SiriusFragmentAnnotation.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSSpectrum.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SiriusFragmentAnnotation
      {
      public:
 
          struct SiriusTargetDecoySpectra
          {
            MSSpectrum target;
            MSSpectrum decoy;
 
            SiriusTargetDecoySpectra() = default;
            SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(target_spectrum), decoy(decoy_spectrum) {}
          };
 
          static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, const double& score_threshold, bool use_exact_mass);
 
          static void extractSiriusFragmentAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
 
          static void extractSiriusDecoyAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
      protected:
          static OpenMS::String extractNativeIDFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
 
          static OpenMS::String extractMIDFromSiriusMS_(const String& path_to_sirius_workspace);
 
          static void extractAnnotationFromSiriusFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
 
          static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
 
          static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
 
          static void extractAnnotationFromDecoyFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
 
  };
} // namespace OpenMS