OpenMS
MzMLSqliteSwathHandler.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hannes Roest $
6 // $Authors: Hannes Roest
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/CONCEPT/Types.h>
12 
15 
16 // forward declarations
17 struct sqlite3;
18 
19 namespace OpenMS
20 {
21 
22  namespace Internal
23  {
24 
33  class OPENMS_DLLAPI MzMLSqliteSwathHandler
34  {
35 
36 public:
37 
43  MzMLSqliteSwathHandler(const String& filename) :
44  filename_(filename)
45  {}
46 
53  std::vector<OpenSwath::SwathMap> readSwathWindows();
54 
60  std::vector<int> readMS1Spectra();
61 
69  std::vector<int> readSpectraForWindow(const OpenSwath::SwathMap & swath_map);
70 
71 protected:
72 
74 
75  /*
76  * These are spectra and chromatogram ids that are global for a specific
77  * database file. Keeping track of them allows us to append spectra and
78  * chromatograms multiple times to a database.
79  */
82 
83  };
84 
85 
86  } // namespace Internal
87 } // namespace OpenMS
88 
Sqlite handler for SWATH data sets.
Definition: MzMLSqliteSwathHandler.h:34
std::vector< int > readMS1Spectra()
Read indices of MS1 spectra from file.
String filename_
Definition: MzMLSqliteSwathHandler.h:73
std::vector< int > readSpectraForWindow(const OpenSwath::SwathMap &swath_map)
Read indices of spectra belonging to specified SWATH window from file.
Int spec_id_
Definition: MzMLSqliteSwathHandler.h:80
MzMLSqliteSwathHandler(const String &filename)
Constructor.
Definition: MzMLSqliteSwathHandler.h:43
std::vector< OpenSwath::SwathMap > readSwathWindows()
Read SWATH windows boundaries from file.
Int chrom_id_
Definition: MzMLSqliteSwathHandler.h:81
A more convenient string class.
Definition: String.h:34
int Int
Signed integer type.
Definition: Types.h:76
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22
Data structure to hold one SWATH map with information about upper / lower isolation window and whethe...
Definition: SwathMap.h:20