ParentMolecule.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/ScoredProcessingResult.h>
 
#include <boost/multi_index_container.hpp>
#include <boost/multi_index/ordered_index.hpp>
#include <boost/multi_index/member.hpp>
 
namespace OpenMS
{
  namespace IdentificationDataInternal
  {
    struct ParentMolecule: public ScoredProcessingResult
    {
      String accession;
 
      enum MoleculeType molecule_type;
 
      // @TODO: if there are modifications in the sequence, "sequence.size()"
      // etc. will be misleading!
      String sequence;
 
      String description;
 
      double coverage; 
 
      bool is_decoy;
 
      explicit ParentMolecule(
        const String& accession,
        MoleculeType molecule_type = MoleculeType::PROTEIN,
        const String& sequence = "", const String& description = "",
        double coverage = 0.0, bool is_decoy = false,
        const AppliedProcessingSteps& steps_and_scores =
        AppliedProcessingSteps()):
        ScoredProcessingResult(steps_and_scores), accession(accession),
        molecule_type(molecule_type), sequence(sequence),
        description(description), coverage(coverage), is_decoy(is_decoy)
      {
      }
 
      ParentMolecule(const ParentMolecule&) = default;
 
      ParentMolecule& operator+=(const ParentMolecule& other)
      {
        ScoredProcessingResult::operator+=(other);
        if (sequence.empty()) sequence = other.sequence;
        if (description.empty()) description = other.description;
        if (!is_decoy) is_decoy = other.is_decoy; // believe it when it's set
        // @TODO: what about coverage? (not reliable if we're merging data)
 
        return *this;
      }
    };
 
    // parent molecules indexed by their accessions:
    // @TODO: allow querying/iterating over proteins and RNAs separately
    typedef boost::multi_index_container<
      ParentMolecule,
      boost::multi_index::indexed_by<
        boost::multi_index::ordered_unique<boost::multi_index::member<
          ParentMolecule, String, &ParentMolecule::accession>>>
      > ParentMolecules;
    typedef IteratorWrapper<ParentMolecules::iterator> ParentMoleculeRef;
 
  }
}