OpenMS  2.8.0
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 
56  SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum) : target(target_spectrum), decoy(decoy_spectrum) {}
57  };
58 
71  static std::vector<SiriusTargetDecoySpectra> extractAndResolveSiriusAnnotations(const std::vector<String>& sirius_workspace_subdirs, const double& score_threshold, bool use_exact_mass);
72 
96  static void extractSiriusFragmentAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
97 
121  static void extractSiriusDecoyAnnotationMapping(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
122  protected:
131  static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String& path_to_sirius_workspace);
132 
143  static OpenMS::String extractConcatMIDsFromSiriusMS_(const String& path_to_sirius_workspace);
144 
159  static void extractAnnotationFromSiriusFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill, bool use_exact_mass = false);
160 
169  static std::map< Size, String > extractCompoundRankingAndFilename_(const String& path_to_sirius_workspace);
170 
179  static std::map< Size, double > extractCompoundRankingAndScore_(const String& path_to_sirius_workspace);
180 
195  static void extractAnnotationFromDecoyFile_(const String& path_to_sirius_workspace, MSSpectrum& msspectrum_to_fill);
196  };
197 } // namespace OpenMS
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
SiriusTargetDecoySpectra holds the target and/or decoy information for one entry (subdirectory from S...
Definition: SiriusFragmentAnnotation.h:49
SiriusTargetDecoySpectra(MSSpectrum target_spectrum, MSSpectrum decoy_spectrum)
Definition: SiriusFragmentAnnotation.h:56
MSSpectrum target
Definition: SiriusFragmentAnnotation.h:52
MSSpectrum decoy
Definition: SiriusFragmentAnnotation.h:53
Definition: SiriusFragmentAnnotation.h:42
static std::map< Size, double > extractCompoundRankingAndScore_(const String &path_to_sirius_workspace)
extractCompoundRankingAndFilename Extract compound ranking and score (./formula_candidates....
static std::vector< SiriusTargetDecoySpectra > extractAndResolveSiriusAnnotations(const std::vector< String > &sirius_workspace_subdirs, const double &score_threshold, bool use_exact_mass)
extractAndResolveSiriusAnnotations Extract and resolves SIRIUS target and/or decoy annotation for map...
static OpenMS::String extractConcatMIDsFromSiriusMS_(const String &path_to_sirius_workspace)
extractConcatMIDsFromSiriusMS Extract m_ids from SIRIUS output (./spectrum.ms) and concatenates them....
static void extractSiriusFragmentAnnotationMapping(const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
extractSiriusFragmentAnnotationMapping Extract concatenated native ids and concatenated m_ids (unique...
static void extractSiriusDecoyAnnotationMapping(const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill)
extractSiriusDecoyAnnotationMapping Extract concatenated native ids and concatenated m_ids (....
static void extractAnnotationFromDecoyFile_(const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill)
extractAnnotationFromDecoyFile Extract decoy annotation from SIRIUS/PASSATUTTO (./decoys/1_sumformula...
static OpenMS::String extractConcatNativeIDsFromSiriusMS_(const OpenMS::String &path_to_sirius_workspace)
extractConcatNativeIDsFromSiriusMS Extract concatenated native id from SIRIUS output (....
static void extractAnnotationFromSiriusFile_(const String &path_to_sirius_workspace, MSSpectrum &msspectrum_to_fill, bool use_exact_mass=false)
extractAnnotationFromSiriusFile Extract fragment annotation from SIRIUS (./spectra/1_sumformula....
static std::map< Size, String > extractCompoundRankingAndFilename_(const String &path_to_sirius_workspace)
extractCompoundRankingAndFilename Extract compound ranking and filename (./formula_candidates....
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47