SiriusFragmentAnnotation.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FORMAT/CsvFile.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusFragmentAnnotation
      {
      public:
 
          class SiriusTargetDecoySpectra
          {
          public:
 
            MSSpectrum target;
            MSSpectrum decoy;
 
            SiriusTargetDecoySpectra() = default;
            SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(std::move(target_spectrum)), decoy(std::move(decoy_spectrum)) {}
          };
 
          static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, double score_threshold,
                                                                                          bool use_exact_mass, bool decoy_generation);
 
          static std::vector<MSSpectrum> extractAnnotationsFromSiriusFile(const String& path_to_sirius_workspace, Size max_rank = 1, bool decoy = false, bool use_exact_mass = false);
 
          static std::map< std::string, Size > extract_columnname_to_columnindex(const CsvFile& csvfile);
 
      protected:
          static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
 
          static OpenMS::String extractConcatMIDsFromSiriusMS_(const String& path_to_sirius_workspace);
 
          static OpenMS::String extractFeatureIDFromSiriusMS_(const String& path_to_sirius_workspace);
 
 
          static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
 
          static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
 
  };
} // namespace OpenMS