ParentSequence.h

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//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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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 ParentSequence: 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 ParentSequence(
        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)
      {
      }
 
      ParentSequence(const ParentSequence&) = default;
 
      ParentSequence& merge(const ParentSequence& other)
      {
        ScoredProcessingResult::merge(other);
        if (sequence.empty()) 
        {
          sequence = other.sequence;
        } 
        else if (!other.sequence.empty() && sequence != other.sequence) // differ and none is empty
        {
          throw Exception::InvalidValue(__FILE__, __LINE__,
                                        OPENMS_PRETTY_FUNCTION, 
                                        "Trying to overwrite ParentSequence sequence '" + sequence + "' with conflicting value.", 
                                        other.sequence);
        } 
 
        if (description.empty())
        {
          description = other.description;
        } 
        else if (!other.description.empty() && description != other.description) // differ and none is empty
        {
          throw Exception::InvalidValue(__FILE__, __LINE__,
                                        OPENMS_PRETTY_FUNCTION, 
                                        "Trying to overwrite ParentSequence description '" + description + "' with conflicting value.", 
                                        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 sequences indexed by their accessions:
    // @TODO: allow querying/iterating over proteins and RNAs separately
    typedef boost::multi_index_container<
      ParentSequence,
      boost::multi_index::indexed_by<
        boost::multi_index::ordered_unique<boost::multi_index::member<
          ParentSequence, String, &ParentSequence::accession>>>
      > ParentSequences;
    typedef IteratorWrapper<ParentSequences::iterator> ParentSequenceRef;
 
  }
}