CometNativeIDRemapper.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/DATASTRUCTURES/StringUtils.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <string>
#include <unordered_map>
 
namespace OpenMS
{
namespace CometNativeIDRemapper
{
  inline const std::string ORIGINAL_NATIVE_ID = "original_native_id";
 
  inline Size rewriteToIndex(MSExperiment& exp)
  {
    Size idx = 0;
    for (auto& spec : exp.getSpectra())
    {
      spec.setMetaValue(ORIGINAL_NATIVE_ID, spec.getNativeID());
      spec.setNativeID("index=" + StringUtils::toStr(idx++));
    }
    return idx;
  }
 
  inline void translateReferencesBack(const MSExperiment& exp, PeptideIdentificationList& pids)
  {
    if (exp.empty()) { return; }
 
    // Build rewritten-id -> original-id map once (O(N) vs O(N*M) linear scan).
    std::unordered_map<std::string, std::string> id_map;
    id_map.reserve(exp.size());
    for (const auto& spec : exp.getSpectra())
    {
      if (spec.metaValueExists(ORIGINAL_NATIVE_ID)) { id_map.emplace(spec.getNativeID(), spec.getMetaValue(ORIGINAL_NATIVE_ID).toString()); }
    }
    if (id_map.empty()) { return; }
 
    for (auto& pid : pids)
    {
      auto it = id_map.find(pid.getSpectrumReference());
      if (it != id_map.end()) { pid.setSpectrumReference(it->second); }
    }
  }
} // namespace CometNativeIDRemapper
} // namespace OpenMS