| OpenMS 2.5.0

CsiFingerIdMzTabWriter.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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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 CsiFingerIdMzTabWriter
42 {
43 public:
44
72 struct CsiAdapterHit
73 {
74 OpenMS::String inchikey2D;
75 OpenMS::String inchi;
76 unsigned int rank = 0;
77 OpenMS::String molecular_formula;
78 double score = 0.;
79 OpenMS::String name;
80 OpenMS::String smiles;
81 std::vector<String> pubchemids;
82 std::vector<String> links;
83
84 };
85
86 struct CsiAdapterIdentification
87 {
88 double mz = 0.;
89 double rt = 0.;
90 OpenMS::String native_id;
91 int scan_index = -1;
92 int scan_number = -1;
93 OpenMS::String feature_id;
94 std::vector<CsiAdapterHit> hits;
95 };
96
97 struct CsiAdapterRun
98 {
99 std::vector <CsiAdapterIdentification> identifications;
100 };
101
112 static void read(const std::vector<String>& sirius_output_paths,
113 const String& original_input_mzml,
114 const Size& top_n_hits,
115 MzTab& result);
116
117 };
118 }
119
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::smiles
OpenMS::String smiles
Definition: CsiFingerIdMzTabWriter.h:80
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::CsiFingerIdMzTabWriter
Definition: CsiFingerIdMzTabWriter.h:41
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit
Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output t...
Definition: CsiFingerIdMzTabWriter.h:72
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification
Definition: CsiFingerIdMzTabWriter.h:86
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun
Definition: CsiFingerIdMzTabWriter.h:97
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::feature_id
OpenMS::String feature_id
Definition: CsiFingerIdMzTabWriter.h:93
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::native_id
OpenMS::String native_id
Definition: CsiFingerIdMzTabWriter.h:90
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::molecular_formula
OpenMS::String molecular_formula
Definition: CsiFingerIdMzTabWriter.h:77
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterIdentification::hits
std::vector< CsiAdapterHit > hits
Definition: CsiFingerIdMzTabWriter.h:94
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::name
OpenMS::String name
Definition: CsiFingerIdMzTabWriter.h:79
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::inchi
OpenMS::String inchi
Definition: CsiFingerIdMzTabWriter.h:75
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::links
std::vector< String > links
Definition: CsiFingerIdMzTabWriter.h:82
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:855
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::inchikey2D
OpenMS::String inchikey2D
Definition: CsiFingerIdMzTabWriter.h:74
MzTabFile.h
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterRun::identifications
std::vector< CsiAdapterIdentification > identifications
Definition: CsiFingerIdMzTabWriter.h:99
OpenMS::CsiFingerIdMzTabWriter::CsiAdapterHit::pubchemids
std::vector< String > pubchemids
Definition: CsiFingerIdMzTabWriter.h:81
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127