IDMapper.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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 <algorithm>
#include <limits>

namespace OpenMS
{
  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(PeakMap& map, const std::vector<PeptideIdentification>& peptide_ids, const std::vector<ProteinIdentification>& protein_ids, const bool clear_ids = false, const bool map_ms1 = false);

    void annotate(PeakMap& map, FeatureMap fmap, const bool clear_ids = false, const bool map_ms1 = false);

    void annotate(FeatureMap& map, const std::vector<PeptideIdentification>& 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 std::vector<PeptideIdentification>& ids, 
                  const std::vector<ProteinIdentification>& protein_ids, 
                  bool measure_from_subelements = false, 
                  bool annotate_ids_with_subelements = false, 
                  const PeakMap& spectra = PeakMap());


    struct SpectraIdentificationState
    {
      std::vector<Size> no_precursors;
      std::vector<Size> identified;
      std::vector<Size> unidentified;
    }; 

    static SpectraIdentificationState mapPrecursorsToIdentifications(const PeakMap& spectra, 
                                                                     const std::vector<PeptideIdentification>& ids, 
                                                                     double mz_tol = 0.001, 
                                                                     double rt_tol = 0.001)
    {
      SpectraIdentificationState 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 std::vector<PeptideIdentification>& 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