| OpenMS 2.5.0

MzMLSqliteSwathHandler.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 2002-2020.
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: Hannes Roest $
32 // $Authors: Hannes Roest
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Types.h>
38
39 #include <OpenMS/DATASTRUCTURES/String.h>
40 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
41
42 // forward declarations
43 struct sqlite3;
44
45 namespace OpenMS
46 {
47
48 namespace Internal
49 {
50
59 class OPENMS_DLLAPI MzMLSqliteSwathHandler
60 {
61
62 public:
63
69 MzMLSqliteSwathHandler(const String& filename) :
70 filename_(filename)
71 {}
72
79 std::vector<OpenSwath::SwathMap> readSwathWindows();
80
86 std::vector<int> readMS1Spectra();
87
95 std::vector<int> readSpectraForWindow(const OpenSwath::SwathMap & swath_map);
96
97 protected:
98
99 String filename_;
100
101 /*
102 * These are spectra and chromatogram ids that are global for a specific
103 * database file. Keeping track of them allows us to append spectra and
104 * chromatograms multiple times to a database.
105 */
106 Int spec_id_;
107 Int chrom_id_;
108
109 };
110
111
112 } // namespace Internal
113 } // namespace OpenMS
114
OpenMS::Internal::MzMLSqliteSwathHandler::MzMLSqliteSwathHandler
MzMLSqliteSwathHandler(const String &filename)
Constructor.
Definition: MzMLSqliteSwathHandler.h:69
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Internal::MzMLSqliteSwathHandler::filename_
String filename_
Definition: MzMLSqliteSwathHandler.h:99
Types.h
OpenMS::Internal::MzMLSqliteSwathHandler
Sqlite handler for SWATH data sets.
Definition: MzMLSqliteSwathHandler.h:59
OpenMS::Internal::MzMLSqliteSwathHandler::chrom_id_
Int chrom_id_
Definition: MzMLSqliteSwathHandler.h:107
OpenMS::Internal::MzMLSqliteSwathHandler::spec_id_
Int spec_id_
Definition: MzMLSqliteSwathHandler.h:106
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenSwath::SwathMap
Data structure to hold one SWATH map with information about upper / lower isolation window and whethe...
Definition: SwathMap.h:45
int
SwathMap.h