libpappsomspp
Library for mass spectrometry
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timsmsrunreaderms2selected.cpp
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1/**
2 * \file pappsomspp/msrun/private/timsmsrunreaderms2.cpp
3 * \date 10/09/2019
4 * \author Olivier Langella
5 * \brief MSrun file reader for native Bruker TimsTOF specialized for MS2
6 * purpose
7 */
8
9
10/*******************************************************************************
11 * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
12 *
13 * This file is part of the PAPPSOms++ library.
14 *
15 * PAPPSOms++ is free software: you can redistribute it and/or modify
16 * it under the terms of the GNU General Public License as published by
17 * the Free Software Foundation, either version 3 of the License, or
18 * (at your option) any later version.
19 *
20 * PAPPSOms++ is distributed in the hope that it will be useful,
21 * but WITHOUT ANY WARRANTY; without even the implied warranty of
22 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
23 * GNU General Public License for more details.
24 *
25 * You should have received a copy of the GNU General Public License
26 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
27 *
28 ******************************************************************************/
29
33#include <QDebug>
34#include <QtConcurrent>
35
36using namespace pappso;
37
44
52
53void
55{
56 mpa_timsData = new TimsData(mcsp_msRunId.get()->getFileName());
57
58 mp_timsDdaPrecursors = mpa_timsData->getTimsDdaPrecursorsPtr();
59}
60
61void
64{
65 if(mp_timsDdaPrecursors != nullptr)
66 {
68 }
69 else
70 {
71 throw PappsoException(
72 QObject::tr("ERROR in TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr "
73 "mp_timsDdaPrecursors is null"));
74 }
75}
76
77void
80{
81 if(mp_timsDdaPrecursors != nullptr)
82 {
84 }
85 else
86 {
87 throw PappsoException(
88 QObject::tr("ERROR in TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr "
89 "mp_timsDdaPrecursors is null"));
90 }
91}
92
93bool
94TimsMsRunReaderMs2Selected::accept(const QString &file_name) const
95{
96 qDebug() << file_name;
97 return true;
98}
99
100
103{
104 QualifiedMassSpectrum mass_spectrum =
105 qualifiedMassSpectrum(spectrum_index, true);
106 return mass_spectrum.getMassSpectrumSPtr();
107}
108
109
112{
113 QualifiedMassSpectrum mass_spectrum =
114 qualifiedMassSpectrum(spectrum_index, true);
115 return mass_spectrum.getMassSpectrumSPtr();
116}
117
118
121 bool want_binary_data) const
122{
123
124 std::size_t precursor_index = (spectrum_index / 2) + 1;
125
126 TimsDdaPrecursors::SpectrumDescr spectrum_descr =
128
129 if(spectrum_index % 2 == 0)
130 {
131 qDebug();
132 // this is an MS1 spectrum
133 QualifiedMassSpectrum mass_spectrum_ms1;
135 getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
136 qDebug(); // << mass_spectrum_ms1.toString();
137
138 // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
139 return mass_spectrum_ms1;
140 }
141 else
142 {
143 qDebug();
144 QualifiedMassSpectrum mass_spectrum_ms2;
145 if(spectrum_descr.ms2_index != spectrum_index)
146 {
147 qDebug();
148 throw PappsoException(
149 QObject::tr(
150 "ERROR in %1 %2 %3 spectrum_descr.ms2_index != spectrum_index")
151 .arg(__FILE__)
152 .arg(__FUNCTION__)
153 .arg(__LINE__));
154 }
156 getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
157 qDebug(); // << mass_spectrum_ms2.toString();
158
159 // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
160 return mass_spectrum_ms2;
161 }
162}
163
164
165void
168{
169 const bool want_binary_data = handler.needPeakList();
170 // const bool want_binary_data = false;
171
172 // We'll need it to perform the looping in the spectrum list.
173 std::size_t spectrum_list_size = spectrumListSize();
174
175 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
176
177 // Inform the handler of the spectrum list so that it can handle feedback to
178 // the user.
179 handler.spectrumListHasSize(spectrum_list_size);
180
181 std::vector<size_t> selected_precursor{63905,
182 73549,
183 105675,
184 130439,
185 177297,
186 177369,
187 177483,
188 190453,
189 196967,
190 246691,
191 271215,
192 289423,
193 310669};
194 // QFile temp_output("/data/temp.txt");
195 // temp_output.open(QIODevice::WriteOnly | QIODevice::Text);
196 // QTextStream out(&temp_output);
197
198 // Iterate in the full list of spectra.
199 bool readAhead = handler.isReadAhead();
200
201 if(readAhead)
202 {
203
204 std::size_t process_list_size = 300;
205
206 struct tmp_item
207 {
208 QualifiedMassSpectrum qualified_mass_spectrum;
209 std::size_t iter;
210 bool want_binary_data;
211 };
212
213 for(std::size_t i = 0; i < spectrum_list_size; i += process_list_size)
214 {
215 // QTextStream out(&temp_output);
216 qDebug();
217 // If the user of this reader instance wants to stop reading the
218 // spectra, then break this loop.
219 if(handler.shouldStop())
220 {
221 qDebug() << "The operation was cancelled. Breaking the loop.";
222 break;
223 }
224 std::vector<tmp_item> item_list;
225 for(std::size_t iter = 0;
226 (iter < process_list_size) && ((iter + i) < spectrum_list_size);
227 iter++)
228 {
229 if(std::find(selected_precursor.begin(),
230 selected_precursor.end(),
231 iter + i) != selected_precursor.end())
232 {
233 bool get_data = want_binary_data;
234 if((iter + i) % 2 == 0)
235 { // MS1
236 get_data = handler.needMsLevelPeakList(1);
237 }
238 else
239 {
240 get_data = handler.needMsLevelPeakList(2);
241 }
242
243 item_list.push_back(
244 {QualifiedMassSpectrum(), iter + i, get_data});
245 }
246 }
247 qDebug() << item_list.size();
248 // Use QtConcurrentBlocking::mapped to apply the scale function to all
249 // the images in the list.
250 QtConcurrent::blockingMap(
251 item_list.begin(), item_list.end(), [this](tmp_item &one_item) {
252 qDebug() << one_item.iter;
253 one_item.qualified_mass_spectrum =
254 qualifiedMassSpectrum(one_item.iter, one_item.want_binary_data);
255
256 // qDebug() << one_item.qualified_mass_spectrum.size() << " " <<
257 // one_item.qualified_mass_spectrum.getMassSpectrumSPtr().get()->toString();
258 });
259
260 qDebug() << item_list.size();
261 for(auto &item : item_list)
262 {
263 // qDebug() <<
264 // item.qualified_mass_spectrum.getMassSpectrumSPtr()
265 // .get()
266 // ->toString();
267 handler.setQualifiedMassSpectrum(item.qualified_mass_spectrum);
268 qDebug();
269 }
270 }
271 }
272 else
273 {
274 for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
275 {
276 qDebug();
277 // If the user of this reader instance wants to stop reading the
278 // spectra, then break this loop.
279 if(handler.shouldStop())
280 {
281 qDebug() << "The operation was cancelled. Breaking the loop.";
282 break;
283 }
284 bool get_data = want_binary_data;
285 if(iter % 2 == 0)
286 { // MS1
287 if(!handler.needMsLevelPeakList(1))
288 {
289 get_data = false;
290 }
291 }
292 QualifiedMassSpectrum qualified_mass_spectrum =
293 qualifiedMassSpectrum(iter, get_data);
294 handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
295 qDebug();
296 }
297 }
298 // End of
299 // for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
300
301 // Now let the loading handler know that the loading of the data has
302 // ended. The handler might need this "signal" to perform additional tasks
303 // or to cleanup cruft.
304
305 // qDebug() << "Loading ended";
306 // temp_output.close();
307 handler.loadingEnded();
308}
309
310void
312 [[maybe_unused]] const MsRunReadConfig &config,
314{
315 return readSpectrumCollection(handler);
316}
317
318std::size_t
323
324
325bool
327{
328 return false;
329}
const MsRunIdCstSPtr & getMsRunId() const
Class representing a fully specified mass spectrum.
MassSpectrumSPtr getMassSpectrumSPtr() const
Get the MassSpectrumSPtr.
interface to collect spectrums from the MsRunReader class
virtual bool isReadAhead() const
tells if we want to read ahead spectrum
virtual bool needPeakList() const =0
tells if we need the peak list (if we want the binary data) for each spectrum
virtual bool needMsLevelPeakList(unsigned int ms_level) const final
tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level
virtual void setQualifiedMassSpectrum(const QualifiedMassSpectrum &spectrum)=0
void getQualifiedMs1MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
void getQualifiedMs2MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters ...
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr &filter)
filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters ...
TimsDdaPrecursors::SpectrumDescr getSpectrumDescrWithPrecursorId(std::size_t precursor_id) const
get an intermediate structure describing a spectrum
std::size_t getTotalPrecursorCount() const
get the number of precursors analyzed by PASEF
virtual MassSpectrumCstSPtr massSpectrumCstSPtr(std::size_t spectrum_index) override
virtual std::size_t spectrumListSize() const override
get the totat number of spectrum conained in the MSrun data file
virtual void readSpectrumCollection2(const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override
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,...
void setMs2FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
void setMs1FilterCstSPtr(pappso::FilterInterfaceCstSPtr filter)
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
TimsMsRunReaderMs2Selected(MsRunIdCstSPtr &msrun_id_csp)
virtual bool hasScanNumbers() const override
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided func...
virtual void readSpectrumCollection(SpectrumCollectionHandlerInterface &handler) override
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
TimsDdaPrecursors * mp_timsDdaPrecursors
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:46
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< const FilterInterface > FilterInterfaceCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
handle specific data for DDA MS runs