libpappsomspp
Library for mass spectrometry
timsframesmsrunreader.cpp
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1/**
2 * \file pappsomspp/msrun/private/timsmsrunreader.h
3 * \date 05/09/2019
4 * \author Olivier Langella
5 * \brief MSrun file reader for native Bruker TimsTOF raw data
6 */
7
8/*******************************************************************************
9 * 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
29#include "../../exception/exceptionnotimplemented.h"
30#include <QDebug>
31
32using namespace pappso;
33
34TimsFramesMsRunReader::TimsFramesMsRunReader(MsRunIdCstSPtr &msrun_id_csp)
35 : MsRunReader(msrun_id_csp)
36{
37 qDebug() << "Now initializing the TimsFramesMsRunReader.";
38
39 initialize();
40}
41
43{
44 msp_timsData = nullptr;
45}
46
47void
49{
50 msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
51 if(msp_timsData == nullptr)
52 {
53 throw PappsoException(
54 QObject::tr("ERROR in TimsFramesMsRunReader::initialize "
55 "msp_timsData is null for MsRunId %1")
56 .arg(mcsp_msRunId.get()->toString()));
57 }
58}
59
60
61bool
62TimsFramesMsRunReader::accept(const QString &file_name) const
63{
64 qDebug() << file_name;
65 return true;
66}
67
68
71 [[maybe_unused]] std::size_t spectrum_index)
72{
74 QObject::tr("Not yet implemented in TimsFramesMsRunReader %1.\n")
75 .arg(__LINE__));
76
78}
79
80
83{
84 return msp_timsData->getMassSpectrumCstSPtrByRawIndex(spectrum_index);
85}
86
87
90 bool want_binary_data) const
91{
92
93 QualifiedMassSpectrum mass_spectrum;
94
95 msp_timsData->getQualifiedMassSpectrumByRawIndex(
96 getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
97 return mass_spectrum;
98}
99
100
101void
104{
105 // Here we want to only handle mass spectra as combined scans spectra, that
106 // is, for each frame, we want all the mobility scans to be cumulated (at the
107 // integer level, that is, without conversion of all the integers to m/z
108 // values) so as to yield a *single* mass spectrum per frame.
109
110 // We can iterate in the vector of frames records and for each frame ask that
111 // all its scans be combined into a single mass spectrum.
112
113 const std::vector<FrameIdDescr> frame_id_descr_list =
114 msp_timsData->getFrameIdDescrList();
115
116 // The scan index is the index of the scan in the *whole* mass data file, it
117 // is a sequential number of scan over all the frames.
118 std::size_t scan_index = 0; // iterate in each spectrum
119
120 // We'll need it to perform the looping in the spectrum list.
121 std::size_t frames_count = msp_timsData->getTotalNumberOfFrames();
122
123 qDebug() << "The spectrum list has this much frames:" << frames_count;
124
125 // Inform the handler of the spectrum list so that it can handle feedback to
126 // the user.
127 handler.spectrumListHasSize(frames_count);
128
129 for(const FrameIdDescr &current_frame : frame_id_descr_list)
130 {
131 TimsFrameCstSPtr tims_frame =
132 msp_timsData->getTimsFrameCstSPtrCached(current_frame.m_frameId);
133
134 // Get to know the size of the frame, that is, the number of mobility
135 // scans in it.
136
137 quint32 scan_count = tims_frame->getTotalNumberOfScans();
138
139 Trace spectrum = tims_frame->cumulateScanToTrace(0, scan_count - 1);
140
141 QualifiedMassSpectrum mass_spectrum;
142
143 MassSpectrumId spectrum_id;
144
145 spectrum_id.setSpectrumIndex(scan_index);
146
147 spectrum_id.setMsRunId(getMsRunId());
148
149 // Can modify to help our case
150 spectrum_id.setNativeId(QString("frame=%1 index=%2")
151 .arg(current_frame.m_frameId)
152 .arg(scan_index));
153
154 mass_spectrum.setMassSpectrumId(spectrum_id);
155
156 // We want to document the retention time!
157 mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
158
159 // We do want to document the ms level of the spectrum and possibly the
160 // precursor's m/z and charge.
161 unsigned int frame_ms_level = tims_frame.get()->getMsLevel();
162 mass_spectrum.setMsLevel(frame_ms_level);
163
164 if(frame_ms_level > 1)
165 {
166 // FIXME
167 // We want to document the precusor's m/z, z and index.
168 }
169
170 mass_spectrum.setDtInMilliSeconds(-1);
171
172 mass_spectrum.setEmptyMassSpectrum(false);
173
174 mass_spectrum.setMassSpectrumSPtr(
175 std::make_shared<MassSpectrum>(spectrum));
176
177 handler.setQualifiedMassSpectrum(mass_spectrum);
178
179 scan_index += scan_count;
180 }
181}
182
183
184void
186 [[maybe_unused]] SpectrumCollectionHandlerInterface &handler,
187 [[maybe_unused]] unsigned int ms_level)
188{
189
190 qDebug();
191}
192
193
194std::size_t
196{
197 return msp_timsData->getTotalNumberOfScans();
198}
199
200
201bool
203{
204 return false;
205}
206
207
208bool
210{
211 msp_timsData = nullptr;
212 return true;
213}
214
215bool
217{
218 if(msp_timsData == nullptr)
219 {
220 initialize();
221 }
222 return true;
223}
224
225
228 std::size_t spectrum_index [[maybe_unused]],
229 pappso::PrecisionPtr precision [[maybe_unused]]) const
230{
231 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
232 .arg(__FILE__)
233 .arg(__FUNCTION__)
234 .arg(__LINE__));
235}
236
239 const pappso::QualifiedMassSpectrum &mass_spectrum [[maybe_unused]],
240 pappso::PrecisionPtr precision [[maybe_unused]]) const
241{
242 throw ExceptionNotImplemented(QObject::tr("Not implemented %1 %2 %3")
243 .arg(__FILE__)
244 .arg(__FUNCTION__)
245 .arg(__LINE__));
246}
247
250{
252 return msp_timsData;
253}
254
255
256Trace
258{
259 // Use the Sqlite database to fetch the total ion current chromatogram (TIC
260 // chromatogram).
261
263
264 return msp_timsData->getTicChromatogram();
265}
266
267
268Trace
270{
271
272 // We want to compute the TIC chromatogram, not load the chromatogram that is
273 // located in the SQL database.
274 //
275 // For this, we need to iterated into the frames and ask for MS1 spectra only.
276 // msp_timsData has that information:
277 //
278 // std::vector<FrameIdDescr> m_frameIdDescrList;
279 //
280 // and
281
282 // struct FrameIdDescr
283 // {
284 // std::size_t m_frameId; // frame id
285 // std::size_t m_size; // frame size (number of TOF scans in frame)
286 // std::size_t m_cumulSize; // cumulative size
287 // };
288
289 Trace tic_chromatogram;
290
291 const std::vector<FrameIdDescr> frame_descr_list =
292 msp_timsData->getFrameIdDescrList();
293
294 for(FrameIdDescr frame_id_descr : frame_descr_list)
295 {
296 TimsFrameCstSPtr tims_frame_csp =
297 msp_timsData->getTimsFrameCstSPtrCached(frame_id_descr.m_frameId);
298 std::size_t scan_begin = 0;
299 std::size_t scan_end = tims_frame_csp->getTotalNumberOfScans() - 1;
300
301 // By convention, a TIC chromatogram is only performed using MS1 spectra.
302 if(tims_frame_csp->getMsLevel() == 1)
303 {
304
305 double rt = tims_frame_csp->getTime();
306
307 tic_chromatogram.append(DataPoint(
308 rt,
309 tims_frame_csp->cumulateScansIntensities(scan_begin, scan_end)));
310 }
311 else
312 continue;
313 }
314
315 return tic_chromatogram;
316}
317
void setNativeId(const QString &native_id)
void setMsRunId(MsRunIdCstSPtr other)
void setSpectrumIndex(std::size_t index)
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition: msrunreader.h:192
MsRunIdCstSPtr mcsp_msRunId
Definition: msrunreader.h:301
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
void setDtInMilliSeconds(pappso_double rt)
Set the drift time in milliseconds.
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
void setMsLevel(uint ms_level)
Set the mass spectrum level.
void setMassSpectrumSPtr(MassSpectrumSPtr massSpectrum)
Set the MassSpectrumSPtr.
void setRtInSeconds(pappso_double rt)
Set the retention time in seconds.
void setEmptyMassSpectrum(bool is_empty_mass_spectrum)
interface to collect spectrums from the MsRunReader class
Definition: msrunreader.h:56
virtual void spectrumListHasSize(std::size_t size)
Definition: msrunreader.cpp:53
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual pappso::XicCoordSPtr newXicCoordSPtrFromQualifiedMassSpectrum(const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum
virtual QualifiedMassSpectrum qualifiedMassSpectrum(std::size_t spectrum_index, bool want_binary_data=true) const override
get a QualifiedMassSpectrum class given its scan number
virtual MassSpectrumSPtr massSpectrumSPtr(std::size_t spectrum_index) override
get a MassSpectrumSPtr class given its spectrum index
virtual Trace getTicChromatogram() override
get a TIC chromatogram
virtual bool releaseDevice() override
release data back end device if a the data back end is released, the developper has to use acquireDev...
virtual void initialize() override
virtual TimsDataSp getTimsDataSPtr()
give an access to the underlying raw data pointer
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual bool acquireDevice() override
acquire data back end device
virtual bool accept(const QString &file_name) const override
tells if the reader is able to handle this file must be implemented by private MS run reader,...
virtual pappso::XicCoordSPtr newXicCoordSPtrFromSpectrumIndex(std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
get a xic coordinate object from a given spectrum index
virtual void readSpectrumCollectionByMsLevel(SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
A simple container of DataPoint instances.
Definition: trace.h:148
size_t append(const DataPoint &data_point)
appends a datapoint and return new size
Definition: trace.cpp:614
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
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
@ rt
Retention time.
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42
std::shared_ptr< XicCoord > XicCoordSPtr
Definition: xiccoord.h:43