MetaboTargetedAssay.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: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <map> //insert

#include <OpenMS/ANALYSIS/MRM/ReactionMonitoringTransition.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>
#include <OpenMS/ANALYSIS/ID/SiriusMSConverter.h> //SiriusMSFile
#include <OpenMS/FORMAT/DATAACCESS/SiriusFragmentAnnotation.h> //SiriusTargetDecoySpectra

#include <OpenMS/CONCEPT/Exception.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MetaboTargetedAssay
  {
    public:
    double precursor_int; 
    double transition_quality_score; 
    double precursor_mz; 
    double compound_rt; 
    String molecular_formula; 
    int compound_file; 
    String compound_name; 
    String compound_adduct; 
    TargetedExperiment::Compound potential_cmp; 
    std::vector<ReactionMonitoringTransition> potential_rmts; 

    class CompoundTargetDecoyPair
    {
    public:
      SiriusMSFile::CompoundInfo compound_info;
      SiriusFragmentAnnotation::SiriusTargetDecoySpectra target_decoy_spectra;

      CompoundTargetDecoyPair() = default;
      CompoundTargetDecoyPair(SiriusMSFile::CompoundInfo info, SiriusFragmentAnnotation::SiriusTargetDecoySpectra td_spectra) :
          compound_info(std::move(info)),
          target_decoy_spectra(std::move(td_spectra))
      {}
    };

    class CompoundSpectrumPair
    {
    public:
      SiriusMSFile::CompoundInfo compound_info;
      MSSpectrum spectrum;

      CompoundSpectrumPair() = default;
      CompoundSpectrumPair(SiriusMSFile::CompoundInfo info, MSSpectrum spectrum) :
          compound_info(std::move(info)),
          spectrum(std::move(spectrum))
      {}
    };

    struct TargetDecoyGroup
    {
      int target_index = -1;
      int decoy_index = -1;
      double target_mz = 0.0;
      double target_rt = 0.0;
      double decoy_mz = 0.0;
      double decoy_rt = 0.0;
      int target_file_number = 0;
      int decoy_file_number = 0;
    };

    static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssay(const MSExperiment& spectra,
                                                                       const FeatureMapping::FeatureToMs2Indices& feature_ms2_index,
                                                                       const double& precursor_rt_tol,
                                                                       const double& precursor_mz_distance,
                                                                       const double& cosine_sim_threshold,
                                                                       const double& transition_threshold,
                                                                       const double& min_fragment_mz,
                                                                       const double& max_fragment_mz,
                                                                       const bool& method_consensus_spectrum,
                                                                       const bool& exclude_ms2_precursor,
                                                                       const unsigned int& file_counter);

    static std::vector<MetaboTargetedAssay> extractMetaboTargetedAssayFragmentAnnotation(const std::vector< CompoundTargetDecoyPair >& v_cmp_spec,
                                                                                         const double& transition_threshold,
                                                                                         const double& min_fragment_mz,
                                                                                         const double& max_fragment_mz,
                                                                                         const bool& use_exact_mass,
                                                                                         const bool& exclude_ms2_precursor,
                                                                                         const unsigned int& file_counter);

    static std::vector< MetaboTargetedAssay::CompoundTargetDecoyPair > pairCompoundWithAnnotatedTDSpectraPairs(const std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                                                                                                               const std::vector<SiriusFragmentAnnotation::SiriusTargetDecoySpectra>& annotated_spectra);
    static std::vector< MetaboTargetedAssay::CompoundSpectrumPair > pairCompoundWithAnnotatedSpectra(const std::vector<SiriusMSFile::CompoundInfo>& v_cmpinfo,
                                                                                                     const std::vector<MSSpectrum>& annotated_spectra);

    static std::unordered_map< UInt64, std::vector<MetaboTargetedAssay> > buildAmbiguityGroup(const std::vector<MetaboTargetedAssay>& v_mta,
                                                                                              const double& ar_mz_tol,
                                                                                              const double& ar_rt_tol,
                                                                                              const String& ar_mz_tol_unit_res, size_t in_files_size);

    static void resolveAmbiguityGroup(std::unordered_map< UInt64, std::vector<MetaboTargetedAssay> >& map_mta_filter,
                                      const double& total_occurrence_filter,
                                      size_t in_files_size);

  protected:

    static constexpr float noise_threshold_constant_ = 1.1;

    static bool intensityLess_(const Peak1D& a, const Peak1D& b);

    static int getChargeFromAdduct_(const String& adduct);

    static void filterBasedOnTotalOccurrence_(std::vector<MetaboTargetedAssay>& mta, double total_occurrence_filter, size_t in_files_size);

    static void filterBasedOnMolFormAdductOccurrence_(std::vector<MetaboTargetedAssay>& mta);

    static void sortByPrecursorInt(std::vector<MetaboTargetedAssay>& vec_mta);
  };

} // namespace OpenMS