool use_centroid_rt = false, bool use_centroid_mz = false, const PeakMap& spectra = PeakMap());
 
    void annotate(ConsensusMap& map, const PeptideIdentificationList& ids, 
                  const std::vector<ProteinIdentification>& protein_ids, 
                  bool measure_from_subelements = false, 
                  bool annotate_ids_with_subelements = false, 
                  const PeakMap& spectra = PeakMap());
 
 
    struct PeptideIdentificationListState
    {
      std::vector<Size> no_precursors;
      std::vector<Size> identified;
      std::vector<Size> unidentified;
    }; 
 
    static PeptideIdentificationListState mapPrecursorsToIdentifications(const PeakMap& spectra, 
                                                                     const PeptideIdentificationList& ids, 
                                                                     double mz_tol = 0.001, 
                                                                     double rt_tol = 0.001)
    {
      PeptideIdentificationListState ret;
      for (Size spectrum_index = 0; spectrum_index < spectra.size(); ++spectrum_index)
      {
        const MSSpectrum& spectrum = spectra[spectrum_index];
        if (!spectrum.getPrecursors().empty())
        {
          bool identified(false);
          const std::vector<Precursor>& precursors = spectrum.getPrecursors();
 
          // check if precursor has been identified
          for (Size i_p = 0; i_p < precursors.size(); ++i_p)
          {
            // check by precursor mass and spectrum RT
            double mz_p = precursors[i_p].getMZ();
            double rt_s = spectrum.getRT();
          
            for (Size i_id = 0; i_id != ids.size(); ++i_id)
            {
              const PeptideIdentification& pid = ids[i_id];
 
              // do not count empty ids as identification of a spectrum
              if (pid.getHits().empty()) continue;
 
              double mz_id = pid.getMZ();
              double rt_id = pid.getRT();
 
              if ( fabs(mz_id - mz_p) < mz_tol && fabs(rt_s - rt_id) < rt_tol )
              {
                identified = true;
                break; 
              }
            }
          }   
          if (!identified) 
          {
            ret.unidentified.push_back(spectrum_index);
          }
          else
          {
            ret.identified.push_back(spectrum_index);
          }
        }
        else
        {
          ret.no_precursors.push_back(spectrum_index);
        }
      }
      return ret;
    }
 
 
protected:
    void updateMembers_() override;
 
    double rt_tolerance_;
    double mz_tolerance_;
    Measure measure_;
    bool ignore_charge_;
 
    double getAbsoluteMZTolerance_(const double mz) const;
 
    bool isMatch_(const double rt_distance, const double mz_theoretical, const double mz_observed) const;
 
    void checkHits_(const PeptideIdentificationList& ids) const;
 
    void getIDDetails_(const PeptideIdentification& id, double& rt_pep, DoubleList& mz_values, IntList& charges, bool use_avg_mass = false) const;
 
    void increaseBoundingBox_(DBoundingBox<2>& box);
 
    bool checkMassType_(const std::vector<DataProcessing>& processing) const;
 
  };
 
} // namespace OpenMS