ModificationDefinitionIO.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: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
 
#include <map>
#include <set>
#include <string>
#include <vector>
 
namespace OpenMS
{
  class ConsensusMap;
  class FeatureMap;
  class ResidueModification;
 
  class OPENMS_DLLAPI ModificationDefinitionIO
  {
  public:
    static bool isDefinition(const ResidueModification* mod);
 
    static std::map<std::string, std::set<const ResidueModification*>> collect(
      const std::vector<ProteinIdentification>& protein_ids,
      const PeptideIdentificationList& peptide_ids);
 
    static std::map<std::string, std::set<const ResidueModification*>> collect(const FeatureMap& map);
 
    static std::map<std::string, std::set<const ResidueModification*>> collect(const ConsensusMap& map);
 
    static std::string encode(const std::set<const ResidueModification*>& defs);
 
    static void attach(ProteinIdentification::SearchParameters& sp,
                       const std::set<const ResidueModification*>& defs);
 
    static std::map<std::string, std::string> encodeByRun(
      const std::vector<ProteinIdentification>& protein_ids,
      const std::map<std::string, std::set<const ResidueModification*>>& defs);
 
    static Size registerFrom(const std::string& records);
 
    static Size registerFrom(const ProteinIdentification::SearchParameters& sp);
  };
} // namespace OpenMS