libpappsomspp
Library for mass spectrometry
timsdata.h
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1/**
2 * \file pappsomspp/vendors/tims/timsdata.h
3 * \date 27/08/2019
4 * \author Olivier Langella
5 * \brief main Tims data handler
6 */
7
8/*******************************************************************************
9œ* Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#pragma once
29
30#include <QDir>
31#include <QSqlDatabase>
32#include "timsbindec.h"
33#include "timsframe.h"
34#include "../../massspectrum/qualifiedmassspectrum.h"
35#include "../../processing/filters/filterinterface.h"
36#include "../../msrun/xiccoord/xiccoordtims.h"
37#include "../../msrun/msrunreader.h"
38#include <deque>
39#include <QMutex>
40#include <QSqlQuery>
42
43namespace pappso
44{
45
46class TimsData;
47
48/** \brief shared pointer on a TimsData object
49 */
50typedef std::shared_ptr<TimsData> TimsDataSp;
51
52/**
53 * @todo write docs
54 */
56{
57 public:
58 /** @brief build using the tims data directory
59 */
60 TimsData(QDir timsDataDirectory);
61
62 /**
63 * Copy constructor
64 *
65 * @param other TODO
66 */
67 TimsData(const TimsData &other);
68
69 /**
70 * Destructor
71 */
72 virtual ~TimsData();
73
74
75 /** @brief get a mass spectrum given its spectrum index
76 * @param raw_index a number begining at 0, corresponding to a Tims Scan in
77 * the order they lies in the binary data file
78 */
80 getMassSpectrumCstSPtrByRawIndex(std::size_t raw_index);
81
82 /** @brief get a mass spectrum given the tims frame database id and scan
83 * number within tims frame
84 */
85 pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t timsId,
86 std::size_t scanNum);
87
88 /** @brief get the total number of scans
89 */
90 std::size_t getTotalNumberOfScans() const;
91
92 /** @brief get the number of precursors analyzes by PASEF
93 */
94 std::size_t getTotalNumberOfPrecursors() const;
95
96 /** @brief guess possible precursor ids given a charge, m/z, retention time
97 * and k0
98 * @return a list of possible precursor ids
99 */
100 std::vector<std::size_t> getPrecursorsFromMzRtCharge(int charge,
101 double mz_val,
102 double rt_sec,
103 double k0);
104
105 unsigned int getMsLevelBySpectrumIndex(std::size_t spectrum_index);
106
107 void getQualifiedMassSpectrumByRawIndex(const MsRunIdCstSPtr &msrun_id,
108 QualifiedMassSpectrum &mass_spectrum,
109 std::size_t spectrum_index,
110 bool want_binary_data);
111
112 Trace getTicChromatogram() const;
113
115 {
116 std::size_t parent_frame = 0;
117 std::size_t precursor_id = 0;
118 std::size_t scan_mobility_start = 0;
119 std::size_t scan_mobility_end = 0;
120 std::size_t ms1_index = 0;
121 std::size_t ms2_index = 0;
122 double isolationMz = 0;
123 double isolationWidth = 0;
124 float collisionEnergy = 0;
125 std::vector<std::size_t> tims_frame_list;
127 };
128
129 void
130 getQualifiedMs2MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id,
131 QualifiedMassSpectrum &mass_spectrum,
132 const SpectrumDescr &spectrum_descr,
133 bool want_binary_data);
134
135 void
136 getQualifiedMs1MassSpectrumByPrecursorId(const MsRunIdCstSPtr &msrun_id,
137 QualifiedMassSpectrum &mass_spectrum,
138 const SpectrumDescr &spectrum_descr,
139 bool want_binary_data);
140
141 /** @brief filter interface to apply just after raw MS2 specturm extraction
142 * the filter can be a list of filters inside a FilterSuite object
143 */
144 void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter);
145
146 /** @brief filter interface to apply just after raw MS1 specturm extraction
147 * the filter can be a list of filters inside a FilterSuite object
148 */
149 void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter);
150
151 /** @brief enable or disable simple centroid filter on raw tims data for MS2
152 */
153 void setMs2BuiltinCentroid(bool centroid);
154
155
156 /** @brief tells if simple centroid filter on raw tims data for MS2 is enabled
157 * or not
158 */
159 bool getMs2BuiltinCentroid() const;
160
161
162 std::vector<std::size_t> getTimsMS1FrameIdRange(double rt_begin,
163 double rt_end) const;
164
165
166 /** @brief get a Tims frame with his database ID
167 * but look in the cache first
168 *
169 * thread safe
170 */
171 TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId);
172
173 /** @brief get a Tims frame with his database ID
174 *
175 * this function is not thread safe
176 */
177 TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId);
178
179 XicCoordTims getXicCoordTimsFromPrecursorId(std::size_t precursor_id,
180 PrecisionPtr precision_ptr);
181
182
183 /** @brief function to visit an MsRunReader and get each Spectrum in a
184 * spectrum collection handler by Ms Levels
185 *
186 * this function will retrieve processed qualified spectrum depending on each
187 * Bruker precursors
188 */
189 void ms2ReaderSpectrumCollectionByMsLevel(
190 const MsRunIdCstSPtr &msrun_id,
192 unsigned int ms_level);
193
194
195 /** @brief function to visit an MsRunReader and get each raw Spectrum in a
196 * spectrum collection handler by Ms Levels
197 *
198 * this function will retrieve every scans as a qualified mass spectrum
199 */
200 void rawReaderSpectrumCollectionByMsLevel(
201 const MsRunIdCstSPtr &msrun_id,
203 unsigned int ms_level);
204
205 /** @brief get cumulated raw signal for a given precursor
206 * only to use to see the raw signal
207 *
208 * @param precursor_index precursor index to extract signal from
209 * @result a map of integers, x=time of flights, y= intensities
210 */
211 std::map<quint32, quint32>
212 getRawMs2ByPrecursorId(std::size_t precursor_index);
213
214 /** @brief get raw signal for a spectrum index
215 * only to use to see the raw signal
216 *
217 * @param spectrum_index spcetrum index
218 * @result a map of integers, x=time of flights, y= intensities
219 */
220 std::map<quint32, quint32>
221 getRawMsBySpectrumIndex(std::size_t spectrum_index);
222
223
224 /** @brief retention timeline
225 * get retention times along the MSrun in seconds
226 * @return vector of retention times (seconds)
227 */
228 virtual std::vector<double> getRetentionTimeLine() const;
229
230 /** @brief get an intermediate structure describing a spectrum
231 */
232 SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id);
233
234 /** @brief set only one is_mono_thread to true
235 *
236 * this avoid to use qtconcurrent
237 */
238 void setMonoThread(bool is_mono_thread);
239
240
241 private:
242 SpectrumDescr getSpectrumDescrWithScanCoordinate(
243 const std::pair<std::size_t, std::size_t> &scan_coordinate);
244
245
246 std::pair<std::size_t, std::size_t>
247 getScanCoordinateFromRawIndex(std::size_t spectrum_index) const;
248
249 std::size_t getRawIndexFromCoordinate(std::size_t frame_id,
250 std::size_t scan_num) const;
251
252 QSqlDatabase openDatabaseConnection() const;
253
254
255 /** @brief get a Tims frame base (no binary data file access) with his
256 * database ID
257 */
258 TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr(std::size_t timsId);
259
260
261 TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtrCached(std::size_t timsId);
262
263
264 std::vector<std::size_t>
265 getMatchPrecursorIdByKo(std::vector<std::vector<double>> ids,
266 double ko_value);
267
268 /** @todo documentation
269 */
270 std::vector<std::size_t>
271 getClosestPrecursorIdByMz(std::vector<std::vector<double>> ids,
272 double mz_value);
273
274
275 /** @brief private function to fill m_frameIdDescrList
276 */
277 void fillFrameIdDescrList();
278
279
280 private:
281 void ms2ReaderGenerateMS1MS2Spectrum(
282 const MsRunIdCstSPtr &msrun_id,
283 std::vector<QualifiedMassSpectrum> &qualified_mass_spectrum_list,
285 const SpectrumDescr &spectrum_descr,
286 unsigned int ms_level);
287
288 void fillSpectrumDescriptionWithSqlRecord(SpectrumDescr &spectrum_descr,
289 QSqlQuery &qprecursor_list);
290
291 private:
293 TimsBinDec *mpa_timsBinDec = nullptr;
294 // QSqlDatabase *mpa_qdb = nullptr;
298 std::size_t m_cacheSize = 60;
299 std::deque<TimsFrameCstSPtr> m_timsFrameCache;
300 std::deque<TimsFrameBaseCstSPtr> m_timsFrameBaseCache;
301
302 pappso::FilterInterfaceCstSPtr mcsp_ms2Filter = nullptr;
303 pappso::FilterInterfaceCstSPtr mcsp_ms1Filter = nullptr;
304
305 /** @brief enable builtin centroid on raw tims integers by default
306 */
307 bool m_builtinMs2Centroid = true;
308
309
310 std::map<int, QSqlRecord> m_mapMzCalibrationRecord;
311 std::map<int, QSqlRecord> m_mapTimsCalibrationRecord;
312 std::vector<TimsFrameRecord> m_mapFramesRecord;
313 std::map<std::size_t, QSqlRecord> m_mapXicCoordRecord;
314
316
317
319 {
320 std::size_t m_frameId; // frame id
321 std::size_t m_size; // frame size (number of TOF scans in frame)
322 std::size_t m_cumulSize; // cumulative size
323 };
324
325
326 /** @brief store every frame id and corresponding sizes
327 */
328 std::vector<FrameIdDescr> m_frameIdDescrList;
329
330 /** @brief index to find quickly a frameId in the description list with the
331 * raw index of spectrum modulo 1000
332 * @key thousands of TOF scans
333 * @value corresponding m_frameIdDescrList index
334 */
335 std::map<std::size_t, std::size_t> m_thousandIndexToFrameIdDescrListIndex;
336
337
338 /** @brief tells if someone is loading a frame id
339 */
340 std::vector<std::size_t> m_someoneIsLoadingFrameId;
341
342 bool m_isMonoThread = false;
343
345
346 QMutex m_mutex;
347};
348} // namespace pappso
Class representing a fully specified mass spectrum.
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
std::vector< FrameIdDescr > m_frameIdDescrList
store every frame id and corresponding sizes
Definition: timsdata.h:328
std::map< std::size_t, QSqlRecord > m_mapXicCoordRecord
Definition: timsdata.h:313
std::size_t m_totalNumberOfFrames
Definition: timsdata.h:297
std::size_t m_totalNumberOfScans
Definition: timsdata.h:295
std::deque< TimsFrameCstSPtr > m_timsFrameCache
Definition: timsdata.h:299
std::vector< TimsFrameRecord > m_mapFramesRecord
Definition: timsdata.h:312
std::map< int, QSqlRecord > m_mapMzCalibrationRecord
Definition: timsdata.h:310
std::map< int, QSqlRecord > m_mapTimsCalibrationRecord
Definition: timsdata.h:311
QMutex m_mutex
Definition: timsdata.h:346
std::vector< std::size_t > m_someoneIsLoadingFrameId
tells if someone is loading a frame id
Definition: timsdata.h:340
bool m_hasPrecursorTable
Definition: timsdata.h:344
QDir m_timsDataDirectory
Definition: timsdata.h:292
MzCalibrationStore * mpa_mzCalibrationStore
Definition: timsdata.h:315
std::deque< TimsFrameBaseCstSPtr > m_timsFrameBaseCache
Definition: timsdata.h:300
std::map< std::size_t, std::size_t > m_thousandIndexToFrameIdDescrListIndex
index to find quickly a frameId in the description list with the raw index of spectrum modulo 1000 @k...
Definition: timsdata.h:335
std::size_t m_totalNumberOfPrecursors
Definition: timsdata.h:296
A simple container of DataPoint instances.
Definition: trace.h:38
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
Definition: timsframebase.h:41
std::shared_ptr< const MsRunId > MsRunIdCstSPtr
Definition: msrunid.h:45
std::shared_ptr< TimsData > TimsDataSp
shared pointer on a TimsData object
Definition: timsdata.h:50
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
Definition: massspectrum.h:55
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42
std::vector< std::size_t > tims_frame_list
Definition: timsdata.h:125
PrecursorIonData precursor_ion_data
Definition: timsdata.h:126
coordinates of the XIC to extract and the resulting XIC after extraction
Definition: xiccoordtims.h:51
binary file handler of Bruker's TimsTof raw data
handle a single Bruker's TimsTof frame