ObservationMatch.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    may be used to endorse or promote products derived from this software
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// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/ID/Observation.h>
#include <OpenMS/METADATA/ID/MetaData.h>
#include <OpenMS/METADATA/ID/IdentifiedMolecule.h>
#include <OpenMS/METADATA/PeptideHit.h> // for "PeakAnnotation"
#include <OpenMS/CHEMISTRY/AdductInfo.h>
 
#include <boost/multi_index_container.hpp>
#include <boost/multi_index/ordered_index.hpp>
#include <boost/multi_index/composite_key.hpp>
 
namespace OpenMS
{
  namespace IdentificationDataInternal
  {
    // @TODO: move "PeakAnnotation" out of "PeptideHit"
    typedef std::vector<PeptideHit::PeakAnnotation> PeakAnnotations;
    typedef std::map<std::optional<ProcessingStepRef>,
                     PeakAnnotations> PeakAnnotationSteps;
 
    // @TODO: this allows adducts with duplicate names, but requires different
    // sum formulas/charges - is this what we want?
    struct AdductCompare
    {
      bool operator()(const AdductInfo& left, const AdductInfo& right) const
      {
        return (std::make_pair(left.getCharge(), left.getEmpiricalFormula()) <
                std::make_pair(right.getCharge(), right.getEmpiricalFormula()));
      }
    };
 
    typedef std::set<AdductInfo, AdductCompare> Adducts;
    typedef IteratorWrapper<Adducts::iterator> AdductRef;
    typedef std::optional<AdductRef> AdductOpt;
 
    struct ObservationMatch: public ScoredProcessingResult
    {
      IdentifiedMolecule identified_molecule_var;
 
      ObservationRef observation_ref;
 
      Int charge;
 
      AdductOpt adduct_opt; 
 
      // peak annotations (fragment ion matches), potentially from different
      // data processing steps:
      PeakAnnotationSteps peak_annotations;
 
      explicit ObservationMatch(
        IdentifiedMolecule identified_molecule_var,
        ObservationRef observation_ref, Int charge = 0,
        const std::optional<AdductRef>& adduct_opt = std::nullopt,
        const AppliedProcessingSteps& steps_and_scores = AppliedProcessingSteps(),
        const PeakAnnotationSteps& peak_annotations = PeakAnnotationSteps()):
        ScoredProcessingResult(steps_and_scores),
        identified_molecule_var(identified_molecule_var),
        observation_ref(observation_ref), charge(charge), adduct_opt(adduct_opt),
        peak_annotations(peak_annotations)
      {
      }
 
      ObservationMatch(const ObservationMatch&) = default;
 
      ObservationMatch& merge(const ObservationMatch& other)
      {
        ScoredProcessingResult::merge(other);
        if (charge == 0)
        {
          charge = other.charge;
        }
        else if (charge != other.charge)
        {
          throw Exception::InvalidValue(__FILE__, __LINE__,
                                        OPENMS_PRETTY_FUNCTION,
                                        "Trying to overwrite ObservationMatch charge with conflicting value.",
                                        String(charge));
        }
 
        if (!adduct_opt)
        {
          adduct_opt = other.adduct_opt;
        }
        else if (adduct_opt != other.adduct_opt)
        {
          throw Exception::InvalidValue(__FILE__, __LINE__,
                                        OPENMS_PRETTY_FUNCTION,
                                        "Trying to overwrite ObservationMatch adduct_opt with conflicting value.",
                                        (*adduct_opt)->getName());
        }
 
        peak_annotations.insert(other.peak_annotations.begin(),
                                other.peak_annotations.end());
        return *this;
      }
    };
 
    // all matches for the same observation should be consecutive, so make sure
    // the observation is used as the first member in the composite key:
    typedef boost::multi_index_container<
      ObservationMatch,
      boost::multi_index::indexed_by<
        boost::multi_index::ordered_unique<
          boost::multi_index::composite_key<
            ObservationMatch,
            boost::multi_index::member<ObservationMatch, ObservationRef,
                                       &ObservationMatch::observation_ref>,
            boost::multi_index::member<
              ObservationMatch, IdentifiedMolecule,
              &ObservationMatch::identified_molecule_var>,
            boost::multi_index::member<ObservationMatch, AdductOpt,
                                       &ObservationMatch::adduct_opt>>>>
      > ObservationMatches;
 
    typedef IteratorWrapper<ObservationMatches::iterator> ObservationMatchRef;
  }
}