OpenMS  3.0.0
SiriusMzTabWriter.h
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31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
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34 
35 #pragma once
36 
38 #include <OpenMS/FORMAT/CsvFile.h>
39 
40 namespace OpenMS
41 {
42  class OPENMS_DLLAPI SiriusMzTabWriter
43  {
44  public:
45 
77  {
78  public:
82  int rank = 0;
83  double iso_score = 0.0;
84  double tree_score = 0.0;
85  double sirius_score = 0.0;
86  int explainedpeaks = 0;
87  double explainedintensity = 0.0;
88  double median_mass_error_fragment_peaks_ppm = 0.0;
89  double median_absolute_mass_error_fragment_peaks_ppm = 0.0;
90  double mass_error_precursor_ppm = 0.0;
91  };
92 
94  {
95  public:
96  double mz = 0.;
97  double rt = 0.;
99  int scan_index = -1;
100  int scan_number = -1;
102  std::vector<SiriusAdapterHit> hits;
103  };
104 
106  {
107  public:
108  std::vector<SiriusAdapterIdentification> identifications;
109  };
110 
112  {
113  public:
114  StringList ext_n_id; // multiple possible MS2 spectra
115  double ext_mz = 0.0;
116  double ext_rt = 0.0;
117  };
118 
122  static int extractScanIndex(const String& path);
123 
127  static int extractScanNumber(const String& path);
128 
132  static String extractFeatureId(const String& path);
133 
137  static std::map< std::string, Size > extract_columnname_to_columnindex(CsvFile& csvfile);
138 
142  static SiriusSpectrumMSInfo extractSpectrumMSInfo(const String& single_sirius_path);
143 
154  static void read(const std::vector<String>& sirius_output_paths,
155  const String& original_input_mzml,
156  const Size& top_n_hits,
157  MzTab& result);
158 
159  };
160 
161  namespace SiriusVersion
162  {
165  inline const std::string CURRENT_VERSION = "4.9.0";
166  }
167 
168 }
169 
MzTabFile.h
OpenMS::SiriusMzTabWriter::SiriusAdapterHit::adduct
OpenMS::String adduct
Definition: SiriusMzTabWriter.h:80
OpenMS::SiriusMzTabWriter::SiriusAdapterHit
Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an m...
Definition: SiriusMzTabWriter.h:76
OpenMS::SiriusMzTabWriter::SiriusAdapterHit::precursor_formula
OpenMS::String precursor_formula
Definition: SiriusMzTabWriter.h:81
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::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:477
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::native_ids
OpenMS::StringList native_ids
Definition: SiriusMzTabWriter.h:98
OpenMS::SiriusMzTabWriter
Definition: SiriusMzTabWriter.h:42
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification
Definition: SiriusMzTabWriter.h:93
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SiriusVersion::CURRENT_VERSION
const std::string CURRENT_VERSION
Definition: SiriusMzTabWriter.h:165
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::hits
std::vector< SiriusAdapterHit > hits
Definition: SiriusMzTabWriter.h:102
OpenMS::SiriusMzTabWriter::SiriusSpectrumMSInfo::ext_n_id
StringList ext_n_id
Definition: SiriusMzTabWriter.h:114
CsvFile.h
OpenMS::SiriusMzTabWriter::SiriusAdapterRun
Definition: SiriusMzTabWriter.h:105
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::CsvFile
This class handles csv files. Currently only loading is implemented.
Definition: CsvFile.h:49
OpenMS::SiriusMzTabWriter::SiriusAdapterRun::identifications
std::vector< SiriusAdapterIdentification > identifications
Definition: SiriusMzTabWriter.h:108
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::feature_id
OpenMS::String feature_id
Definition: SiriusMzTabWriter.h:101
OpenMS::SiriusMzTabWriter::SiriusAdapterHit::formula
OpenMS::String formula
Definition: SiriusMzTabWriter.h:79
OpenMS::SiriusMzTabWriter::SiriusSpectrumMSInfo
Definition: SiriusMzTabWriter.h:111