SiriusFragmentAnnotation.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Oliver Alka $
// $Authors: Oliver Alka $
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#pragma once

#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);
          static std::vector<MSSpectrum> extractSiriusAnnotationsTgtOnly(const std::vector<String>& sirius_workspace_subdirs, double score_threshold, bool use_exact_mass, bool resolve);


          static std::vector<MSSpectrum> extractAnnotationsFromSiriusFile(const String& path_to_sirius_workspace, Size max_rank = 1, bool decoy = false, bool use_exact_mass = false);

      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