libpappsomspp
Library for mass spectrometry
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pappso::TimsDdaPrecursors Class Reference

#include <timsddaprecursors.h>

Classes

struct  SpectrumDescr

Public Member Functions

 TimsDdaPrecursors (QSqlQuery &query, TimsData *tims_data_origin)
 ~TimsDdaPrecursors ()
std::size_t getTotalPrecursorCount () const
 get the number of precursors analyzed by PASEF
XicCoordTims getXicCoordTimsFromPrecursorId (std::size_t precursor_id, PrecisionPtr precision_ptr)
TimsDdaPrecursors::SpectrumDescr getSpectrumDescrWithPrecursorId (std::size_t precursor_id) const
 get an intermediate structure describing a spectrum
std::vector< TimsDdaPrecursors::SpectrumDescr > getSpectrumDescrListByFrameId (std::size_t frame_id) const
 get a list of TimsDdaPrecursors::SpectrumDescr for a frame
void getQualifiedMs2MassSpectrumBySpectrumDescr (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
void getQualifiedMs1MassSpectrumBySpectrumDescr (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 inside a FilterSuite object
void setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
 filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters inside a FilterSuite object
void setMs2BuiltinCentroid (bool centroid)
 enable or disable simple centroid filter on raw tims data for MS2
bool getMs2BuiltinCentroid () const
 tells if simple centroid filter on raw tims data for MS2 is enabled or not
void ms2ReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)
 function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
void setMonoThread (bool is_mono_thread)
 set only one is_mono_thread to true
void rawReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)
 function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels
std::vector< std::size_t > getPrecursorsByMzRtCharge (int charge, double mz_val, double rt_sec, double k0)
 guess possible precursor ids given a charge, m/z, retention time and k0
std::vector< std::size_t > getMatchPrecursorIdByKo (std::vector< std::vector< double > > ids, double ko_value)
std::vector< std::size_t > getClosestPrecursorIdByMz (std::vector< std::vector< double > > ids, double mz_value)
TimsDataFastMap & getCombinedMs2ScansByPrecursorId (std::size_t precursor_id)
 get cumulated raw signal for a given precursorCMakeLists.txt.userCMakeLists.txt.userCMakeLists.txt.user only to use to see the raw signal

Protected Member Functions

SpectrumDescr getSpectrumDescrWithScanCoordinates (const std::pair< std::size_t, std::size_t > &scan_coordinates)

Private Member Functions

void ms2ReaderGenerateMS1MS2Spectrum (const MsRunIdCstSPtr &msrun_id, std::vector< QualifiedMassSpectrum > &qualified_mass_spectrum_list, SpectrumCollectionHandlerInterface &handler, const SpectrumDescr &spectrum_descr, unsigned int ms_level)
void fillSpectrumDescriptionWithSqlRecord (SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list)

Private Attributes

friend TimsData
TimsData * mp_timsDataOrigin
std::size_t m_totalPrecursorCount
std::map< std::size_t, QSqlRecord > m_mapXicCoordRecord
pappso::FilterInterfaceCstSPtr mcsp_ms2Filter = nullptr
pappso::FilterInterfaceCstSPtr mcsp_ms1Filter = nullptr
bool m_builtinMs2Centroid = true
 enable builtin centroid on raw tims integers by default
bool m_isMonoThread = false
QMutex m_mutex

Detailed Description

Todo
TimsData helper that stores all related DDA informations

Definition at line 37 of file timsddaprecursors.h.

Constructor & Destructor Documentation

◆ TimsDdaPrecursors()

pappso::TimsDdaPrecursors::TimsDdaPrecursors ( QSqlQuery & query,
TimsData * tims_data_origin )

Default constructor

Definition at line 38 of file timsddaprecursors.cpp.

39 : mp_timsDataOrigin(tims_data_origin)
40{
41
42 // get number of precursors
43 qDebug();
44 m_totalPrecursorCount = 0;
45 if(!query.exec("SELECT COUNT( DISTINCT Id) FROM Precursors;"))
46 {
47 qDebug();
48 throw pappso::ExceptionNotFound(QObject::tr("ERROR : no Precursors in SqlLite database"));
49 }
50 else
51 {
52 if(query.next())
53 {
54 m_totalPrecursorCount = query.value(0).toLongLong();
55 }
56 }
57
58 qDebug();
59
60 mcsp_ms2Filter =
61 std::make_shared<FilterSuiteString>("chargeDeconvolution|0.02dalton mzExclusion|0.01dalton");
62
63
64 std::shared_ptr<FilterTriangle> ms1filter = std::make_shared<FilterTriangle>();
65 ms1filter.get()->setTriangleSlope(50, 0.01);
66 mcsp_ms1Filter = ms1filter;
67}
pappso::TimsDdaPrecursors::mcsp_ms1Filter
pappso::FilterInterfaceCstSPtr mcsp_ms1Filter
Definition timsddaprecursors.h:216
pappso::TimsDdaPrecursors::mcsp_ms2Filter
pappso::FilterInterfaceCstSPtr mcsp_ms2Filter
Definition timsddaprecursors.h:215

References m_totalPrecursorCount, mcsp_ms1Filter, mcsp_ms2Filter, mp_timsDataOrigin, and TimsData.

Referenced by ms2ReaderSpectrumCollectionByMsLevel().

◆ ~TimsDdaPrecursors()

pappso::TimsDdaPrecursors::~TimsDdaPrecursors ( )

Destructor

Definition at line 69 of file timsddaprecursors.cpp.

70{
71}

Member Function Documentation

◆ fillSpectrumDescriptionWithSqlRecord()

void pappso::TimsDdaPrecursors::fillSpectrumDescriptionWithSqlRecord ( TimsDdaPrecursors::SpectrumDescr & spectrum_descr,
QSqlQuery & qprecursor_list )
private

Definition at line 552 of file timsddaprecursors.cpp.

554{
555
556 spectrum_descr.tims_frame_list.clear();
557 spectrum_descr.tims_frame_list.push_back(qprecursor_list.value(0).toLongLong());
558 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
559 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
560 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
561 spectrum_descr.precursor_ion_data = PrecursorIonData(qprecursor_list.value(10).toDouble(),
562 qprecursor_list.value(11).toInt(),
563 qprecursor_list.value(13).toDouble());
564
565 spectrum_descr.precursor_id = qprecursor_list.value(6).toLongLong();
566 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
567 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
568
569 spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong();
570 spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong();
571
572 spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble();
573 spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble();
574 spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat();
575 spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong();
576}

References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.

Referenced by rawReaderSpectrumCollectionByMsLevel().

◆ getClosestPrecursorIdByMz()

std::vector< std::size_t > pappso::TimsDdaPrecursors::getClosestPrecursorIdByMz ( std::vector< std::vector< double > > ids,
double mz_value )
Todo
documentation

Definition at line 1476 of file timsddaprecursors.cpp.

1477{
1478 std::vector<std::size_t> best_precursor;
1479 double best_value = 1;
1480 int count = 1;
1481 int best_val_position = 0;
1482
1483 for(std::vector<double> values : ids)
1484 {
1485 double new_val = abs(mz_value - values[4]);
1486 if(new_val < best_value)
1487 {
1488 best_value = new_val;
1489 best_val_position = count;
1490 }
1491 count++;
1492 }
1493 best_precursor.push_back(ids[best_val_position][1]);
1494 return best_precursor;
1495}

Referenced by getPrecursorsByMzRtCharge().

◆ getCombinedMs2ScansByPrecursorId()

TimsDataFastMap & pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId ( std::size_t precursor_id)

get cumulated raw signal for a given precursorCMakeLists.txt.userCMakeLists.txt.userCMakeLists.txt.user only to use to see the raw signal

Parameters
precursor_indexprecursor index to extract signal from
Returns
a map of integers, x=time of flights, y= intensities

Definition at line 164 of file timsddaprecursors.cpp.

165{
166
167 qDebug();
168 TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
169 raw_spectrum.clear();
170 try
171 {
172 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
173
174 QSqlQuery q(qdb);
175 q.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
176 "PasefFrameMsMsInfo INNER JOIN Precursors ON "
177 "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
178 "Precursors.Id=%1;")
179 .arg(precursor_id));
180 if(q.lastError().isValid())
181 {
182 qDebug();
183 throw PappsoException(
184 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
185 "command %2:\n%3\n%4\n%5")
186 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
187 .arg(q.lastQuery())
188 .arg(qdb.lastError().databaseText())
189 .arg(qdb.lastError().driverText())
190 .arg(qdb.lastError().nativeErrorCode()));
191 }
192 qDebug();
193 // m_mutex.unlock();
194 if(q.size() == 0)
195 {
196
197 throw ExceptionNotFound(
198 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
199 "id=%1 not found")
200 .arg(precursor_id));
201 }
202 else
203 {
204 // qDebug() << " q.size()="<< q.size();
205 qDebug();
206 bool first = true;
207 std::size_t scan_mobility_start = 0;
208 std::size_t scan_mobility_end = 0;
209 std::vector<std::size_t> tims_frame_list;
210
211 while(q.next())
212 {
213 tims_frame_list.push_back(q.value(0).toLongLong());
214 if(first)
215 {
216
217 scan_mobility_start = q.value(1).toLongLong();
218 scan_mobility_end = q.value(2).toLongLong();
219
220 first = false;
221 }
222 }
223 // QMutexLocker locker(&m_mutex_spectrum);
224 qDebug();
225 TimsFrameCstSPtr tims_frame, previous_frame;
226 // TracePlusCombiner combiner;
227 // MapTrace combiner_result;
228 for(std::size_t tims_id : tims_frame_list)
229 {
230 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(tims_id);
231 qDebug();
232 /*combiner.combine(combiner_result,
233 tims_frame.get()->cumulateScanToTrace(
234 scan_mobility_start, scan_mobility_end));*/
235 if(previous_frame.get() != nullptr)
236 {
237 if(previous_frame.get()->hasSameCalibrationData(*tims_frame.get()))
238 {
239 }
240 else
241 {
242 throw ExceptionNotFound(
243 QObject::tr("ERROR in %1 %2, different calibration data "
244 "between frame id %3 and frame id %4")
245 .arg(__FILE__)
246 .arg(__FUNCTION__)
247 .arg(previous_frame.get()->getId())
248 .arg(tims_frame.get()->getId()));
249 }
250 }
251 tims_frame.get()->combineScansInTofIndexIntensityMap(
252 raw_spectrum, scan_mobility_start, scan_mobility_end);
253 qDebug();
254
255 previous_frame = tims_frame;
256 }
257 qDebug() << " precursor_index=" << precursor_id << " num_rows=" << tims_frame_list.size()
258 << " sql=" << q.lastQuery() << " " << (std::size_t)QThread::currentThreadId();
259 if(first == true)
260 {
261 throw ExceptionNotFound(
262 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
263 "id=%1 not found")
264 .arg(precursor_id));
265 }
266 qDebug();
267 }
268 }
269
270 catch(PappsoException &error)
271 {
272 throw PappsoException(QObject::tr("ERROR in %1 (precursor_index=%2):\n%3")
273 .arg(__FUNCTION__)
274 .arg(precursor_id)
275 .arg(error.qwhat()));
276 }
277 catch(std::exception &error)
278 {
279 qDebug() << QString("Failure %1 ").arg(error.what());
280 }
281 return raw_spectrum;
282 qDebug();
283}
pappso::TimsDataFastMap::getTimsDataFastMapInstance
static TimsDataFastMap & getTimsDataFastMapInstance()
Definition timsdatafastmap.cpp:40
pappso::TimsFrameCstSPtr
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition timsframe.h:44

References pappso::TimsDataFastMap::clear(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), mp_timsDataOrigin, pappso::PappsoException::qwhat(), and pappso::PappsoException::what().

◆ getMatchPrecursorIdByKo()

std::vector< std::size_t > pappso::TimsDdaPrecursors::getMatchPrecursorIdByKo ( std::vector< std::vector< double > > ids,
double ko_value )

Definition at line 1451 of file timsddaprecursors.cpp.

1452{
1453 std::vector<std::size_t> precursor_id;
1454 for(std::vector<double> index : ids)
1455 {
1456 auto coordinate = mp_timsDataOrigin->getScanCoordinatesByGlobalScanIndex(index[0]);
1457
1458 TimsFrameBaseCstSPtr tims_frame;
1459 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(coordinate.first);
1460
1461 double bko = tims_frame.get()->getOneOverK0Transformation(index[2]);
1462 double eko = tims_frame.get()->getOneOverK0Transformation(index[3]);
1463
1464 // qInfo() << "diff" << (bko + eko) / 2;
1465 double mean_ko = (bko + eko) / 2;
1466
1467 if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1)
1468 {
1469 precursor_id.push_back(index[1]);
1470 }
1471 }
1472 return precursor_id;
1473}
pappso::TimsFrameBaseCstSPtr
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
Definition timsframebase.h:43

References mp_timsDataOrigin.

◆ getMs2BuiltinCentroid()

bool pappso::TimsDdaPrecursors::getMs2BuiltinCentroid ( ) const

tells if simple centroid filter on raw tims data for MS2 is enabled or not

Definition at line 884 of file timsddaprecursors.cpp.

885{
886 return m_builtinMs2Centroid;
887}
pappso::TimsDdaPrecursors::m_builtinMs2Centroid
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default
Definition timsddaprecursors.h:220

References m_builtinMs2Centroid.

◆ getPrecursorsByMzRtCharge()

std::vector< std::size_t > pappso::TimsDdaPrecursors::getPrecursorsByMzRtCharge ( int charge,
double mz_val,
double rt_sec,
double k0 )

guess possible precursor ids given a charge, m/z, retention time and k0

Returns
a list of possible precursor ids

Definition at line 1374 of file timsddaprecursors.cpp.

1375{
1376
1377 std::vector<std::size_t> precursor_ids;
1378 std::vector<std::vector<double>> ids;
1379
1380 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1381 QSqlQuery q(QString("SELECT Frames.Time, Precursors.MonoisotopicMz, Precursors.Charge, "
1382 "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
1383 "PasefFrameMsMsInfo.scanNumEnd "
1384 "FROM Frames "
1385 "INNER JOIN PasefFrameMsMsInfo ON Frames.Id = "
1386 "PasefFrameMsMsInfo.Frame "
1387 "INNER JOIN Precursors ON "
1388 "PasefFrameMsMsInfo.Precursor= Precursors.Id "
1389 "WHERE Precursors.Charge == %1 "
1390 "AND Precursors.MonoisotopicMz > %2 -0.01 "
1391 "AND Precursors.MonoisotopicMz < %2 +0.01 "
1392 "AND Frames.Time >= %3 -1 "
1393 "AND Frames.Time < %3 +1; ")
1394 .arg(charge)
1395 .arg(mz_val)
1396 .arg(rt_sec));
1397 q.exec();
1398 if(q.lastError().isValid())
1399 {
1400
1401 throw PappsoException(
1402 QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
1403 "executing SQL "
1404 "command %3:\n%4\n%5\n%6")
1405 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1406 .arg(qdb.databaseName())
1407 .arg(q.lastQuery())
1408 .arg(qdb.lastError().databaseText())
1409 .arg(qdb.lastError().driverText())
1410 .arg(qdb.lastError().nativeErrorCode()));
1411 }
1412 while(q.next())
1413 {
1414 // qInfo() << q.value(0).toDouble() << q.value(1).toDouble()
1415 // << q.value(2).toDouble() << q.value(3).toDouble();
1416
1417 std::vector<double> sql_values;
1418 sql_values.push_back(q.value(4).toDouble()); // frame id
1419 sql_values.push_back(q.value(3).toDouble()); // precursor id
1420 sql_values.push_back(q.value(5).toDouble()); // scan num begin
1421 sql_values.push_back(q.value(6).toDouble()); // scan num end
1422 sql_values.push_back(q.value(1).toDouble()); // mz_value
1423
1424 ids.push_back(sql_values);
1425
1426
1427 if(std::find(precursor_ids.begin(), precursor_ids.end(), q.value(3).toDouble()) ==
1428 precursor_ids.end())
1429 {
1430 precursor_ids.push_back(q.value(3).toDouble());
1431 }
1432 }
1433
1434 if(precursor_ids.size() > 1)
1435 {
1436 // std::vector<std::size_t> precursor_ids_ko =
1437 // getMatchPrecursorIdByKo(ids, values[3]);
1438 if(precursor_ids.size() > 1)
1439 {
1440 precursor_ids = getClosestPrecursorIdByMz(ids, k0);
1441 }
1442 return precursor_ids;
1443 }
1444 else
1445 {
1446 return precursor_ids;
1447 }
1448}
pappso::TimsDdaPrecursors::getClosestPrecursorIdByMz
std::vector< std::size_t > getClosestPrecursorIdByMz(std::vector< std::vector< double > > ids, double mz_value)
Definition timsddaprecursors.cpp:1476

References getClosestPrecursorIdByMz(), and mp_timsDataOrigin.

◆ getQualifiedMs1MassSpectrumBySpectrumDescr()

void pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr ( const MsRunIdCstSPtr & msrun_id,
QualifiedMassSpectrum & mass_spectrum,
const SpectrumDescr & spectrum_descr,
bool want_binary_data )

Definition at line 579 of file timsddaprecursors.cpp.

583{
584
585
586 qDebug() << " ms2_index=" << spectrum_descr.ms2_index
587 << " precursor_index=" << spectrum_descr.precursor_id;
588
589 TracePlusCombiner combiner;
590 MapTrace combiner_result;
591
592 try
593 {
594 mass_spectrum.setMsLevel(1);
595 mass_spectrum.setPrecursorSpectrumIndex(0);
596 mass_spectrum.setEmptyMassSpectrum(true);
597
598 MassSpectrumId spectrum_id;
599 spectrum_id.setSpectrumIndex(spectrum_descr.ms1_index);
600 spectrum_id.setNativeId(QString("frame_id=%1 begin=%2 end=%3 precursor=%4 idxms1=%5")
601 .arg(spectrum_descr.parent_frame)
602 .arg(spectrum_descr.scan_mobility_start)
603 .arg(spectrum_descr.scan_mobility_end)
604 .arg(spectrum_descr.precursor_id)
605 .arg(spectrum_descr.ms1_index));
606
607 spectrum_id.setMsRunId(msrun_id);
608
609 mass_spectrum.setMassSpectrumId(spectrum_id);
610
611
612 TimsFrameBaseCstSPtr tims_frame;
613 if(want_binary_data)
614 {
615 qDebug() << "bindec";
616 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(spectrum_descr.parent_frame);
617 }
618 else
619 {
620 tims_frame =
621 mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(spectrum_descr.parent_frame);
622 }
623 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
624
625 mass_spectrum.setParameterValue(
626 QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
627 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_start));
628
629 mass_spectrum.setParameterValue(
630 QualifiedMassSpectrumParameter::IonMobOneOverK0End,
631 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_end));
632
633
634 if(want_binary_data)
635 {
636 combiner.combine(combiner_result,
637 tims_frame.get()->cumulateScansToTrace(
638 spectrum_descr.scan_mobility_start, spectrum_descr.scan_mobility_end));
639
640 Trace trace(combiner_result);
641 qDebug();
642
643 if(trace.size() > 0)
644 {
645 if(mcsp_ms1Filter != nullptr)
646 {
647 mcsp_ms1Filter->filter(trace);
648 }
649
650 qDebug();
651 mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
652 mass_spectrum.setEmptyMassSpectrum(false);
653 }
654 else
655 {
656 mass_spectrum.setMassSpectrumSPtr(nullptr);
657 mass_spectrum.setEmptyMassSpectrum(true);
658 }
659 }
660 qDebug();
661 }
662
663 catch(PappsoException &error)
664 {
665 throw error;
666 }
667 catch(std::exception &error)
668 {
669 qDebug() << QString("Failure %1 ").arg(error.what());
670 }
671}

References pappso::TracePlusCombiner::combine(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, mcsp_ms1Filter, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::PappsoException::what().

Referenced by ms2ReaderGenerateMS1MS2Spectrum().

◆ getQualifiedMs2MassSpectrumBySpectrumDescr()

void pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr ( const MsRunIdCstSPtr & msrun_id,
QualifiedMassSpectrum & mass_spectrum,
const SpectrumDescr & spectrum_descr,
bool want_binary_data )

Definition at line 686 of file timsddaprecursors.cpp.

690{
691
692
693 try
694 {
695 qDebug();
696 MassSpectrumId spectrum_id;
697
698 spectrum_id.setSpectrumIndex(spectrum_descr.ms2_index);
699 spectrum_id.setNativeId(QString("precursor=%1 idxms2=%2")
700 .arg(spectrum_descr.precursor_id)
701 .arg(spectrum_descr.ms2_index));
702 spectrum_id.setMsRunId(msrun_id);
703
704 mass_spectrum.setMassSpectrumId(spectrum_id);
705
706 mass_spectrum.setMsLevel(2);
707 qDebug() << "spectrum_descr.precursor_id=" << spectrum_descr.precursor_id
708 << " spectrum_descr.ms1_index=" << spectrum_descr.ms1_index
709 << " spectrum_descr.ms2_index=" << spectrum_descr.ms2_index;
710 mass_spectrum.setPrecursorSpectrumIndex(spectrum_descr.ms1_index);
711
712 mass_spectrum.setEmptyMassSpectrum(true);
713
714 qDebug();
715
716
717 mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
718
719 mass_spectrum.setPrecursorNativeId(
720 QString("frame_id=%1 begin=%2 end=%3 precursor=%4 idxms1=%5")
721 .arg(spectrum_descr.parent_frame)
722 .arg(spectrum_descr.scan_mobility_start)
723 .arg(spectrum_descr.scan_mobility_end)
724 .arg(spectrum_descr.precursor_id)
725 .arg(spectrum_descr.ms1_index));
726
727 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMz,
728 spectrum_descr.isolationMz);
729 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth,
730 spectrum_descr.isolationWidth);
731
732 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::CollisionEnergy,
733 spectrum_descr.collisionEnergy);
734 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
735 (quint64)spectrum_descr.precursor_id);
736
737 // QMutexLocker locker(&m_mutex_spectrum);
738 qDebug();
739 TimsFrameBaseCstSPtr tims_frame, previous_frame;
740 // TracePlusCombiner combiner;
741 // MapTrace combiner_result;
742 TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
743 raw_spectrum.clear();
744 bool first = true;
745 for(std::size_t tims_id : spectrum_descr.tims_frame_list)
746 {
747 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " tims_id=" << tims_id
748 << (std::size_t)QThread::currentThreadId();
749
750 if(want_binary_data)
751 {
752 qDebug() << "bindec";
753 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(tims_id);
754 }
755 else
756 {
757 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(tims_id);
758 }
759 qDebug() << (std::size_t)QThread::currentThreadId();
760
761 if(first)
762 {
763 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
764
765 mass_spectrum.setParameterValue(
766 QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
767 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_start));
768
769 mass_spectrum.setParameterValue(
770 QualifiedMassSpectrumParameter::IonMobOneOverK0End,
771 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_end));
772
773 first = false;
774 }
775
776
777 if(want_binary_data)
778 {
779 qDebug();
780 /*combiner.combine(combiner_result,
781 tims_frame.get()->cumulateScanToTrace(
782 scan_mobility_start, scan_mobility_end));*/
783 if(previous_frame.get() != nullptr)
784 {
785 if(previous_frame.get()->hasSameCalibrationData(*tims_frame.get()))
786 {
787 }
788 else
789 {
790 throw ExceptionNotFound(
791 QObject::tr("ERROR in %1 %2, different calibration data "
792 "between frame id %3 and frame id %4")
793 .arg(__FILE__)
794 .arg(__FUNCTION__)
795 .arg(previous_frame.get()->getId())
796 .arg(tims_frame.get()->getId()));
797 }
798 }
799 qDebug() << (std::size_t)QThread::currentThreadId();
800
801 tims_frame.get()->combineScansInTofIndexIntensityMap(
802 raw_spectrum, spectrum_descr.scan_mobility_start, spectrum_descr.scan_mobility_end);
803 qDebug() << (std::size_t)QThread::currentThreadId();
804 }
805 previous_frame = tims_frame;
806 }
807 qDebug() << " precursor_index=" << spectrum_descr.precursor_id
808 << " num_rows=" << spectrum_descr.tims_frame_list.size()
809 << (std::size_t)QThread::currentThreadId();
810 if(first == true)
811 {
812 throw ExceptionNotFound(
813 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
814 "id=%1 not found")
815 .arg(spectrum_descr.precursor_id));
816 }
817 if(want_binary_data)
818 {
819 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
820 // peak_pick.filter(trace);
821 Trace trace;
822 if(m_builtinMs2Centroid)
823 {
824 // raw_spectrum.removeArtefactualSpike();
825 raw_spectrum.builtInCentroid();
826 }
827
828 trace = tims_frame.get()->getTraceFromTofIndexIntensityMap(raw_spectrum);
829
830 if(trace.size() > 0)
831 {
832 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " " << trace.size()
833 << " " << (std::size_t)QThread::currentThreadId();
834
835 if(mcsp_ms2Filter != nullptr)
836 {
837 // FilterTriangle filter;
838 // filter.setTriangleSlope(50, 0.02);
839 // filter.filter(trace);
840 // trace.filter(FilterHighPass(10));
841 mcsp_ms2Filter->filter(trace);
842 }
843
844 // FilterScaleFactorY filter_scale((double)1 /
845 // (double)tims_frame_list.size());
846 // filter_scale.filter(trace);
847 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
848 mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
849 mass_spectrum.setEmptyMassSpectrum(false);
850 }
851 else
852 {
853 mass_spectrum.setMassSpectrumSPtr(nullptr);
854 mass_spectrum.setEmptyMassSpectrum(true);
855 }
856
857 qDebug();
858 }
859 qDebug();
860 }
861
862 catch(PappsoException &error)
863 {
864 throw PappsoException(QObject::tr("ERROR in %1 (ms2_index=%2 precursor_index=%3):\n%4")
865 .arg(__FUNCTION__)
866 .arg(spectrum_descr.ms2_index)
867 .arg(spectrum_descr.precursor_id)
868 .arg(error.qwhat()));
869 }
870 catch(std::exception &error)
871 {
872 qDebug() << QString("Failure %1 ").arg(error.what());
873 }
874 qDebug();
875}
pappso::QualifiedMassSpectrumParameter::IsolationMzWidth
@ IsolationMzWidth
m/z isolation window width (left + right)
Definition qualifiedmassspectrum.h:59
pappso::QualifiedMassSpectrumParameter::CollisionEnergy
@ CollisionEnergy
Bruker's timsTOF collision energy.
Definition qualifiedmassspectrum.h:61
pappso::QualifiedMassSpectrumParameter::BrukerPrecursorIndex
@ BrukerPrecursorIndex
Bruker's timsTOF precursor index.
Definition qualifiedmassspectrum.h:62

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::CollisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::IsolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::IsolationMzWidth, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, m_builtinMs2Centroid, mcsp_ms2Filter, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list, and pappso::PappsoException::what().

Referenced by ms2ReaderGenerateMS1MS2Spectrum().

◆ getSpectrumDescrListByFrameId()

std::vector< TimsDdaPrecursors::SpectrumDescr > pappso::TimsDdaPrecursors::getSpectrumDescrListByFrameId ( std::size_t frame_id) const

get a list of TimsDdaPrecursors::SpectrumDescr for a frame

Parameters
frame_idthe frame_id

Definition at line 74 of file timsddaprecursors.cpp.

75{
76 std::vector<TimsDdaPrecursors::SpectrumDescr> spectrum_descr_list;
77
78 try
79 {
80 // QMutexLocker lock(&m_mutex);
81 // Go get records!
82
83
84 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
85
86 QSqlQuery q(qdb);
87 q.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
88 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
89 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
90 "PasefFrameMsMsInfo.IsolationMz, " // 3
91 "PasefFrameMsMsInfo.IsolationWidth, " // 4
92 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
93 "PasefFrameMsMsInfo.Precursor, " // 6
94 "Precursors.Id, " // 7
95 "Precursors.LargestPeakMz, " // 8
96 "Precursors.AverageMz, " // 9
97 "Precursors.MonoisotopicMz, " // 10
98 "Precursors.Charge, " // 11
99 "Precursors.ScanNumber, " // 12
100 "Precursors.Intensity, " // 13
101 "Precursors.Parent " // 14
102 "FROM PasefFrameMsMsInfo "
103 "INNER JOIN Precursors ON "
104
105
106 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
107 "WHERE PasefFrameMsMsInfo.Frame=%1;")
108 .arg(frame_id));
109 if(q.lastError().isValid())
110 {
111 qDebug();
112 throw PappsoException(
113 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
114 "command %2:\n%3\n%4\n%5")
115 .arg(mp_timsDataOrigin->m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
116 .arg(q.lastQuery())
117 .arg(qdb.lastError().databaseText())
118 .arg(qdb.lastError().driverText())
119 .arg(qdb.lastError().nativeErrorCode()));
120 }
121
122 q.last(); // strange bug : get the last sql record and get back,
123 // otherwise it will not retrieve all records.
124 q.first();
125 // std::size_t i = 0;
126 do
127 {
128 TimsDdaPrecursors::SpectrumDescr spectrum_descr;
129 spectrum_descr.tims_frame_list.clear();
130 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
131 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
132 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
133 spectrum_descr.precursor_ion_data =
134 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
135
136 spectrum_descr.precursor_id = q.value(6).toLongLong();
137 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
138 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
139
140 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
141 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
142
143 spectrum_descr.isolationMz = q.value(3).toDouble();
144 spectrum_descr.isolationWidth = q.value(4).toDouble();
145 spectrum_descr.collisionEnergy = q.value(5).toFloat();
146 spectrum_descr.parent_frame = q.value(14).toLongLong();
147
148 spectrum_descr_list.push_back(spectrum_descr);
149 }
150 while(q.next());
151 }
152 catch(PappsoException &error)
153 {
154 throw error;
155 }
156 catch(std::exception &error)
157 {
158 qDebug() << QString("Failure %1 ").arg(error.what());
159 }
160 return spectrum_descr_list;
161}

References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list, and pappso::PappsoException::what().

Referenced by pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getSpectrumDescrWithPrecursorId()

TimsDdaPrecursors::SpectrumDescr pappso::TimsDdaPrecursors::getSpectrumDescrWithPrecursorId ( std::size_t precursor_id) const

get an intermediate structure describing a spectrum

Definition at line 397 of file timsddaprecursors.cpp.

398{
399
400 SpectrumDescr spectrum_descr;
401 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
402 QSqlQuery q(qdb);
403 q.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
404 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
405 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
406 "PasefFrameMsMsInfo.IsolationMz, " // 3
407 "PasefFrameMsMsInfo.IsolationWidth, " // 4
408 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
409 "PasefFrameMsMsInfo.Precursor, " // 6
410 "Precursors.Id, " // 7
411 "Precursors.LargestPeakMz, " // 8
412 "Precursors.AverageMz, " // 9
413 "Precursors.MonoisotopicMz, " // 10
414 "Precursors.Charge, " // 11
415 "Precursors.ScanNumber, " // 12
416 "Precursors.Intensity, " // 13
417 "Precursors.Parent " // 14
418 "FROM PasefFrameMsMsInfo "
419 "INNER JOIN Precursors ON "
420
421
422 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
423 "WHERE Precursors.Id=%1;")
424 .arg(precursor_id));
425 if(q.lastError().isValid())
426 {
427
428 throw PappsoException(
429 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
430 "command %2:\n%3\n%4\n%5")
431 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
432 .arg(q.lastQuery())
433 .arg(qdb.lastError().databaseText())
434 .arg(qdb.lastError().driverText())
435 .arg(qdb.lastError().nativeErrorCode()));
436 }
437
438
439 bool first = true;
440 while(q.next())
441 {
442
443 qDebug() << " cumul tims frame:" << q.value(0).toLongLong();
444 spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong());
445 if(first)
446 {
447 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
448 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
449 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
450 spectrum_descr.precursor_ion_data =
451 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
452
453 spectrum_descr.precursor_id = q.value(6).toLongLong();
454 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
455 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
456
457 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
458 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
459
460 spectrum_descr.isolationMz = q.value(3).toDouble();
461 spectrum_descr.isolationWidth = q.value(4).toDouble();
462 spectrum_descr.collisionEnergy = q.value(5).toFloat();
463 spectrum_descr.parent_frame = q.value(14).toLongLong();
464
465
466 first = false;
467 }
468 }
469 if(spectrum_descr.precursor_id == 0)
470 {
471 throw ExceptionNotFound(QObject::tr("ERROR in %1 %2 : precursor id (%3) NOT FOUND ")
472 .arg(__FILE__)
473 .arg(__FUNCTION__)
474 .arg(precursor_id));
475 }
476 return spectrum_descr;
477}

References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.

◆ getSpectrumDescrWithScanCoordinates()

TimsDdaPrecursors::SpectrumDescr pappso::TimsDdaPrecursors::getSpectrumDescrWithScanCoordinates ( const std::pair< std::size_t, std::size_t > & scan_coordinates)
protected

Definition at line 480 of file timsddaprecursors.cpp.

482{
483
484 SpectrumDescr spectrum_descr;
485 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
486 QSqlQuery q(qdb);
487 q.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
488 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
489 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
490 "PasefFrameMsMsInfo.IsolationMz, " // 3
491 "PasefFrameMsMsInfo.IsolationWidth, " // 4
492 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
493 "PasefFrameMsMsInfo.Precursor, " // 6
494 "Precursors.Id, " // 7
495 "Precursors.LargestPeakMz, " // 8
496 "Precursors.AverageMz, " // 9
497 "Precursors.MonoisotopicMz, " // 10
498 "Precursors.Charge, " // 11
499 "Precursors.ScanNumber, " // 12
500 "Precursors.Intensity, " // 13
501 "Precursors.Parent " // 14
502 "FROM PasefFrameMsMsInfo "
503 "INNER JOIN Precursors ON "
504 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
505 "WHERE "
506 "PasefFrameMsMsInfo.Frame=%1 and "
507 "(PasefFrameMsMsInfo.ScanNumBegin "
508 "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);")
509 .arg(scan_coordinates.first)
510 .arg(scan_coordinates.second));
511 if(q.lastError().isValid())
512 {
513
514 throw PappsoException(
515 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
516 "command %2:\n%3\n%4\n%5")
517 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
518 .arg(q.lastQuery())
519 .arg(qdb.lastError().databaseText())
520 .arg(qdb.lastError().driverText())
521 .arg(qdb.lastError().nativeErrorCode()));
522 }
523
524 if(q.next())
525 {
526
527 qDebug() << " cumul tims frame:" << q.value(0).toLongLong();
528 spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong());
529 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
530 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
531 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
532 spectrum_descr.precursor_ion_data =
533 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
534
535 spectrum_descr.precursor_id = q.value(6).toLongLong();
536 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
537 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
538
539 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
540 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
541
542 spectrum_descr.isolationMz = q.value(3).toDouble();
543 spectrum_descr.isolationWidth = q.value(4).toDouble();
544 spectrum_descr.collisionEnergy = q.value(5).toFloat();
545 spectrum_descr.parent_frame = q.value(14).toLongLong();
546 }
547 return spectrum_descr;
548}

References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.

◆ getTotalPrecursorCount()

std::size_t pappso::TimsDdaPrecursors::getTotalPrecursorCount ( ) const

get the number of precursors analyzed by PASEF

Definition at line 286 of file timsddaprecursors.cpp.

287{
288 return m_totalPrecursorCount;
289}

References m_totalPrecursorCount.

◆ getXicCoordTimsFromPrecursorId()

XicCoordTims pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId ( std::size_t precursor_id,
PrecisionPtr precision_ptr )

Definition at line 292 of file timsddaprecursors.cpp.

294{
295
296 qDebug();
297 XicCoordTims xic_coord_tims_struct;
298
299 try
300 {
301 if(m_mapXicCoordRecord.size() == 0)
302 {
303 QMutexLocker lock(&m_mutex);
304 // Go get records!
305
306 // We proceed in this way:
307
308 // 1. For each Precursor reference to the Precursors table's ID
309 // found in the PasefFrameMsMsInfo table, store the precursor ID for
310 // step 2.
311
312 // 2. From the Precursors table's ID from step 1, get the
313 // MonoisotopicMz.
314
315 // 3. From the PasefFrameMsMsInfo table, for the Precursors table's
316 // ID reference, get a reference to the Frames table's ID. Thanks to
317 // the Frames ID, look for the Time value (acquisition retention
318 // time) for the MS/MS spectrum. The Time value in the Frames tables
319 // always corresponds to a Frame of MsMsType 8 (that is, MS/MS),
320 // which is expected since we are looking into MS/MS data.
321
322 // 4. From the PasefFrameMsMsInfo table, associate the values
323 // ScanNumBegin and ScanNumEnd, the mobility bins in which the
324 // precursor was found.
325
326
327 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
328 QSqlQuery q(qdb);
329 q.exec(
330 QString("SELECT Precursors.id, "
331 "min(Frames.Time), "
332 "min(PasefFrameMsMsInfo.ScanNumBegin), "
333 "max(PasefFrameMsMsInfo.ScanNumEnd), "
334 "Precursors.MonoisotopicMz "
335 "FROM "
336 "PasefFrameMsMsInfo INNER JOIN Precursors ON "
337 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
338 "INNER JOIN Frames ON "
339 "PasefFrameMsMsInfo.Frame=Frames.Id "
340 "GROUP BY Precursors.id;"));
341 if(q.lastError().isValid())
342 {
343 qDebug();
344 throw PappsoException(
345 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
346 "command %2:\n%3\n%4\n%5")
347 .arg(mp_timsDataOrigin->m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
348 .arg(q.lastQuery())
349 .arg(qdb.lastError().databaseText())
350 .arg(qdb.lastError().driverText())
351 .arg(qdb.lastError().nativeErrorCode()));
352 }
353
354 q.last(); // strange bug : get the last sql record and get back,
355 // otherwise it will not retrieve all records.
356 q.first();
357 // std::size_t i = 0;
358 do
359 {
360 QSqlRecord record = q.record();
361 m_mapXicCoordRecord.insert(std::pair<std::size_t, QSqlRecord>(
362 (std::size_t)record.value(0).toULongLong(), record));
363 }
364 while(q.next());
365 }
366
367
368 auto it_map_xiccoord = m_mapXicCoordRecord.find(precursor_id);
369 if(it_map_xiccoord == m_mapXicCoordRecord.end())
370 {
371
372 throw ExceptionNotFound(
373 QObject::tr("ERROR Precursors database id %1 not found").arg(precursor_id));
374 }
375
376 auto &q = it_map_xiccoord->second;
377 xic_coord_tims_struct.mzRange = MzRange(q.value(4).toDouble(), precision_ptr);
378 xic_coord_tims_struct.scanNumBegin = q.value(2).toUInt();
379 xic_coord_tims_struct.scanNumEnd = q.value(3).toUInt();
380 xic_coord_tims_struct.rtTarget = q.value(1).toDouble();
381 // xic_structure.charge = q.value(5).toUInt();
382 xic_coord_tims_struct.xicSptr = std::make_shared<Xic>();
383 }
384 catch(PappsoException &error)
385 {
386 throw error;
387 }
388 catch(std::exception &error)
389 {
390 qDebug() << QString("Failure %1 ").arg(error.what());
391 }
392 return xic_coord_tims_struct;
393}
pappso::TimsDdaPrecursors::m_mapXicCoordRecord
std::map< std::size_t, QSqlRecord > m_mapXicCoordRecord
Definition timsddaprecursors.h:212

References m_mapXicCoordRecord, m_mutex, mp_timsDataOrigin, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::XicCoordTims::scanNumBegin, pappso::XicCoordTims::scanNumEnd, pappso::PappsoException::what(), and pappso::XicCoord::xicSptr.

◆ ms2ReaderGenerateMS1MS2Spectrum()

void pappso::TimsDdaPrecursors::ms2ReaderGenerateMS1MS2Spectrum ( const MsRunIdCstSPtr & msrun_id,
std::vector< QualifiedMassSpectrum > & qualified_mass_spectrum_list,
SpectrumCollectionHandlerInterface & handler,
const SpectrumDescr & spectrum_descr,
unsigned int ms_level )
private

Definition at line 1112 of file timsddaprecursors.cpp.

1118{
1119
1120 qDebug() << " ms_level=" << ms_level;
1121 // The handler will receive the index of the mass spectrum in the
1122 // current run via the mass spectrum id member datum.
1123 if((ms_level == 0) || (ms_level == 1))
1124 {
1125 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1126 getQualifiedMs1MassSpectrumBySpectrumDescr(msrun_id,
1127 qualified_mass_spectrum_list.back(),
1128 spectrum_descr,
1129 handler.needMsLevelPeakList(1));
1130 }
1131 if((ms_level == 0) || (ms_level == 2))
1132 {
1133 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1134 getQualifiedMs2MassSpectrumBySpectrumDescr(msrun_id,
1135 qualified_mass_spectrum_list.back(),
1136 spectrum_descr,
1137 handler.needMsLevelPeakList(2));
1138 }
1139 qDebug();
1140}
pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr
void getQualifiedMs1MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
Definition timsddaprecursors.cpp:579
pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr
void getQualifiedMs2MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
Definition timsddaprecursors.cpp:686

References getQualifiedMs1MassSpectrumBySpectrumDescr(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList().

Referenced by ms2ReaderSpectrumCollectionByMsLevel().

◆ ms2ReaderSpectrumCollectionByMsLevel()

void pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel ( const MsRunIdCstSPtr & msrun_id,
SpectrumCollectionHandlerInterface & handler,
unsigned int ms_level )

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

this function will retrieve processed qualified spectrum depending on each Bruker precursors

Definition at line 890 of file timsddaprecursors.cpp.

893{
894 qDebug() << " ms_level=" << ms_level;
895
896 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
897 QSqlQuery qprecursor_list(qdb);
898 qprecursor_list.exec(
899 QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
900 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
901 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
902 "PasefFrameMsMsInfo.IsolationMz, " // 3
903 "PasefFrameMsMsInfo.IsolationWidth, " // 4
904 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
905 "PasefFrameMsMsInfo.Precursor, " // 6
906 "Precursors.Id, " // 7
907 "Precursors.LargestPeakMz, " // 8
908 "Precursors.AverageMz, " // 9
909 "Precursors.MonoisotopicMz, " // 10
910 "Precursors.Charge, " // 11
911 "Precursors.ScanNumber, " // 12
912 "Precursors.Intensity, " // 13
913 "Precursors.Parent " // 14
914 "FROM PasefFrameMsMsInfo "
915 "INNER JOIN Precursors ON "
916 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
917 "ORDER BY PasefFrameMsMsInfo.Precursor, PasefFrameMsMsInfo.Frame ;"));
918 if(qprecursor_list.lastError().isValid())
919 {
920
921 throw PappsoException(
922 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
923 "command %2:\n%3\n%4\n%5")
924 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
925 .arg(qprecursor_list.lastQuery())
926 .arg(qdb.lastError().databaseText())
927 .arg(qdb.lastError().driverText())
928 .arg(qdb.lastError().nativeErrorCode()));
929 }
930
931
932 qDebug() << "qprecursor_list.size()=" << qprecursor_list.size();
933 qDebug() << QObject::tr(
934 "TIMS sqlite database file %1, executing SQL "
935 "command %2:\n%3\n%4\n%5")
936 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
937 .arg(qprecursor_list.lastQuery())
938 .arg(qdb.lastError().databaseText())
939 .arg(qdb.lastError().driverText())
940 .arg(qdb.lastError().nativeErrorCode());
941
942 qDebug() << "qprecursor_list.isActive()=" << qprecursor_list.isActive();
943 qDebug() << "qprecursor_list.isSelect()=" << qprecursor_list.isSelect();
944 bool first = true;
945 SpectrumDescr spectrum_descr;
946
947 /*
948std::size_t i = 0;
949while(qprecursor_list.next())
950 {
951 qDebug() << "i=" << i;
952 i++;
953 }*/
954
955 qprecursor_list.last(); // strange bug : get the last sql record and get
956 // back, otherwise it will not retrieve all records.
957
958 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
959 qprecursor_list.first();
960 std::vector<TimsDdaPrecursors::SpectrumDescr> spectrum_description_list;
961 spectrum_descr.precursor_id = 0;
962 // std::size_t i = 0;
963
964 do
965 {
966
967 if(spectrum_descr.precursor_id != (std::size_t)qprecursor_list.value(6).toLongLong())
968 {
969 // new precursor
970 if(spectrum_descr.precursor_id > 0)
971 {
972 spectrum_description_list.push_back(spectrum_descr);
973 }
974
975 spectrum_descr.tims_frame_list.clear();
976 first = true;
977 }
978 qDebug() << " qprecursor_list.value(6).toLongLong() ="
979 << qprecursor_list.value(6).toLongLong();
980 spectrum_descr.precursor_id = (std::size_t)qprecursor_list.value(6).toLongLong();
981 qDebug() << " spectrum_descr.precursor_id =" << spectrum_descr.precursor_id;
982 qDebug() << " cumul tims frame:" << qprecursor_list.value(0).toLongLong();
983 spectrum_descr.tims_frame_list.push_back(qprecursor_list.value(0).toLongLong());
984 qDebug() << " first =" << first;
985 if(first)
986 {
987 qDebug();
988 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
989 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
990 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
991 spectrum_descr.precursor_ion_data =
992 PrecursorIonData(qprecursor_list.value(10).toDouble(),
993 qprecursor_list.value(11).toInt(),
994 qprecursor_list.value(13).toDouble());
995
996 // spectrum_descr.precursor_id = q.value(6).toLongLong();
997 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
998 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
999
1000 spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong();
1001 spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong();
1002
1003 spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble();
1004 spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble();
1005 spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat();
1006 spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong();
1007
1008
1009 first = false;
1010 }
1011 // qDebug() << "qprecursor_list.executedQuery()="
1012 // << qprecursor_list.executedQuery();
1013 // qDebug() << "qprecursor_list.last()=" << qprecursor_list.last();
1014 // i++;
1015 }
1016 while(qprecursor_list.next());
1017
1018 // last One
1019
1020 // new precursor
1021 if(spectrum_descr.precursor_id > 0)
1022 {
1023 spectrum_description_list.push_back(spectrum_descr);
1024 }
1025
1026
1027 QString local_filepath =
1028 mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf");
1029
1030 if(m_isMonoThread)
1031 {
1032 for(SpectrumDescr &spectrum_descr : spectrum_description_list)
1033 {
1034
1035 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1036 ms2ReaderGenerateMS1MS2Spectrum(
1037 msrun_id, mass_spectrum_list, handler, spectrum_descr, ms_level);
1038
1039 for(auto &qualified_spectrum : mass_spectrum_list)
1040 {
1041 handler.setQualifiedMassSpectrum(qualified_spectrum);
1042 }
1043
1044 if(handler.shouldStop())
1045 {
1046 qDebug() << "The operation was cancelled. Breaking the loop.";
1047 throw ExceptionInterrupted(
1048 QObject::tr("reading TimsTOF job cancelled by the user :\n%1").arg(local_filepath));
1049 }
1050 }
1051 }
1052 else
1053 {
1054
1055
1056 TimsDdaPrecursors *itself = this;
1057 SpectrumCollectionHandlerInterface *pointer_handler = &handler;
1058
1059
1060 std::function<std::vector<QualifiedMassSpectrum>(const TimsDdaPrecursors::SpectrumDescr &)>
1061 map_function_generate_spectrum = [itself, msrun_id, pointer_handler, ms_level](
1062 const TimsDdaPrecursors::SpectrumDescr &spectrum_descr)
1063 -> std::vector<QualifiedMassSpectrum> {
1064 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1065 itself->ms2ReaderGenerateMS1MS2Spectrum(
1066 msrun_id, mass_spectrum_list, *pointer_handler, spectrum_descr, ms_level);
1067
1068
1069 return mass_spectrum_list;
1070 };
1071
1072 std::function<void(std::size_t,
1073 const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list)>
1074 reduce_function_spectrum_list =
1075 [pointer_handler, local_filepath](
1076 std::size_t res, const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list) {
1077 for(auto &qualified_spectrum : qualified_spectrum_list)
1078 {
1079 pointer_handler->setQualifiedMassSpectrum(qualified_spectrum);
1080 }
1081
1082 if(pointer_handler->shouldStop())
1083 {
1084 qDebug() << "The operation was cancelled. Breaking the loop.";
1085 throw ExceptionInterrupted(
1086 QObject::tr("reading TimsTOF job on %1 cancelled by the user")
1087 .arg(local_filepath));
1088 }
1089 res++;
1090 };
1091
1092
1093 QFuture<std::size_t> res;
1094 res = QtConcurrent::mappedReduced<std::size_t>(spectrum_description_list.begin(),
1095 spectrum_description_list.end(),
1096 map_function_generate_spectrum,
1097 reduce_function_spectrum_list,
1098 QtConcurrent::OrderedReduce);
1099 res.waitForFinished();
1100 }
1101 handler.loadingEnded();
1102 mp_timsDataOrigin->getTimsBinDecPtr()->closeLinearRead();
1103}
pappso::TimsDdaPrecursors::ms2ReaderGenerateMS1MS2Spectrum
void ms2ReaderGenerateMS1MS2Spectrum(const MsRunIdCstSPtr &msrun_id, std::vector< QualifiedMassSpectrum > &qualified_mass_spectrum_list, SpectrumCollectionHandlerInterface &handler, const SpectrumDescr &spectrum_descr, unsigned int ms_level)
Definition timsddaprecursors.cpp:1112
pappso::TimsDdaPrecursors::TimsDdaPrecursors
TimsDdaPrecursors(QSqlQuery &query, TimsData *tims_data_origin)
Definition timsddaprecursors.cpp:38

References TimsDdaPrecursors(), pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::SpectrumCollectionHandlerInterface::loadingEnded(), m_isMonoThread, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.

◆ rawReaderSpectrumCollectionByMsLevel()

void pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel ( const MsRunIdCstSPtr & msrun_id,
SpectrumCollectionHandlerInterface & handler,
unsigned int ms_level )

function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels

this function will retrieve every scans as a qualified mass spectrum

Definition at line 1143 of file timsddaprecursors.cpp.

1146{
1147
1148
1149 // We'll need it to perform the looping in the spectrum list.
1150 std::size_t spectrum_list_size = mp_timsDataOrigin->getTotalScanCount();
1151
1152 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
1153
1154 // Inform the handler of the spectrum list so that it can handle feedback to
1155 // the user.
1156 handler.spectrumListHasSize(spectrum_list_size);
1157
1158 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1159 QSqlQuery qprecursor_list(qdb);
1160 qprecursor_list.exec(
1161 QString("SELECT DISTINCT "
1162 "PasefFrameMsMsInfo.Frame, " // 0
1163 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
1164 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
1165 "PasefFrameMsMsInfo.IsolationMz, " // 3
1166 "PasefFrameMsMsInfo.IsolationWidth, " // 4
1167 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
1168 "PasefFrameMsMsInfo.Precursor, " // 6
1169 "Precursors.Id, " // 7
1170 "Precursors.LargestPeakMz, " // 8
1171 "Precursors.AverageMz, " // 9
1172 "Precursors.MonoisotopicMz, " // 10
1173 "Precursors.Charge, " // 11
1174 "Precursors.ScanNumber, " // 12
1175 "Precursors.Intensity, " // 13
1176 "Precursors.Parent " // 14
1177 "FROM PasefFrameMsMsInfo "
1178 "INNER JOIN Precursors ON "
1179 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
1180 "ORDER BY PasefFrameMsMsInfo.Frame, PasefFrameMsMsInfo.ScanNumBegin ;"));
1181 if(qprecursor_list.lastError().isValid())
1182 {
1183 throw PappsoException(
1184 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
1185 "command %2:\n%3\n%4\n%5")
1186 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1187 .arg(qprecursor_list.lastQuery())
1188 .arg(qdb.lastError().databaseText())
1189 .arg(qdb.lastError().driverText())
1190 .arg(qdb.lastError().nativeErrorCode()));
1191 }
1192
1193
1194 std::size_t i = 0; // iterate on each Spectrum
1195
1196 qprecursor_list.last(); // strange bug : get the last sql record and get
1197 // back, unless it will not retrieve all records.
1198
1199 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
1200 qprecursor_list.first();
1201
1202 TimsFrameBaseCstSPtr tims_frame;
1203 SpectrumDescr spectrum_descr;
1204
1205 for(const FrameIdDescr &current_frame : mp_timsDataOrigin->getFrameIdDescrList())
1206 {
1207
1208 // If the user of this reader instance wants to stop reading the
1209 // spectra, then break this loop.
1210 if(handler.shouldStop())
1211 {
1212 qDebug() << "The operation was cancelled. Breaking the loop.";
1213 throw ExceptionInterrupted(
1214 QObject::tr("reading TimsTOF job cancelled by the user :\n%1")
1215 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf")));
1216 }
1217
1218 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(current_frame.m_frameId);
1219 unsigned int tims_ms_level = tims_frame.get()->getMsLevel();
1220
1221 if((ms_level != 0) && (ms_level != tims_ms_level))
1222 { // bypass
1223 i += current_frame.m_scanCount;
1224 }
1225 else
1226 {
1227 bool want_binary_data = handler.needMsLevelPeakList(tims_ms_level);
1228 qDebug() << "want_binary_data=" << want_binary_data;
1229 if(want_binary_data)
1230 {
1231 qDebug() << "bindec";
1232 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(current_frame.m_frameId);
1233 }
1234
1235 bool possible_precursor = false;
1236 if(tims_ms_level == 2)
1237 {
1238 // seek the precursor record:
1239 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1240 {
1241 qprecursor_list.next();
1242
1243 if(qprecursor_list.value(0).toULongLong() == current_frame.m_frameId)
1244 {
1245 possible_precursor = true;
1246 }
1247 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1248 }
1249 }
1250
1251 for(std::size_t scan_num = 0; scan_num < current_frame.m_scanCount; scan_num++)
1252 {
1253 bool has_a_precursor = false;
1254 if(possible_precursor)
1255 {
1256 if(spectrum_descr.scan_mobility_end < scan_num)
1257 {
1258 // seek the precursor record:
1259 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1260 {
1261 qprecursor_list.next();
1262
1263 if(qprecursor_list.value(0).toULongLong() != current_frame.m_frameId)
1264 {
1265 possible_precursor = false;
1266 }
1267 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1268 }
1269 }
1270
1271 if(possible_precursor && (spectrum_descr.scan_mobility_start < scan_num))
1272 {
1273 // we are in
1274 has_a_precursor = true;
1275 }
1276 } // end to determine if we are in a precursor for this
1277 // spectrum
1278
1279 QualifiedMassSpectrum mass_spectrum;
1280
1281
1282 MassSpectrumId spectrum_id;
1283
1284 spectrum_id.setSpectrumIndex(i);
1285 spectrum_id.setMsRunId(msrun_id);
1286 spectrum_id.setNativeId(QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1287 .arg(current_frame.m_frameId)
1288 .arg(scan_num)
1289 .arg(i));
1290
1291 mass_spectrum.setMassSpectrumId(spectrum_id);
1292
1293 mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
1294 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
1295
1296 mass_spectrum.setDtInMilliSeconds(
1297 tims_frame.get()->getDriftTimeInMilliseconds(scan_num));
1298 // 1/K0
1299 mass_spectrum.setParameterValue(
1300 QualifiedMassSpectrumParameter::IonMobOneOverK0,
1301 tims_frame.get()->getOneOverK0Transformation(scan_num));
1302
1303 mass_spectrum.setEmptyMassSpectrum(true);
1304 if(want_binary_data)
1305 {
1306 try
1307 {
1308 mass_spectrum.setMassSpectrumSPtr(
1309 tims_frame.get()->getMassSpectrumSPtr(scan_num));
1310 }
1311 catch(PappsoException &error)
1312 {
1313 throw PappsoException(
1314 QObject::tr("ERROR in %1 (scan_num=%2 spectrum_index=%3):\n%4")
1315 .arg(__FUNCTION__)
1316 .arg(scan_num)
1317 .arg(spectrum_id.getSpectrumIndex())
1318 .arg(error.qwhat()));
1319 }
1320 if(mass_spectrum.size() > 0)
1321 {
1322 mass_spectrum.setEmptyMassSpectrum(false);
1323 }
1324 }
1325 else
1326 {
1327 // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0)
1328 //{
1329 mass_spectrum.setEmptyMassSpectrum(false);
1330 // }
1331 }
1332 if(has_a_precursor)
1333 {
1334 if(spectrum_descr.precursor_id > 0)
1335 {
1336
1337 mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
1338
1339 std::size_t prec_spectrum_index =
1340 mp_timsDataOrigin->getGlobalScanIndexByScanCoordinates(
1341 spectrum_descr.parent_frame, scan_num);
1342
1343 mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
1344 mass_spectrum.setPrecursorNativeId(
1345 QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1346 .arg(spectrum_descr.parent_frame)
1347 .arg(scan_num)
1348 .arg(prec_spectrum_index));
1349
1350 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMz,
1351 spectrum_descr.isolationMz);
1352 mass_spectrum.setParameterValue(
1353 QualifiedMassSpectrumParameter::IsolationMzWidth,
1354 spectrum_descr.isolationWidth);
1355
1356 mass_spectrum.setParameterValue(
1357 QualifiedMassSpectrumParameter::CollisionEnergy,
1358 spectrum_descr.collisionEnergy);
1359 mass_spectrum.setParameterValue(
1360 QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
1361 (quint64)spectrum_descr.precursor_id);
1362 }
1363 }
1364
1365 handler.setQualifiedMassSpectrum(mass_spectrum);
1366 i++;
1367 }
1368 }
1369 }
1370}
pappso::TimsDdaPrecursors::fillSpectrumDescriptionWithSqlRecord
void fillSpectrumDescriptionWithSqlRecord(SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list)
Definition timsddaprecursors.cpp:552

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, fillSpectrumDescriptionWithSqlRecord(), pappso::MassSpectrumId::getSpectrumIndex(), pappso::IonMobOneOverK0, pappso::IsolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::IsolationMzWidth, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::QualifiedMassSpectrum::size(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().

◆ setMonoThread()

void pappso::TimsDdaPrecursors::setMonoThread ( bool is_mono_thread)

set only one is_mono_thread to true

this avoid to use qtconcurrent

Definition at line 1106 of file timsddaprecursors.cpp.

1107{
1108 m_isMonoThread = is_mono_thread;
1109}

References m_isMonoThread.

◆ setMs1FilterCstSPtr()

void pappso::TimsDdaPrecursors::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr & filter)

filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters inside a FilterSuite object

Definition at line 680 of file timsddaprecursors.cpp.

681{
682 mcsp_ms1Filter = filter;
683}
pappso::ProjectParamCategory::filter
@ filter
concerning filters (psm, peptide, protein validation)
Definition projectparameters.h:48

References pappso::filter, and mcsp_ms1Filter.

◆ setMs2BuiltinCentroid()

void pappso::TimsDdaPrecursors::setMs2BuiltinCentroid ( bool centroid)

enable or disable simple centroid filter on raw tims data for MS2

Definition at line 878 of file timsddaprecursors.cpp.

879{
880 m_builtinMs2Centroid = centroid;
881}

References m_builtinMs2Centroid.

◆ setMs2FilterCstSPtr()

void pappso::TimsDdaPrecursors::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr & filter)

filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters inside a FilterSuite object

Definition at line 675 of file timsddaprecursors.cpp.

676{
677 mcsp_ms2Filter = filter;
678}

References pappso::filter, and mcsp_ms2Filter.

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsDdaPrecursors::m_builtinMs2Centroid = true
private

enable builtin centroid on raw tims integers by default

Definition at line 220 of file timsddaprecursors.h.

Referenced by getMs2BuiltinCentroid(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and setMs2BuiltinCentroid().

◆ m_isMonoThread

bool pappso::TimsDdaPrecursors::m_isMonoThread = false
private

Definition at line 222 of file timsddaprecursors.h.

Referenced by ms2ReaderSpectrumCollectionByMsLevel(), and setMonoThread().

◆ m_mapXicCoordRecord

std::map<std::size_t, QSqlRecord> pappso::TimsDdaPrecursors::m_mapXicCoordRecord
private

Definition at line 212 of file timsddaprecursors.h.

Referenced by getXicCoordTimsFromPrecursorId().

◆ m_mutex

QMutex pappso::TimsDdaPrecursors::m_mutex
private

Definition at line 224 of file timsddaprecursors.h.

Referenced by getXicCoordTimsFromPrecursorId().

◆ m_totalPrecursorCount

std::size_t pappso::TimsDdaPrecursors::m_totalPrecursorCount
private

Definition at line 209 of file timsddaprecursors.h.

Referenced by TimsDdaPrecursors(), and getTotalPrecursorCount().

◆ mcsp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsDdaPrecursors::mcsp_ms1Filter = nullptr
private

Definition at line 216 of file timsddaprecursors.h.

Referenced by TimsDdaPrecursors(), getQualifiedMs1MassSpectrumBySpectrumDescr(), and setMs1FilterCstSPtr().

◆ mcsp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsDdaPrecursors::mcsp_ms2Filter = nullptr
private

Definition at line 215 of file timsddaprecursors.h.

Referenced by TimsDdaPrecursors(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and setMs2FilterCstSPtr().

◆ mp_timsDataOrigin

TimsData* pappso::TimsDdaPrecursors::mp_timsDataOrigin
private

Definition at line 207 of file timsddaprecursors.h.

Referenced by TimsDdaPrecursors(), getCombinedMs2ScansByPrecursorId(), getMatchPrecursorIdByKo(), getPrecursorsByMzRtCharge(), getQualifiedMs1MassSpectrumBySpectrumDescr(), getQualifiedMs2MassSpectrumBySpectrumDescr(), getSpectrumDescrListByFrameId(), getSpectrumDescrWithPrecursorId(), getSpectrumDescrWithScanCoordinates(), getXicCoordTimsFromPrecursorId(), ms2ReaderSpectrumCollectionByMsLevel(), and rawReaderSpectrumCollectionByMsLevel().

◆ TimsData

friend pappso::TimsDdaPrecursors::TimsData
private

Definition at line 39 of file timsddaprecursors.h.

Referenced by TimsDdaPrecursors().

The documentation for this class was generated from the following files: