| OpenMS 2.5.0

SiriusMzTabWriter.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/FORMAT/MzTabFile.h>
38
39 namespace OpenMS
40 {
41 class OPENMS_DLLAPI SiriusMzTabWriter
42 {
43 public:
44
73 struct SiriusAdapterHit
74 {
75 OpenMS::String formula;
76 OpenMS::String adduct;
77 int rank = 0;
78 double score = 0.;
79 double treescore = 0.;
80 double isoscore = 0.;
81 int explainedpeaks = 0;
82 double explainedintensity = 0.;
83 };
84
85 struct SiriusAdapterIdentification
86 {
87 double mz = 0.;
88 double rt = 0.;
89 OpenMS::String native_id;
90 int scan_index = -1;
91 int scan_number = -1;
92 OpenMS::String feature_id;
93 std::vector<SiriusAdapterHit> hits;
94 };
95
96 struct SiriusAdapterRun
97 {
98 std::vector<SiriusAdapterIdentification> identifications;
99 };
100
104 static int extract_scan_index(const String& path);
105
116 static void read(const std::vector<String>& sirius_output_paths,
117 const String& original_input_mzml,
118 const Size& top_n_hits,
119 MzTab& result);
120
121 };
122
123 }
124
OpenMS::SiriusMzTabWriter::SiriusAdapterRun::identifications
std::vector< SiriusAdapterIdentification > identifications
Definition: SiriusMzTabWriter.h:98
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::hits
std::vector< SiriusAdapterHit > hits
Definition: SiriusMzTabWriter.h:93
OpenMS::SiriusMzTabWriter::SiriusAdapterHit
Internal structure used in SiriusAdapter that is used for the conversion of the sirius output to an m...
Definition: SiriusMzTabWriter.h:73
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification
Definition: SiriusMzTabWriter.h:85
OpenMS::SiriusMzTabWriter::SiriusAdapterRun
Definition: SiriusMzTabWriter.h:96
OpenMS::SiriusMzTabWriter
Definition: SiriusMzTabWriter.h:41
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::feature_id
OpenMS::String feature_id
Definition: SiriusMzTabWriter.h:92
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:855
MzTabFile.h
OpenMS::SiriusMzTabWriter::SiriusAdapterHit::adduct
OpenMS::String adduct
Definition: SiriusMzTabWriter.h:76
OpenMS::SiriusMzTabWriter::SiriusAdapterIdentification::native_id
OpenMS::String native_id
Definition: SiriusMzTabWriter.h:89
OpenMS::SiriusMzTabWriter::SiriusAdapterHit::formula
OpenMS::String formula
Definition: SiriusMzTabWriter.h:75
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127