OpenMS  3.0.0
SiriusFragmentAnnotation.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
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34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41  class OPENMS_DLLAPI SiriusFragmentAnnotation
42  {
43  public:
44 
49  {
50  public:
51 
54 
55  SiriusTargetDecoySpectra() = default;
56  SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(std::move(target_spectrum)), decoy(std::move(decoy_spectrum)) {}
57  };
58 
71  static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, double score_threshold,
72  bool use_exact_mass);
73  static std::vector<MSSpectrum> extractSiriusAnnotationsTgtOnly(const std::vector<String>& sirius_workspace_subdirs, double score_threshold, bool use_exact_mass, bool resolve);
74 
75 
107  static std::vector<MSSpectrum> extractAnnotationsFromSiriusFile(const String& path_to_sirius_workspace, Size max_rank = 1, bool decoy = false, bool use_exact_mass = false);
108 
109  protected:
118  static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
119 
130  static OpenMS::String extractConcatMIDsFromSiriusMS_(const String& path_to_sirius_workspace);
131 
140  static OpenMS::String extractFeatureIDFromSiriusMS_(const String& path_to_sirius_workspace);
141 
150  static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
151 
160  static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
161 
162  };
163 } // namespace OpenMS
OpenMS::SiriusFragmentAnnotation::SiriusTargetDecoySpectra::decoy
MSSpectrum decoy
Definition: SiriusFragmentAnnotation.h:53
OpenMS::SiriusFragmentAnnotation::SiriusTargetDecoySpectra::SiriusTargetDecoySpectra
SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum)
Definition: SiriusFragmentAnnotation.h:56
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SiriusFragmentAnnotation
Definition: SiriusFragmentAnnotation.h:41
OpenMS::SiriusFragmentAnnotation::SiriusTargetDecoySpectra::target
MSSpectrum target
Definition: SiriusFragmentAnnotation.h:52
OpenMS::SiriusFragmentAnnotation::SiriusTargetDecoySpectra
SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from S...
Definition: SiriusFragmentAnnotation.h:48
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSSpectrum.h