OpenMS  2.8.0
CsiFingerIdMzTabWriter.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Oliver Alka $
32 // $Authors: Oliver Alka $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41  class OPENMS_DLLAPI CsiFingerIdMzTabWriter
42  {
43  public:
44 
73  {
74  public:
77  unsigned int rank = 0;
78  unsigned int formula_rank = 0;
81  double score = 0.;
86  std::vector<String> pubchemids;
87  std::vector<String> links;
88 
89  };
90 
92  {
93  public:
94  double mz = 0.;
95  double rt = 0.;
97  int scan_index = -1;
98  int scan_number = -1;
100  std::vector<CsiAdapterHit> hits;
101  };
102 
104  {
105  public:
106  std::vector <CsiAdapterIdentification> identifications;
107  };
108 
119  static void read(const std::vector<String>& sirius_output_paths,
120  const String& original_input_mzml,
121  const Size& top_n_hits,
122  MzTab& result);
123 
124  };
125 }
Definition: CsiFingerIdMzTabWriter.h:42
std::vector< CsiAdapterHit > hits
Definition: CsiFingerIdMzTabWriter.h:100
OpenMS::String molecular_formula
Definition: CsiFingerIdMzTabWriter.h:80
OpenMS::String feature_id
Definition: CsiFingerIdMzTabWriter.h:99
OpenMS::String adduct
Definition: CsiFingerIdMzTabWriter.h:79
OpenMS::String inchikey2D
Definition: CsiFingerIdMzTabWriter.h:75
std::vector< String > pubchemids
Definition: CsiFingerIdMzTabWriter.h:86
OpenMS::String inchi
Definition: CsiFingerIdMzTabWriter.h:76
OpenMS::String xlogp
Definition: CsiFingerIdMzTabWriter.h:84
std::vector< String > links
Definition: CsiFingerIdMzTabWriter.h:87
static void read(const std::vector< String > &sirius_output_paths, const String &original_input_mzml, const Size &top_n_hits, MzTab &result)
Conversion of CSI:FingerID output to mzTab.
OpenMS::String dbflags
Definition: CsiFingerIdMzTabWriter.h:85
std::vector< CsiAdapterIdentification > identifications
Definition: CsiFingerIdMzTabWriter.h:106
OpenMS::StringList native_ids
Definition: CsiFingerIdMzTabWriter.h:96
OpenMS::String smiles
Definition: CsiFingerIdMzTabWriter.h:83
OpenMS::String name
Definition: CsiFingerIdMzTabWriter.h:82
Internal structure used in SiriusAdapter that is used for the conversion of the Csi:FingerID output t...
Definition: CsiFingerIdMzTabWriter.h:73
Definition: CsiFingerIdMzTabWriter.h:92
Definition: CsiFingerIdMzTabWriter.h:104
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:478
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47