OpenSwathLibraryIDNormalizer.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <optional>
#include <string>
#include <unordered_map>
 
namespace OpenMS
{
  class OPENMS_DLLAPI OpenSwathLibraryIDNormalizer
  {
  public:
    struct SourceIDMapping
    {
      std::unordered_map<std::string, std::string> precursor_source_to_canonical;
 
      std::unordered_map<std::string, std::string> precursor_canonical_to_source;
 
      std::unordered_map<std::string, std::string> transition_canonical_to_source;
    };
 
    static SourceIDMapping normalizeSourceIDs(OpenSwath::LightTargetedExperiment& exp);
 
    static void materializeDecoyPrefix(OpenSwath::LightTargetedExperiment& exp,
                                       const SourceIDMapping& source_ids,
                                       const std::string& decoy_prefix);
 
    static std::optional<std::string> canonicalTargetForDecoyPrecursor(
      const std::string& decoy_ref,
      const SourceIDMapping& source_ids,
      const std::string& decoy_prefix);
 
    static bool hasCanonicalIDs(const OpenSwath::LightTargetedExperiment& exp);
 
    static bool hasCanonicalIDFormat(const OpenSwath::LightTargetedExperiment& exp) noexcept;
 
    static void validateCanonicalIDs(const OpenSwath::LightTargetedExperiment& exp);
  };
} // namespace OpenMS