MoleculeQueryMatch.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/METADATA/ID/MetaData.h>
#include <OpenMS/METADATA/ID/IdentifiedCompound.h>
#include <OpenMS/METADATA/ID/IdentifiedSequence.h>
#include <OpenMS/METADATA/PeptideHit.h> // for "PeakAnnotation"
 
#include <boost/multi_index_container.hpp>
#include <boost/multi_index/ordered_index.hpp>
#include <boost/multi_index/composite_key.hpp>
#include <boost/variant.hpp>
 
namespace OpenMS
{
  namespace IdentificationDataInternal
  {
    // @TODO: move "PeakAnnotation" out of "PeptideHit"
    typedef std::vector<PeptideHit::PeakAnnotation> PeakAnnotations;
    typedef std::map<boost::optional<ProcessingStepRef>,
                     PeakAnnotations> PeakAnnotationSteps;
 
    typedef boost::variant<IdentifiedPeptideRef, IdentifiedCompoundRef,
                           IdentifiedOligoRef> IdentifiedMoleculeRef;
 
    struct MoleculeQueryMatch: public ScoredProcessingResult
    {
      IdentifiedMoleculeRef identified_molecule_ref;
 
      DataQueryRef data_query_ref;
 
      Int charge;
 
      // peak annotations (fragment ion matches), potentially from different
      // data processing steps:
      PeakAnnotationSteps peak_annotations;
 
      explicit MoleculeQueryMatch(
        IdentifiedMoleculeRef identified_molecule_ref,
        DataQueryRef data_query_ref, Int m_charge = 0,
        const AppliedProcessingSteps& steps_and_scores = AppliedProcessingSteps(),
        const PeakAnnotationSteps& peak_annotations = PeakAnnotationSteps()
      )
        : ScoredProcessingResult(steps_and_scores),
          identified_molecule_ref(identified_molecule_ref),
          data_query_ref(data_query_ref), charge(m_charge),
          peak_annotations(peak_annotations)
      {
      }
 
      MoleculeQueryMatch(const MoleculeQueryMatch&) = default;
 
      MoleculeType getMoleculeType() const
      {
        if (boost::get<IdentifiedPeptideRef>(&identified_molecule_ref))
        {
          return MoleculeType::PROTEIN;
        }
        if (boost::get<IdentifiedCompoundRef>(&identified_molecule_ref))
        {
          return MoleculeType::COMPOUND;
        }
        if (boost::get<IdentifiedOligoRef>(&identified_molecule_ref))
        {
          return MoleculeType::RNA;
        }
        return MoleculeType::SIZE_OF_MOLECULETYPE; // this shouldn't happen
      }
 
      IdentifiedPeptideRef getIdentifiedPeptideRef() const
      {
        if (const IdentifiedPeptideRef* ref_ptr =
            boost::get<IdentifiedPeptideRef>(&identified_molecule_ref))
        {
          return *ref_ptr;
        }
        String msg = "matched molecule is not a peptide";
        throw Exception::IllegalArgument(__FILE__, __LINE__,
                                         OPENMS_PRETTY_FUNCTION, msg);
      }
 
      IdentifiedCompoundRef getIdentifiedCompoundRef() const
      {
        if (const IdentifiedCompoundRef* ref_ptr =
            boost::get<IdentifiedCompoundRef>(&identified_molecule_ref))
        {
          return *ref_ptr;
        }
        String msg = "matched molecule is not a compound";
        throw Exception::IllegalArgument(__FILE__, __LINE__,
                                         OPENMS_PRETTY_FUNCTION, msg);
      }
 
      IdentifiedOligoRef getIdentifiedOligoRef() const
      {
        if (const IdentifiedOligoRef* ref_ptr =
            boost::get<IdentifiedOligoRef>(&identified_molecule_ref))
        {
          return *ref_ptr;
        }
        String msg = "matched molecule is not an oligonucleotide";
        throw Exception::IllegalArgument(__FILE__, __LINE__,
                                         OPENMS_PRETTY_FUNCTION, msg);
      }
 
      MoleculeQueryMatch& operator+=(const MoleculeQueryMatch& other)
      {
        ScoredProcessingResult::operator+=(other);
        if (charge == 0) charge = other.charge;
        peak_annotations.insert(other.peak_annotations.begin(),
                                other.peak_annotations.end());
        return *this;
      }
    };
 
    // all matches for the same data query should be consecutive!
    typedef boost::multi_index_container<
      MoleculeQueryMatch,
      boost::multi_index::indexed_by<
        boost::multi_index::ordered_unique<
          boost::multi_index::composite_key<
            MoleculeQueryMatch,
            boost::multi_index::member<MoleculeQueryMatch, DataQueryRef,
                                       &MoleculeQueryMatch::data_query_ref>,
            boost::multi_index::member<
              MoleculeQueryMatch, IdentifiedMoleculeRef,
              &MoleculeQueryMatch::identified_molecule_ref>>>>
      > MoleculeQueryMatches;
    typedef IteratorWrapper<MoleculeQueryMatches::iterator> QueryMatchRef;
 
  }
}