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 1482 of file timsddaprecursors.cpp.

1483{
1484 std::vector<std::size_t> best_precursor;
1485 double best_value = 1;
1486 int count = 1;
1487 int best_val_position = 0;
1488
1489 for(std::vector<double> values : ids)
1490 {
1491 double new_val = abs(mz_value - values[4]);
1492 if(new_val < best_value)
1493 {
1494 best_value = new_val;
1495 best_val_position = count;
1496 }
1497 count++;
1498 }
1499 best_precursor.push_back(ids[best_val_position][1]);
1500 return best_precursor;
1501}

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 1457 of file timsddaprecursors.cpp.

1458{
1459 std::vector<std::size_t> precursor_id;
1460 for(std::vector<double> index : ids)
1461 {
1462 auto coordinate = mp_timsDataOrigin->getScanCoordinatesByGlobalScanIndex(index[0]);
1463
1464 TimsFrameBaseCstSPtr tims_frame;
1465 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(coordinate.first);
1466
1467 double bko = tims_frame.get()->getOneOverK0Transformation(index[2]);
1468 double eko = tims_frame.get()->getOneOverK0Transformation(index[3]);
1469
1470 // qInfo() << "diff" << (bko + eko) / 2;
1471 double mean_ko = (bko + eko) / 2;
1472
1473 if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1)
1474 {
1475 precursor_id.push_back(index[1]);
1476 }
1477 }
1478 return precursor_id;
1479}
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 886 of file timsddaprecursors.cpp.

887{
888 return m_builtinMs2Centroid;
889}
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 1380 of file timsddaprecursors.cpp.

1381{
1382
1383 std::vector<std::size_t> precursor_ids;
1384 std::vector<std::vector<double>> ids;
1385
1386 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1387 QSqlQuery q(QString("SELECT Frames.Time, Precursors.MonoisotopicMz, Precursors.Charge, "
1388 "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
1389 "PasefFrameMsMsInfo.scanNumEnd "
1390 "FROM Frames "
1391 "INNER JOIN PasefFrameMsMsInfo ON Frames.Id = "
1392 "PasefFrameMsMsInfo.Frame "
1393 "INNER JOIN Precursors ON "
1394 "PasefFrameMsMsInfo.Precursor= Precursors.Id "
1395 "WHERE Precursors.Charge == %1 "
1396 "AND Precursors.MonoisotopicMz > %2 -0.01 "
1397 "AND Precursors.MonoisotopicMz < %2 +0.01 "
1398 "AND Frames.Time >= %3 -1 "
1399 "AND Frames.Time < %3 +1; ")
1400 .arg(charge)
1401 .arg(mz_val)
1402 .arg(rt_sec));
1403 q.exec();
1404 if(q.lastError().isValid())
1405 {
1406
1407 throw PappsoException(
1408 QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
1409 "executing SQL "
1410 "command %3:\n%4\n%5\n%6")
1411 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1412 .arg(qdb.databaseName())
1413 .arg(q.lastQuery())
1414 .arg(qdb.lastError().databaseText())
1415 .arg(qdb.lastError().driverText())
1416 .arg(qdb.lastError().nativeErrorCode()));
1417 }
1418 while(q.next())
1419 {
1420 // qInfo() << q.value(0).toDouble() << q.value(1).toDouble()
1421 // << q.value(2).toDouble() << q.value(3).toDouble();
1422
1423 std::vector<double> sql_values;
1424 sql_values.push_back(q.value(4).toDouble()); // frame id
1425 sql_values.push_back(q.value(3).toDouble()); // precursor id
1426 sql_values.push_back(q.value(5).toDouble()); // scan num begin
1427 sql_values.push_back(q.value(6).toDouble()); // scan num end
1428 sql_values.push_back(q.value(1).toDouble()); // mz_value
1429
1430 ids.push_back(sql_values);
1431
1432
1433 if(std::find(precursor_ids.begin(), precursor_ids.end(), q.value(3).toDouble()) ==
1434 precursor_ids.end())
1435 {
1436 precursor_ids.push_back(q.value(3).toDouble());
1437 }
1438 }
1439
1440 if(precursor_ids.size() > 1)
1441 {
1442 // std::vector<std::size_t> precursor_ids_ko =
1443 // getMatchPrecursorIdByKo(ids, values[3]);
1444 if(precursor_ids.size() > 1)
1445 {
1446 precursor_ids = getClosestPrecursorIdByMz(ids, k0);
1447 }
1448 return precursor_ids;
1449 }
1450 else
1451 {
1452 return precursor_ids;
1453 }
1454}
pappso::TimsDdaPrecursors::getClosestPrecursorIdByMz
std::vector< std::size_t > getClosestPrecursorIdByMz(std::vector< std::vector< double > > ids, double mz_value)
Definition timsddaprecursors.cpp:1482

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::IsolationWindowTargetMz,
728 spectrum_descr.isolationMz);
729 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationWindowLowerOffset,
730 spectrum_descr.isolationWidth);
731 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationWindowUpperOffset,
732 spectrum_descr.isolationWidth);
733
734 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::CollisionEnergy,
735 spectrum_descr.collisionEnergy);
736 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
737 (quint64)spectrum_descr.precursor_id);
738
739 // QMutexLocker locker(&m_mutex_spectrum);
740 qDebug();
741 TimsFrameBaseCstSPtr tims_frame, previous_frame;
742 // TracePlusCombiner combiner;
743 // MapTrace combiner_result;
744 TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
745 raw_spectrum.clear();
746 bool first = true;
747 for(std::size_t tims_id : spectrum_descr.tims_frame_list)
748 {
749 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " tims_id=" << tims_id
750 << (std::size_t)QThread::currentThreadId();
751
752 if(want_binary_data)
753 {
754 qDebug() << "bindec";
755 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(tims_id);
756 }
757 else
758 {
759 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(tims_id);
760 }
761 qDebug() << (std::size_t)QThread::currentThreadId();
762
763 if(first)
764 {
765 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
766
767 mass_spectrum.setParameterValue(
768 QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
769 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_start));
770
771 mass_spectrum.setParameterValue(
772 QualifiedMassSpectrumParameter::IonMobOneOverK0End,
773 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_end));
774
775 first = false;
776 }
777
778
779 if(want_binary_data)
780 {
781 qDebug();
782 /*combiner.combine(combiner_result,
783 tims_frame.get()->cumulateScanToTrace(
784 scan_mobility_start, scan_mobility_end));*/
785 if(previous_frame.get() != nullptr)
786 {
787 if(previous_frame.get()->hasSameCalibrationData(*tims_frame.get()))
788 {
789 }
790 else
791 {
792 throw ExceptionNotFound(
793 QObject::tr("ERROR in %1 %2, different calibration data "
794 "between frame id %3 and frame id %4")
795 .arg(__FILE__)
796 .arg(__FUNCTION__)
797 .arg(previous_frame.get()->getId())
798 .arg(tims_frame.get()->getId()));
799 }
800 }
801 qDebug() << (std::size_t)QThread::currentThreadId();
802
803 tims_frame.get()->combineScansInTofIndexIntensityMap(
804 raw_spectrum, spectrum_descr.scan_mobility_start, spectrum_descr.scan_mobility_end);
805 qDebug() << (std::size_t)QThread::currentThreadId();
806 }
807 previous_frame = tims_frame;
808 }
809 qDebug() << " precursor_index=" << spectrum_descr.precursor_id
810 << " num_rows=" << spectrum_descr.tims_frame_list.size()
811 << (std::size_t)QThread::currentThreadId();
812 if(first == true)
813 {
814 throw ExceptionNotFound(
815 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
816 "id=%1 not found")
817 .arg(spectrum_descr.precursor_id));
818 }
819 if(want_binary_data)
820 {
821 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
822 // peak_pick.filter(trace);
823 Trace trace;
824 if(m_builtinMs2Centroid)
825 {
826 // raw_spectrum.removeArtefactualSpike();
827 raw_spectrum.builtInCentroid();
828 }
829
830 trace = tims_frame.get()->getTraceFromTofIndexIntensityMap(raw_spectrum);
831
832 if(trace.size() > 0)
833 {
834 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " " << trace.size()
835 << " " << (std::size_t)QThread::currentThreadId();
836
837 if(mcsp_ms2Filter != nullptr)
838 {
839 // FilterTriangle filter;
840 // filter.setTriangleSlope(50, 0.02);
841 // filter.filter(trace);
842 // trace.filter(FilterHighPass(10));
843 mcsp_ms2Filter->filter(trace);
844 }
845
846 // FilterScaleFactorY filter_scale((double)1 /
847 // (double)tims_frame_list.size());
848 // filter_scale.filter(trace);
849 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
850 mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
851 mass_spectrum.setEmptyMassSpectrum(false);
852 }
853 else
854 {
855 mass_spectrum.setMassSpectrumSPtr(nullptr);
856 mass_spectrum.setEmptyMassSpectrum(true);
857 }
858
859 qDebug();
860 }
861 qDebug();
862 }
863
864 catch(PappsoException &error)
865 {
866 throw PappsoException(QObject::tr("ERROR in %1 (ms2_index=%2 precursor_index=%3):\n%4")
867 .arg(__FUNCTION__)
868 .arg(spectrum_descr.ms2_index)
869 .arg(spectrum_descr.precursor_id)
870 .arg(error.qwhat()));
871 }
872 catch(std::exception &error)
873 {
874 qDebug() << QString("Failure %1 ").arg(error.what());
875 }
876 qDebug();
877}
pappso::QualifiedMassSpectrumParameter::IsolationWindowTargetMz
@ IsolationWindowTargetMz
Isolation m/z value isolation window target m/z (thomson).
Definition qualifiedmassspectrum.h:57
pappso::QualifiedMassSpectrumParameter::IsolationWindowUpperOffset
@ IsolationWindowUpperOffset
isolation window upper offset (thomson)
Definition qualifiedmassspectrum.h:59
pappso::QualifiedMassSpectrumParameter::CollisionEnergy
@ CollisionEnergy
Bruker's timsTOF collision energy.
Definition qualifiedmassspectrum.h:62
pappso::QualifiedMassSpectrumParameter::IsolationWindowLowerOffset
@ IsolationWindowLowerOffset
isolation window lower offset (thomson)
Definition qualifiedmassspectrum.h:58
pappso::QualifiedMassSpectrumParameter::BrukerPrecursorIndex
@ BrukerPrecursorIndex
Bruker's timsTOF precursor index.
Definition qualifiedmassspectrum.h:63

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::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::IsolationWindowLowerOffset, pappso::IsolationWindowTargetMz, pappso::IsolationWindowUpperOffset, 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 1114 of file timsddaprecursors.cpp.

1120{
1121
1122 qDebug() << " ms_level=" << ms_level;
1123 // The handler will receive the index of the mass spectrum in the
1124 // current run via the mass spectrum id member datum.
1125 if((ms_level == 0) || (ms_level == 1))
1126 {
1127 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1128 getQualifiedMs1MassSpectrumBySpectrumDescr(msrun_id,
1129 qualified_mass_spectrum_list.back(),
1130 spectrum_descr,
1131 handler.needMsLevelPeakList(1));
1132 }
1133 if((ms_level == 0) || (ms_level == 2))
1134 {
1135 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1136 getQualifiedMs2MassSpectrumBySpectrumDescr(msrun_id,
1137 qualified_mass_spectrum_list.back(),
1138 spectrum_descr,
1139 handler.needMsLevelPeakList(2));
1140 }
1141 qDebug();
1142}
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 892 of file timsddaprecursors.cpp.

895{
896 qDebug() << " ms_level=" << ms_level;
897
898 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
899 QSqlQuery qprecursor_list(qdb);
900 qprecursor_list.exec(
901 QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
902 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
903 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
904 "PasefFrameMsMsInfo.IsolationMz, " // 3
905 "PasefFrameMsMsInfo.IsolationWidth, " // 4
906 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
907 "PasefFrameMsMsInfo.Precursor, " // 6
908 "Precursors.Id, " // 7
909 "Precursors.LargestPeakMz, " // 8
910 "Precursors.AverageMz, " // 9
911 "Precursors.MonoisotopicMz, " // 10
912 "Precursors.Charge, " // 11
913 "Precursors.ScanNumber, " // 12
914 "Precursors.Intensity, " // 13
915 "Precursors.Parent " // 14
916 "FROM PasefFrameMsMsInfo "
917 "INNER JOIN Precursors ON "
918 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
919 "ORDER BY PasefFrameMsMsInfo.Precursor, PasefFrameMsMsInfo.Frame ;"));
920 if(qprecursor_list.lastError().isValid())
921 {
922
923 throw PappsoException(
924 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
925 "command %2:\n%3\n%4\n%5")
926 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
927 .arg(qprecursor_list.lastQuery())
928 .arg(qdb.lastError().databaseText())
929 .arg(qdb.lastError().driverText())
930 .arg(qdb.lastError().nativeErrorCode()));
931 }
932
933
934 qDebug() << "qprecursor_list.size()=" << qprecursor_list.size();
935 qDebug() << QObject::tr(
936 "TIMS sqlite database file %1, executing SQL "
937 "command %2:\n%3\n%4\n%5")
938 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
939 .arg(qprecursor_list.lastQuery())
940 .arg(qdb.lastError().databaseText())
941 .arg(qdb.lastError().driverText())
942 .arg(qdb.lastError().nativeErrorCode());
943
944 qDebug() << "qprecursor_list.isActive()=" << qprecursor_list.isActive();
945 qDebug() << "qprecursor_list.isSelect()=" << qprecursor_list.isSelect();
946 bool first = true;
947 SpectrumDescr spectrum_descr;
948
949 /*
950std::size_t i = 0;
951while(qprecursor_list.next())
952 {
953 qDebug() << "i=" << i;
954 i++;
955 }*/
956
957 qprecursor_list.last(); // strange bug : get the last sql record and get
958 // back, otherwise it will not retrieve all records.
959
960 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
961 qprecursor_list.first();
962 std::vector<TimsDdaPrecursors::SpectrumDescr> spectrum_description_list;
963 spectrum_descr.precursor_id = 0;
964 // std::size_t i = 0;
965
966 do
967 {
968
969 if(spectrum_descr.precursor_id != (std::size_t)qprecursor_list.value(6).toLongLong())
970 {
971 // new precursor
972 if(spectrum_descr.precursor_id > 0)
973 {
974 spectrum_description_list.push_back(spectrum_descr);
975 }
976
977 spectrum_descr.tims_frame_list.clear();
978 first = true;
979 }
980 qDebug() << " qprecursor_list.value(6).toLongLong() ="
981 << qprecursor_list.value(6).toLongLong();
982 spectrum_descr.precursor_id = (std::size_t)qprecursor_list.value(6).toLongLong();
983 qDebug() << " spectrum_descr.precursor_id =" << spectrum_descr.precursor_id;
984 qDebug() << " cumul tims frame:" << qprecursor_list.value(0).toLongLong();
985 spectrum_descr.tims_frame_list.push_back(qprecursor_list.value(0).toLongLong());
986 qDebug() << " first =" << first;
987 if(first)
988 {
989 qDebug();
990 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
991 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
992 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
993 spectrum_descr.precursor_ion_data =
994 PrecursorIonData(qprecursor_list.value(10).toDouble(),
995 qprecursor_list.value(11).toInt(),
996 qprecursor_list.value(13).toDouble());
997
998 // spectrum_descr.precursor_id = q.value(6).toLongLong();
999 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
1000 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
1001
1002 spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong();
1003 spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong();
1004
1005 spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble();
1006 spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble();
1007 spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat();
1008 spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong();
1009
1010
1011 first = false;
1012 }
1013 // qDebug() << "qprecursor_list.executedQuery()="
1014 // << qprecursor_list.executedQuery();
1015 // qDebug() << "qprecursor_list.last()=" << qprecursor_list.last();
1016 // i++;
1017 }
1018 while(qprecursor_list.next());
1019
1020 // last One
1021
1022 // new precursor
1023 if(spectrum_descr.precursor_id > 0)
1024 {
1025 spectrum_description_list.push_back(spectrum_descr);
1026 }
1027
1028
1029 QString local_filepath =
1030 mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf");
1031
1032 if(m_isMonoThread)
1033 {
1034 for(SpectrumDescr &spectrum_descr : spectrum_description_list)
1035 {
1036
1037 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1038 ms2ReaderGenerateMS1MS2Spectrum(
1039 msrun_id, mass_spectrum_list, handler, spectrum_descr, ms_level);
1040
1041 for(auto &qualified_spectrum : mass_spectrum_list)
1042 {
1043 handler.setQualifiedMassSpectrum(qualified_spectrum);
1044 }
1045
1046 if(handler.shouldStop())
1047 {
1048 qDebug() << "The operation was cancelled. Breaking the loop.";
1049 throw ExceptionInterrupted(
1050 QObject::tr("reading TimsTOF job cancelled by the user :\n%1").arg(local_filepath));
1051 }
1052 }
1053 }
1054 else
1055 {
1056
1057
1058 TimsDdaPrecursors *itself = this;
1059 SpectrumCollectionHandlerInterface *pointer_handler = &handler;
1060
1061
1062 std::function<std::vector<QualifiedMassSpectrum>(const TimsDdaPrecursors::SpectrumDescr &)>
1063 map_function_generate_spectrum = [itself, msrun_id, pointer_handler, ms_level](
1064 const TimsDdaPrecursors::SpectrumDescr &spectrum_descr)
1065 -> std::vector<QualifiedMassSpectrum> {
1066 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1067 itself->ms2ReaderGenerateMS1MS2Spectrum(
1068 msrun_id, mass_spectrum_list, *pointer_handler, spectrum_descr, ms_level);
1069
1070
1071 return mass_spectrum_list;
1072 };
1073
1074 std::function<void(std::size_t,
1075 const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list)>
1076 reduce_function_spectrum_list =
1077 [pointer_handler, local_filepath](
1078 std::size_t res, const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list) {
1079 for(auto &qualified_spectrum : qualified_spectrum_list)
1080 {
1081 pointer_handler->setQualifiedMassSpectrum(qualified_spectrum);
1082 }
1083
1084 if(pointer_handler->shouldStop())
1085 {
1086 qDebug() << "The operation was cancelled. Breaking the loop.";
1087 throw ExceptionInterrupted(
1088 QObject::tr("reading TimsTOF job on %1 cancelled by the user")
1089 .arg(local_filepath));
1090 }
1091 res++;
1092 };
1093
1094
1095 QFuture<std::size_t> res;
1096 res = QtConcurrent::mappedReduced<std::size_t>(spectrum_description_list.begin(),
1097 spectrum_description_list.end(),
1098 map_function_generate_spectrum,
1099 reduce_function_spectrum_list,
1100 QtConcurrent::OrderedReduce);
1101 res.waitForFinished();
1102 }
1103 handler.loadingEnded();
1104 mp_timsDataOrigin->getTimsBinDecPtr()->closeLinearRead();
1105}
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:1114
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 1145 of file timsddaprecursors.cpp.

1148{
1149
1150
1151 // We'll need it to perform the looping in the spectrum list.
1152 std::size_t spectrum_list_size = mp_timsDataOrigin->getTotalScanCount();
1153
1154 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
1155
1156 // Inform the handler of the spectrum list so that it can handle feedback to
1157 // the user.
1158 handler.spectrumListHasSize(spectrum_list_size);
1159
1160 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1161 QSqlQuery qprecursor_list(qdb);
1162 qprecursor_list.exec(
1163 QString("SELECT DISTINCT "
1164 "PasefFrameMsMsInfo.Frame, " // 0
1165 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
1166 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
1167 "PasefFrameMsMsInfo.IsolationMz, " // 3
1168 "PasefFrameMsMsInfo.IsolationWidth, " // 4
1169 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
1170 "PasefFrameMsMsInfo.Precursor, " // 6
1171 "Precursors.Id, " // 7
1172 "Precursors.LargestPeakMz, " // 8
1173 "Precursors.AverageMz, " // 9
1174 "Precursors.MonoisotopicMz, " // 10
1175 "Precursors.Charge, " // 11
1176 "Precursors.ScanNumber, " // 12
1177 "Precursors.Intensity, " // 13
1178 "Precursors.Parent " // 14
1179 "FROM PasefFrameMsMsInfo "
1180 "INNER JOIN Precursors ON "
1181 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
1182 "ORDER BY PasefFrameMsMsInfo.Frame, PasefFrameMsMsInfo.ScanNumBegin ;"));
1183 if(qprecursor_list.lastError().isValid())
1184 {
1185 throw PappsoException(
1186 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
1187 "command %2:\n%3\n%4\n%5")
1188 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1189 .arg(qprecursor_list.lastQuery())
1190 .arg(qdb.lastError().databaseText())
1191 .arg(qdb.lastError().driverText())
1192 .arg(qdb.lastError().nativeErrorCode()));
1193 }
1194
1195
1196 std::size_t i = 0; // iterate on each Spectrum
1197
1198 qprecursor_list.last(); // strange bug : get the last sql record and get
1199 // back, unless it will not retrieve all records.
1200
1201 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
1202 qprecursor_list.first();
1203
1204 TimsFrameBaseCstSPtr tims_frame;
1205 SpectrumDescr spectrum_descr;
1206
1207 for(const FrameIdDescr &current_frame : mp_timsDataOrigin->getFrameIdDescrList())
1208 {
1209
1210 // If the user of this reader instance wants to stop reading the
1211 // spectra, then break this loop.
1212 if(handler.shouldStop())
1213 {
1214 qDebug() << "The operation was cancelled. Breaking the loop.";
1215 throw ExceptionInterrupted(
1216 QObject::tr("reading TimsTOF job cancelled by the user :\n%1")
1217 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf")));
1218 }
1219
1220 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(current_frame.m_frameId);
1221 unsigned int tims_ms_level = tims_frame.get()->getMsLevel();
1222
1223 if((ms_level != 0) && (ms_level != tims_ms_level))
1224 { // bypass
1225 i += current_frame.m_scanCount;
1226 }
1227 else
1228 {
1229 bool want_binary_data = handler.needMsLevelPeakList(tims_ms_level);
1230 qDebug() << "want_binary_data=" << want_binary_data;
1231 if(want_binary_data)
1232 {
1233 qDebug() << "bindec";
1234 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(current_frame.m_frameId);
1235 }
1236
1237 bool possible_precursor = false;
1238 if(tims_ms_level == 2)
1239 {
1240 // seek the precursor record:
1241 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1242 {
1243 qprecursor_list.next();
1244
1245 if(qprecursor_list.value(0).toULongLong() == current_frame.m_frameId)
1246 {
1247 possible_precursor = true;
1248 }
1249 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1250 }
1251 }
1252
1253 for(std::size_t scan_num = 0; scan_num < current_frame.m_scanCount; scan_num++)
1254 {
1255 bool has_a_precursor = false;
1256 if(possible_precursor)
1257 {
1258 if(spectrum_descr.scan_mobility_end < scan_num)
1259 {
1260 // seek the precursor record:
1261 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1262 {
1263 qprecursor_list.next();
1264
1265 if(qprecursor_list.value(0).toULongLong() != current_frame.m_frameId)
1266 {
1267 possible_precursor = false;
1268 }
1269 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1270 }
1271 }
1272
1273 if(possible_precursor && (spectrum_descr.scan_mobility_start < scan_num))
1274 {
1275 // we are in
1276 has_a_precursor = true;
1277 }
1278 } // end to determine if we are in a precursor for this
1279 // spectrum
1280
1281 QualifiedMassSpectrum mass_spectrum;
1282
1283
1284 MassSpectrumId spectrum_id;
1285
1286 spectrum_id.setSpectrumIndex(i);
1287 spectrum_id.setMsRunId(msrun_id);
1288 spectrum_id.setNativeId(QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1289 .arg(current_frame.m_frameId)
1290 .arg(scan_num)
1291 .arg(i));
1292
1293 mass_spectrum.setMassSpectrumId(spectrum_id);
1294
1295 mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
1296 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
1297
1298 mass_spectrum.setDtInMilliSeconds(
1299 tims_frame.get()->getDriftTimeInMilliseconds(scan_num));
1300 // 1/K0
1301 mass_spectrum.setParameterValue(
1302 QualifiedMassSpectrumParameter::IonMobOneOverK0,
1303 tims_frame.get()->getOneOverK0Transformation(scan_num));
1304
1305 mass_spectrum.setEmptyMassSpectrum(true);
1306 if(want_binary_data)
1307 {
1308 try
1309 {
1310 mass_spectrum.setMassSpectrumSPtr(
1311 tims_frame.get()->getMassSpectrumSPtr(scan_num));
1312 }
1313 catch(PappsoException &error)
1314 {
1315 throw PappsoException(
1316 QObject::tr("ERROR in %1 (scan_num=%2 spectrum_index=%3):\n%4")
1317 .arg(__FUNCTION__)
1318 .arg(scan_num)
1319 .arg(spectrum_id.getSpectrumIndex())
1320 .arg(error.qwhat()));
1321 }
1322 if(mass_spectrum.size() > 0)
1323 {
1324 mass_spectrum.setEmptyMassSpectrum(false);
1325 }
1326 }
1327 else
1328 {
1329 // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0)
1330 //{
1331 mass_spectrum.setEmptyMassSpectrum(false);
1332 // }
1333 }
1334 if(has_a_precursor)
1335 {
1336 if(spectrum_descr.precursor_id > 0)
1337 {
1338
1339 mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
1340
1341 std::size_t prec_spectrum_index =
1342 mp_timsDataOrigin->getGlobalScanIndexByScanCoordinates(
1343 spectrum_descr.parent_frame, scan_num);
1344
1345 mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
1346 mass_spectrum.setPrecursorNativeId(
1347 QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1348 .arg(spectrum_descr.parent_frame)
1349 .arg(scan_num)
1350 .arg(prec_spectrum_index));
1351
1352 mass_spectrum.setParameterValue(
1353 QualifiedMassSpectrumParameter::IsolationWindowTargetMz,
1354 spectrum_descr.isolationMz);
1355 mass_spectrum.setParameterValue(
1356 QualifiedMassSpectrumParameter::IsolationWindowLowerOffset,
1357 spectrum_descr.isolationWidth);
1358 mass_spectrum.setParameterValue(
1359 QualifiedMassSpectrumParameter::IsolationWindowUpperOffset,
1360 spectrum_descr.isolationWidth);
1361
1362 mass_spectrum.setParameterValue(
1363 QualifiedMassSpectrumParameter::CollisionEnergy,
1364 spectrum_descr.collisionEnergy);
1365 mass_spectrum.setParameterValue(
1366 QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
1367 (quint64)spectrum_descr.precursor_id);
1368 }
1369 }
1370
1371 handler.setQualifiedMassSpectrum(mass_spectrum);
1372 i++;
1373 }
1374 }
1375 }
1376}
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::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::IsolationWindowLowerOffset, pappso::IsolationWindowTargetMz, pappso::IsolationWindowUpperOffset, 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 1108 of file timsddaprecursors.cpp.

1109{
1110 m_isMonoThread = is_mono_thread;
1111}

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 880 of file timsddaprecursors.cpp.

881{
882 m_builtinMs2Centroid = centroid;
883}

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: