libpappsomspp
Library for mass spectrometry
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Classes | Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
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 547 of file timsddaprecursors.cpp.

549{
550
551 spectrum_descr.tims_frame_list.clear();
552 spectrum_descr.tims_frame_list.push_back(qprecursor_list.value(0).toLongLong());
553 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
554 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
555 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
556 spectrum_descr.precursor_ion_data = PrecursorIonData(qprecursor_list.value(10).toDouble(),
557 qprecursor_list.value(11).toInt(),
558 qprecursor_list.value(13).toDouble());
559
560 spectrum_descr.precursor_id = qprecursor_list.value(6).toLongLong();
561 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
562 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
563
564 spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong();
565 spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong();
566
567 spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble();
568 spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble();
569 spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat();
570 spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong();
571}

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 1469 of file timsddaprecursors.cpp.

1470{
1471 std::vector<std::size_t> best_precursor;
1472 double best_value = 1;
1473 int count = 1;
1474 int best_val_position = 0;
1475
1476 for(std::vector<double> values : ids)
1477 {
1478 double new_val = abs(mz_value - values[4]);
1479 if(new_val < best_value)
1480 {
1481 best_value = new_val;
1482 best_val_position = count;
1483 }
1484 count++;
1485 }
1486 best_precursor.push_back(ids[best_val_position][1]);
1487 return best_precursor;
1488}

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 163 of file timsddaprecursors.cpp.

164{
165
166 qDebug();
167 TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
168 raw_spectrum.clear();
169 try
170 {
171 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
172
173 QSqlQuery q = qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
174 "PasefFrameMsMsInfo INNER JOIN Precursors ON "
175 "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
176 "Precursors.Id=%1;")
177 .arg(precursor_id));
178 if(q.lastError().isValid())
179 {
180 qDebug();
181 throw PappsoException(
182 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
183 "command %2:\n%3\n%4\n%5")
184 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
185 .arg(q.lastQuery())
186 .arg(qdb.lastError().databaseText())
187 .arg(qdb.lastError().driverText())
188 .arg(qdb.lastError().nativeErrorCode()));
189 }
190 qDebug();
191 // m_mutex.unlock();
192 if(q.size() == 0)
193 {
194
195 throw ExceptionNotFound(
196 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
197 "id=%1 not found")
198 .arg(precursor_id));
199 }
200 else
201 {
202 // qDebug() << " q.size()="<< q.size();
203 qDebug();
204 bool first = true;
205 std::size_t scan_mobility_start = 0;
206 std::size_t scan_mobility_end = 0;
207 std::vector<std::size_t> tims_frame_list;
208
209 while(q.next())
210 {
211 tims_frame_list.push_back(q.value(0).toLongLong());
212 if(first)
213 {
214
215 scan_mobility_start = q.value(1).toLongLong();
216 scan_mobility_end = q.value(2).toLongLong();
217
218 first = false;
219 }
220 }
221 // QMutexLocker locker(&m_mutex_spectrum);
222 qDebug();
223 TimsFrameCstSPtr tims_frame, previous_frame;
224 // TracePlusCombiner combiner;
225 // MapTrace combiner_result;
226 for(std::size_t tims_id : tims_frame_list)
227 {
228 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(tims_id);
229 qDebug();
230 /*combiner.combine(combiner_result,
231 tims_frame.get()->cumulateScanToTrace(
232 scan_mobility_start, scan_mobility_end));*/
233 if(previous_frame.get() != nullptr)
234 {
235 if(previous_frame.get()->hasSameCalibrationData(*tims_frame.get()))
236 {
237 }
238 else
239 {
240 throw ExceptionNotFound(
241 QObject::tr("ERROR in %1 %2, different calibration data "
242 "between frame id %3 and frame id %4")
243 .arg(__FILE__)
244 .arg(__FUNCTION__)
245 .arg(previous_frame.get()->getId())
246 .arg(tims_frame.get()->getId()));
247 }
248 }
249 tims_frame.get()->combineScansInTofIndexIntensityMap(
250 raw_spectrum, scan_mobility_start, scan_mobility_end);
251 qDebug();
252
253 previous_frame = tims_frame;
254 }
255 qDebug() << " precursor_index=" << precursor_id << " num_rows=" << tims_frame_list.size()
256 << " sql=" << q.lastQuery() << " " << (std::size_t)QThread::currentThreadId();
257 if(first == true)
258 {
259 throw ExceptionNotFound(
260 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
261 "id=%1 not found")
262 .arg(precursor_id));
263 }
264 qDebug();
265 }
266 }
267
268 catch(PappsoException &error)
269 {
270 throw PappsoException(QObject::tr("ERROR in %1 (precursor_index=%2):\n%3")
271 .arg(__FUNCTION__)
272 .arg(precursor_id)
273 .arg(error.qwhat()));
274 }
275 catch(std::exception &error)
276 {
277 qDebug() << QString("Failure %1 ").arg(error.what());
278 }
279 return raw_spectrum;
280 qDebug();
281}
pappso::TimsDataFastMap::getTimsDataFastMapInstance
static TimsDataFastMap & getTimsDataFastMapInstance()
Definition timsdatafastmap.cpp:41
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 1444 of file timsddaprecursors.cpp.

1445{
1446 std::vector<std::size_t> precursor_id;
1447 for(std::vector<double> index : ids)
1448 {
1449 auto coordinate = mp_timsDataOrigin->getScanCoordinatesByGlobalScanIndex(index[0]);
1450
1451 TimsFrameBaseCstSPtr tims_frame;
1452 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(coordinate.first);
1453
1454 double bko = tims_frame.get()->getOneOverK0Transformation(index[2]);
1455 double eko = tims_frame.get()->getOneOverK0Transformation(index[3]);
1456
1457 // qInfo() << "diff" << (bko + eko) / 2;
1458 double mean_ko = (bko + eko) / 2;
1459
1460 if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1)
1461 {
1462 precursor_id.push_back(index[1]);
1463 }
1464 }
1465 return precursor_id;
1466}
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 879 of file timsddaprecursors.cpp.

880{
881 return m_builtinMs2Centroid;
882}
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 1367 of file timsddaprecursors.cpp.

1368{
1369
1370 std::vector<std::size_t> precursor_ids;
1371 std::vector<std::vector<double>> ids;
1372
1373 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1374 QSqlQuery q(QString("SELECT Frames.Time, Precursors.MonoisotopicMz, Precursors.Charge, "
1375 "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
1376 "PasefFrameMsMsInfo.scanNumEnd "
1377 "FROM Frames "
1378 "INNER JOIN PasefFrameMsMsInfo ON Frames.Id = "
1379 "PasefFrameMsMsInfo.Frame "
1380 "INNER JOIN Precursors ON "
1381 "PasefFrameMsMsInfo.Precursor= Precursors.Id "
1382 "WHERE Precursors.Charge == %1 "
1383 "AND Precursors.MonoisotopicMz > %2 -0.01 "
1384 "AND Precursors.MonoisotopicMz < %2 +0.01 "
1385 "AND Frames.Time >= %3 -1 "
1386 "AND Frames.Time < %3 +1; ")
1387 .arg(charge)
1388 .arg(mz_val)
1389 .arg(rt_sec));
1390 q.exec();
1391 if(q.lastError().isValid())
1392 {
1393
1394 throw PappsoException(
1395 QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
1396 "executing SQL "
1397 "command %3:\n%4\n%5\n%6")
1398 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1399 .arg(qdb.databaseName())
1400 .arg(q.lastQuery())
1401 .arg(qdb.lastError().databaseText())
1402 .arg(qdb.lastError().driverText())
1403 .arg(qdb.lastError().nativeErrorCode()));
1404 }
1405 while(q.next())
1406 {
1407 // qInfo() << q.value(0).toDouble() << q.value(1).toDouble()
1408 // << q.value(2).toDouble() << q.value(3).toDouble();
1409
1410 std::vector<double> sql_values;
1411 sql_values.push_back(q.value(4).toDouble()); // frame id
1412 sql_values.push_back(q.value(3).toDouble()); // precursor id
1413 sql_values.push_back(q.value(5).toDouble()); // scan num begin
1414 sql_values.push_back(q.value(6).toDouble()); // scan num end
1415 sql_values.push_back(q.value(1).toDouble()); // mz_value
1416
1417 ids.push_back(sql_values);
1418
1419
1420 if(std::find(precursor_ids.begin(), precursor_ids.end(), q.value(3).toDouble()) ==
1421 precursor_ids.end())
1422 {
1423 precursor_ids.push_back(q.value(3).toDouble());
1424 }
1425 }
1426
1427 if(precursor_ids.size() > 1)
1428 {
1429 // std::vector<std::size_t> precursor_ids_ko =
1430 // getMatchPrecursorIdByKo(ids, values[3]);
1431 if(precursor_ids.size() > 1)
1432 {
1433 precursor_ids = getClosestPrecursorIdByMz(ids, k0);
1434 }
1435 return precursor_ids;
1436 }
1437 else
1438 {
1439 return precursor_ids;
1440 }
1441}
pappso::TimsDdaPrecursors::getClosestPrecursorIdByMz
std::vector< std::size_t > getClosestPrecursorIdByMz(std::vector< std::vector< double > > ids, double mz_value)
Definition timsddaprecursors.cpp:1469

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 574 of file timsddaprecursors.cpp.

578{
579
580
581 qDebug() << " ms2_index=" << spectrum_descr.ms2_index
582 << " precursor_index=" << spectrum_descr.precursor_id;
583
584 TracePlusCombiner combiner;
585 MapTrace combiner_result;
586
587 try
588 {
589 mass_spectrum.setMsLevel(1);
590 mass_spectrum.setPrecursorSpectrumIndex(0);
591 mass_spectrum.setEmptyMassSpectrum(true);
592
593 MassSpectrumId spectrum_id;
594 spectrum_id.setSpectrumIndex(spectrum_descr.ms1_index);
595 spectrum_id.setNativeId(QString("frame_id=%1 begin=%2 end=%3 precursor=%4 idxms1=%5")
596 .arg(spectrum_descr.parent_frame)
597 .arg(spectrum_descr.scan_mobility_start)
598 .arg(spectrum_descr.scan_mobility_end)
599 .arg(spectrum_descr.precursor_id)
600 .arg(spectrum_descr.ms1_index));
601
602 spectrum_id.setMsRunId(msrun_id);
603
604 mass_spectrum.setMassSpectrumId(spectrum_id);
605
606
607 TimsFrameBaseCstSPtr tims_frame;
608 if(want_binary_data)
609 {
610 qDebug() << "bindec";
611 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(spectrum_descr.parent_frame);
612 }
613 else
614 {
615 tims_frame =
616 mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(spectrum_descr.parent_frame);
617 }
618 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
619
620 mass_spectrum.setParameterValue(
621 QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
622 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_start));
623
624 mass_spectrum.setParameterValue(
625 QualifiedMassSpectrumParameter::IonMobOneOverK0End,
626 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_end));
627
628
629 if(want_binary_data)
630 {
631 combiner.combine(combiner_result,
632 tims_frame.get()->cumulateScansToTrace(
633 spectrum_descr.scan_mobility_start, spectrum_descr.scan_mobility_end));
634
635 Trace trace(combiner_result);
636 qDebug();
637
638 if(trace.size() > 0)
639 {
640 if(mcsp_ms1Filter != nullptr)
641 {
642 mcsp_ms1Filter->filter(trace);
643 }
644
645 qDebug();
646 mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
647 mass_spectrum.setEmptyMassSpectrum(false);
648 }
649 else
650 {
651 mass_spectrum.setMassSpectrumSPtr(nullptr);
652 mass_spectrum.setEmptyMassSpectrum(true);
653 }
654 }
655 qDebug();
656 }
657
658 catch(PappsoException &error)
659 {
660 throw error;
661 }
662 catch(std::exception &error)
663 {
664 qDebug() << QString("Failure %1 ").arg(error.what());
665 }
666}

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 681 of file timsddaprecursors.cpp.

685{
686
687
688 try
689 {
690 qDebug();
691 MassSpectrumId spectrum_id;
692
693 spectrum_id.setSpectrumIndex(spectrum_descr.ms2_index);
694 spectrum_id.setNativeId(QString("precursor=%1 idxms2=%2")
695 .arg(spectrum_descr.precursor_id)
696 .arg(spectrum_descr.ms2_index));
697 spectrum_id.setMsRunId(msrun_id);
698
699 mass_spectrum.setMassSpectrumId(spectrum_id);
700
701 mass_spectrum.setMsLevel(2);
702 qDebug() << "spectrum_descr.precursor_id=" << spectrum_descr.precursor_id
703 << " spectrum_descr.ms1_index=" << spectrum_descr.ms1_index
704 << " spectrum_descr.ms2_index=" << spectrum_descr.ms2_index;
705 mass_spectrum.setPrecursorSpectrumIndex(spectrum_descr.ms1_index);
706
707 mass_spectrum.setEmptyMassSpectrum(true);
708
709 qDebug();
710
711
712 mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
713
714 mass_spectrum.setPrecursorNativeId(
715 QString("frame_id=%1 begin=%2 end=%3 precursor=%4 idxms1=%5")
716 .arg(spectrum_descr.parent_frame)
717 .arg(spectrum_descr.scan_mobility_start)
718 .arg(spectrum_descr.scan_mobility_end)
719 .arg(spectrum_descr.precursor_id)
720 .arg(spectrum_descr.ms1_index));
721
722 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMz,
723 spectrum_descr.isolationMz);
724 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth,
725 spectrum_descr.isolationWidth);
726
727 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::CollisionEnergy,
728 spectrum_descr.collisionEnergy);
729 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
730 (quint64)spectrum_descr.precursor_id);
731
732 // QMutexLocker locker(&m_mutex_spectrum);
733 qDebug();
734 TimsFrameBaseCstSPtr tims_frame, previous_frame;
735 // TracePlusCombiner combiner;
736 // MapTrace combiner_result;
737 TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
738 raw_spectrum.clear();
739 bool first = true;
740 for(std::size_t tims_id : spectrum_descr.tims_frame_list)
741 {
742 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " tims_id=" << tims_id
743 << (std::size_t)QThread::currentThreadId();
744
745 if(want_binary_data)
746 {
747 qDebug() << "bindec";
748 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(tims_id);
749 }
750 else
751 {
752 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(tims_id);
753 }
754 qDebug() << (std::size_t)QThread::currentThreadId();
755
756 if(first)
757 {
758 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
759
760 mass_spectrum.setParameterValue(
761 QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
762 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_start));
763
764 mass_spectrum.setParameterValue(
765 QualifiedMassSpectrumParameter::IonMobOneOverK0End,
766 tims_frame.get()->getOneOverK0Transformation(spectrum_descr.scan_mobility_end));
767
768 first = false;
769 }
770
771
772 if(want_binary_data)
773 {
774 qDebug();
775 /*combiner.combine(combiner_result,
776 tims_frame.get()->cumulateScanToTrace(
777 scan_mobility_start, scan_mobility_end));*/
778 if(previous_frame.get() != nullptr)
779 {
780 if(previous_frame.get()->hasSameCalibrationData(*tims_frame.get()))
781 {
782 }
783 else
784 {
785 throw ExceptionNotFound(
786 QObject::tr("ERROR in %1 %2, different calibration data "
787 "between frame id %3 and frame id %4")
788 .arg(__FILE__)
789 .arg(__FUNCTION__)
790 .arg(previous_frame.get()->getId())
791 .arg(tims_frame.get()->getId()));
792 }
793 }
794 qDebug() << (std::size_t)QThread::currentThreadId();
795
796 tims_frame.get()->combineScansInTofIndexIntensityMap(
797 raw_spectrum, spectrum_descr.scan_mobility_start, spectrum_descr.scan_mobility_end);
798 qDebug() << (std::size_t)QThread::currentThreadId();
799 }
800 previous_frame = tims_frame;
801 }
802 qDebug() << " precursor_index=" << spectrum_descr.precursor_id
803 << " num_rows=" << spectrum_descr.tims_frame_list.size()
804 << (std::size_t)QThread::currentThreadId();
805 if(first == true)
806 {
807 throw ExceptionNotFound(
808 QObject::tr("ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
809 "id=%1 not found")
810 .arg(spectrum_descr.precursor_id));
811 }
812 if(want_binary_data)
813 {
814 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
815 // peak_pick.filter(trace);
816 Trace trace;
817 if(m_builtinMs2Centroid)
818 {
819 // raw_spectrum.removeArtefactualSpike();
820 raw_spectrum.builtInCentroid();
821 }
822
823 trace = tims_frame.get()->getTraceFromTofIndexIntensityMap(raw_spectrum);
824
825 if(trace.size() > 0)
826 {
827 qDebug() << " precursor_index=" << spectrum_descr.precursor_id << " " << trace.size()
828 << " " << (std::size_t)QThread::currentThreadId();
829
830 if(mcsp_ms2Filter != nullptr)
831 {
832 // FilterTriangle filter;
833 // filter.setTriangleSlope(50, 0.02);
834 // filter.filter(trace);
835 // trace.filter(FilterHighPass(10));
836 mcsp_ms2Filter->filter(trace);
837 }
838
839 // FilterScaleFactorY filter_scale((double)1 /
840 // (double)tims_frame_list.size());
841 // filter_scale.filter(trace);
842 qDebug() << " precursor_index=" << spectrum_descr.precursor_id;
843 mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
844 mass_spectrum.setEmptyMassSpectrum(false);
845 }
846 else
847 {
848 mass_spectrum.setMassSpectrumSPtr(nullptr);
849 mass_spectrum.setEmptyMassSpectrum(true);
850 }
851
852 qDebug();
853 }
854 qDebug();
855 }
856
857 catch(PappsoException &error)
858 {
859 throw PappsoException(QObject::tr("ERROR in %1 (ms2_index=%2 precursor_index=%3):\n%4")
860 .arg(__FUNCTION__)
861 .arg(spectrum_descr.ms2_index)
862 .arg(spectrum_descr.precursor_id)
863 .arg(error.qwhat()));
864 }
865 catch(std::exception &error)
866 {
867 qDebug() << QString("Failure %1 ").arg(error.what());
868 }
869 qDebug();
870}
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.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
87 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
88 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
89 "PasefFrameMsMsInfo.IsolationMz, " // 3
90 "PasefFrameMsMsInfo.IsolationWidth, " // 4
91 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
92 "PasefFrameMsMsInfo.Precursor, " // 6
93 "Precursors.Id, " // 7
94 "Precursors.LargestPeakMz, " // 8
95 "Precursors.AverageMz, " // 9
96 "Precursors.MonoisotopicMz, " // 10
97 "Precursors.Charge, " // 11
98 "Precursors.ScanNumber, " // 12
99 "Precursors.Intensity, " // 13
100 "Precursors.Parent " // 14
101 "FROM PasefFrameMsMsInfo "
102 "INNER JOIN Precursors ON "
103
104
105 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
106 "WHERE PasefFrameMsMsInfo.Frame=%1;")
107 .arg(frame_id));
108 if(q.lastError().isValid())
109 {
110 qDebug();
111 throw PappsoException(
112 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
113 "command %2:\n%3\n%4\n%5")
114 .arg(mp_timsDataOrigin->m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
115 .arg(q.lastQuery())
116 .arg(qdb.lastError().databaseText())
117 .arg(qdb.lastError().driverText())
118 .arg(qdb.lastError().nativeErrorCode()));
119 }
120
121 q.last(); // strange bug : get the last sql record and get back,
122 // otherwise it will not retrieve all records.
123 q.first();
124 // std::size_t i = 0;
125 do
126 {
127 TimsDdaPrecursors::SpectrumDescr spectrum_descr;
128 spectrum_descr.tims_frame_list.clear();
129 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
130 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
131 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
132 spectrum_descr.precursor_ion_data =
133 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
134
135 spectrum_descr.precursor_id = q.value(6).toLongLong();
136 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
137 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
138
139 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
140 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
141
142 spectrum_descr.isolationMz = q.value(3).toDouble();
143 spectrum_descr.isolationWidth = q.value(4).toDouble();
144 spectrum_descr.collisionEnergy = q.value(5).toFloat();
145 spectrum_descr.parent_frame = q.value(14).toLongLong();
146
147 spectrum_descr_list.push_back(spectrum_descr);
148 }
149 while(q.next());
150 }
151 catch(PappsoException &error)
152 {
153 throw error;
154 }
155 catch(std::exception &error)
156 {
157 qDebug() << QString("Failure %1 ").arg(error.what());
158 }
159 return spectrum_descr_list;
160}

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 394 of file timsddaprecursors.cpp.

395{
396
397 SpectrumDescr spectrum_descr;
398 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
399 QSqlQuery q = qdb.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
400 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
401 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
402 "PasefFrameMsMsInfo.IsolationMz, " // 3
403 "PasefFrameMsMsInfo.IsolationWidth, " // 4
404 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
405 "PasefFrameMsMsInfo.Precursor, " // 6
406 "Precursors.Id, " // 7
407 "Precursors.LargestPeakMz, " // 8
408 "Precursors.AverageMz, " // 9
409 "Precursors.MonoisotopicMz, " // 10
410 "Precursors.Charge, " // 11
411 "Precursors.ScanNumber, " // 12
412 "Precursors.Intensity, " // 13
413 "Precursors.Parent " // 14
414 "FROM PasefFrameMsMsInfo "
415 "INNER JOIN Precursors ON "
416
417
418 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
419 "WHERE Precursors.Id=%1;")
420 .arg(precursor_id));
421 if(q.lastError().isValid())
422 {
423
424 throw PappsoException(
425 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
426 "command %2:\n%3\n%4\n%5")
427 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
428 .arg(q.lastQuery())
429 .arg(qdb.lastError().databaseText())
430 .arg(qdb.lastError().driverText())
431 .arg(qdb.lastError().nativeErrorCode()));
432 }
433
434
435 bool first = true;
436 while(q.next())
437 {
438
439 qDebug() << " cumul tims frame:" << q.value(0).toLongLong();
440 spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong());
441 if(first)
442 {
443 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
444 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
445 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
446 spectrum_descr.precursor_ion_data =
447 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
448
449 spectrum_descr.precursor_id = q.value(6).toLongLong();
450 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
451 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
452
453 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
454 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
455
456 spectrum_descr.isolationMz = q.value(3).toDouble();
457 spectrum_descr.isolationWidth = q.value(4).toDouble();
458 spectrum_descr.collisionEnergy = q.value(5).toFloat();
459 spectrum_descr.parent_frame = q.value(14).toLongLong();
460
461
462 first = false;
463 }
464 }
465 if(spectrum_descr.precursor_id == 0)
466 {
467 throw ExceptionNotFound(QObject::tr("ERROR in %1 %2 : precursor id (%3) NOT FOUND ")
468 .arg(__FILE__)
469 .arg(__FUNCTION__)
470 .arg(precursor_id));
471 }
472 return spectrum_descr;
473}

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 476 of file timsddaprecursors.cpp.

478{
479
480 SpectrumDescr spectrum_descr;
481 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
482 QSqlQuery q = qdb.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
483 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
484 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
485 "PasefFrameMsMsInfo.IsolationMz, " // 3
486 "PasefFrameMsMsInfo.IsolationWidth, " // 4
487 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
488 "PasefFrameMsMsInfo.Precursor, " // 6
489 "Precursors.Id, " // 7
490 "Precursors.LargestPeakMz, " // 8
491 "Precursors.AverageMz, " // 9
492 "Precursors.MonoisotopicMz, " // 10
493 "Precursors.Charge, " // 11
494 "Precursors.ScanNumber, " // 12
495 "Precursors.Intensity, " // 13
496 "Precursors.Parent " // 14
497 "FROM PasefFrameMsMsInfo "
498 "INNER JOIN Precursors ON "
499 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
500 "WHERE "
501 "PasefFrameMsMsInfo.Frame=%1 and "
502 "(PasefFrameMsMsInfo.ScanNumBegin "
503 "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);")
504 .arg(scan_coordinates.first)
505 .arg(scan_coordinates.second));
506 if(q.lastError().isValid())
507 {
508
509 throw PappsoException(
510 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
511 "command %2:\n%3\n%4\n%5")
512 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
513 .arg(q.lastQuery())
514 .arg(qdb.lastError().databaseText())
515 .arg(qdb.lastError().driverText())
516 .arg(qdb.lastError().nativeErrorCode()));
517 }
518
519 if(q.next())
520 {
521
522 qDebug() << " cumul tims frame:" << q.value(0).toLongLong();
523 spectrum_descr.tims_frame_list.push_back(q.value(0).toLongLong());
524 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
525 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
526 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
527 spectrum_descr.precursor_ion_data =
528 PrecursorIonData(q.value(10).toDouble(), q.value(11).toInt(), q.value(13).toDouble());
529
530 spectrum_descr.precursor_id = q.value(6).toLongLong();
531 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
532 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
533
534 spectrum_descr.scan_mobility_start = q.value(1).toLongLong();
535 spectrum_descr.scan_mobility_end = q.value(2).toLongLong();
536
537 spectrum_descr.isolationMz = q.value(3).toDouble();
538 spectrum_descr.isolationWidth = q.value(4).toDouble();
539 spectrum_descr.collisionEnergy = q.value(5).toFloat();
540 spectrum_descr.parent_frame = q.value(14).toLongLong();
541 }
542 return spectrum_descr;
543}

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 284 of file timsddaprecursors.cpp.

285{
286 return m_totalPrecursorCount;
287}

References m_totalPrecursorCount.

◆ getXicCoordTimsFromPrecursorId()

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

Definition at line 290 of file timsddaprecursors.cpp.

292{
293
294 qDebug();
295 XicCoordTims xic_coord_tims_struct;
296
297 try
298 {
299 if(m_mapXicCoordRecord.size() == 0)
300 {
301 QMutexLocker lock(&m_mutex);
302 // Go get records!
303
304 // We proceed in this way:
305
306 // 1. For each Precursor reference to the Precursors table's ID
307 // found in the PasefFrameMsMsInfo table, store the precursor ID for
308 // step 2.
309
310 // 2. From the Precursors table's ID from step 1, get the
311 // MonoisotopicMz.
312
313 // 3. From the PasefFrameMsMsInfo table, for the Precursors table's
314 // ID reference, get a reference to the Frames table's ID. Thanks to
315 // the Frames ID, look for the Time value (acquisition retention
316 // time) for the MS/MS spectrum. The Time value in the Frames tables
317 // always corresponds to a Frame of MsMsType 8 (that is, MS/MS),
318 // which is expected since we are looking into MS/MS data.
319
320 // 4. From the PasefFrameMsMsInfo table, associate the values
321 // ScanNumBegin and ScanNumEnd, the mobility bins in which the
322 // precursor was found.
323
324
325 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
326 QSqlQuery q =
327 qdb.exec(QString("SELECT Precursors.id, "
328 "min(Frames.Time), "
329 "min(PasefFrameMsMsInfo.ScanNumBegin), "
330 "max(PasefFrameMsMsInfo.ScanNumEnd), "
331 "Precursors.MonoisotopicMz "
332 "FROM "
333 "PasefFrameMsMsInfo INNER JOIN Precursors ON "
334 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
335 "INNER JOIN Frames ON "
336 "PasefFrameMsMsInfo.Frame=Frames.Id "
337 "GROUP BY Precursors.id;"));
338 if(q.lastError().isValid())
339 {
340 qDebug();
341 throw PappsoException(
342 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
343 "command %2:\n%3\n%4\n%5")
344 .arg(mp_timsDataOrigin->m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
345 .arg(q.lastQuery())
346 .arg(qdb.lastError().databaseText())
347 .arg(qdb.lastError().driverText())
348 .arg(qdb.lastError().nativeErrorCode()));
349 }
350
351 q.last(); // strange bug : get the last sql record and get back,
352 // otherwise it will not retrieve all records.
353 q.first();
354 // std::size_t i = 0;
355 do
356 {
357 QSqlRecord record = q.record();
358 m_mapXicCoordRecord.insert(std::pair<std::size_t, QSqlRecord>(
359 (std::size_t)record.value(0).toULongLong(), record));
360 }
361 while(q.next());
362 }
363
364
365 auto it_map_xiccoord = m_mapXicCoordRecord.find(precursor_id);
366 if(it_map_xiccoord == m_mapXicCoordRecord.end())
367 {
368
369 throw ExceptionNotFound(
370 QObject::tr("ERROR Precursors database id %1 not found").arg(precursor_id));
371 }
372
373 auto &q = it_map_xiccoord->second;
374 xic_coord_tims_struct.mzRange = MzRange(q.value(4).toDouble(), precision_ptr);
375 xic_coord_tims_struct.scanNumBegin = q.value(2).toUInt();
376 xic_coord_tims_struct.scanNumEnd = q.value(3).toUInt();
377 xic_coord_tims_struct.rtTarget = q.value(1).toDouble();
378 // xic_structure.charge = q.value(5).toUInt();
379 xic_coord_tims_struct.xicSptr = std::make_shared<Xic>();
380 }
381 catch(PappsoException &error)
382 {
383 throw error;
384 }
385 catch(std::exception &error)
386 {
387 qDebug() << QString("Failure %1 ").arg(error.what());
388 }
389 return xic_coord_tims_struct;
390}
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 1106 of file timsddaprecursors.cpp.

1112{
1113
1114 qDebug() << " ms_level=" << ms_level;
1115 // The handler will receive the index of the mass spectrum in the
1116 // current run via the mass spectrum id member datum.
1117 if((ms_level == 0) || (ms_level == 1))
1118 {
1119 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1120 getQualifiedMs1MassSpectrumBySpectrumDescr(msrun_id,
1121 qualified_mass_spectrum_list.back(),
1122 spectrum_descr,
1123 handler.needMsLevelPeakList(1));
1124 }
1125 if((ms_level == 0) || (ms_level == 2))
1126 {
1127 qualified_mass_spectrum_list.push_back(QualifiedMassSpectrum());
1128 getQualifiedMs2MassSpectrumBySpectrumDescr(msrun_id,
1129 qualified_mass_spectrum_list.back(),
1130 spectrum_descr,
1131 handler.needMsLevelPeakList(2));
1132 }
1133 qDebug();
1134}
pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr
void getQualifiedMs1MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
Definition timsddaprecursors.cpp:574
pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr
void getQualifiedMs2MassSpectrumBySpectrumDescr(const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data)
Definition timsddaprecursors.cpp:681

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 885 of file timsddaprecursors.cpp.

888{
889 qDebug() << " ms_level=" << ms_level;
890
891 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
892 QSqlQuery qprecursor_list =
893 qdb.exec(QString("SELECT PasefFrameMsMsInfo.Frame, " // 0
894 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
895 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
896 "PasefFrameMsMsInfo.IsolationMz, " // 3
897 "PasefFrameMsMsInfo.IsolationWidth, " // 4
898 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
899 "PasefFrameMsMsInfo.Precursor, " // 6
900 "Precursors.Id, " // 7
901 "Precursors.LargestPeakMz, " // 8
902 "Precursors.AverageMz, " // 9
903 "Precursors.MonoisotopicMz, " // 10
904 "Precursors.Charge, " // 11
905 "Precursors.ScanNumber, " // 12
906 "Precursors.Intensity, " // 13
907 "Precursors.Parent " // 14
908 "FROM PasefFrameMsMsInfo "
909 "INNER JOIN Precursors ON "
910 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
911 "ORDER BY PasefFrameMsMsInfo.Precursor, PasefFrameMsMsInfo.Frame ;"));
912 if(qprecursor_list.lastError().isValid())
913 {
914
915 throw PappsoException(
916 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
917 "command %2:\n%3\n%4\n%5")
918 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
919 .arg(qprecursor_list.lastQuery())
920 .arg(qdb.lastError().databaseText())
921 .arg(qdb.lastError().driverText())
922 .arg(qdb.lastError().nativeErrorCode()));
923 }
924
925
926 qDebug() << "qprecursor_list.size()=" << qprecursor_list.size();
927 qDebug() << QObject::tr(
928 "TIMS sqlite database file %1, executing SQL "
929 "command %2:\n%3\n%4\n%5")
930 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
931 .arg(qprecursor_list.lastQuery())
932 .arg(qdb.lastError().databaseText())
933 .arg(qdb.lastError().driverText())
934 .arg(qdb.lastError().nativeErrorCode());
935
936 qDebug() << "qprecursor_list.isActive()=" << qprecursor_list.isActive();
937 qDebug() << "qprecursor_list.isSelect()=" << qprecursor_list.isSelect();
938 bool first = true;
939 SpectrumDescr spectrum_descr;
940
941 /*
942std::size_t i = 0;
943while(qprecursor_list.next())
944 {
945 qDebug() << "i=" << i;
946 i++;
947 }*/
948
949 qprecursor_list.last(); // strange bug : get the last sql record and get
950 // back, otherwise it will not retrieve all records.
951
952 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
953 qprecursor_list.first();
954 std::vector<TimsDdaPrecursors::SpectrumDescr> spectrum_description_list;
955 spectrum_descr.precursor_id = 0;
956 // std::size_t i = 0;
957
958 do
959 {
960
961 if(spectrum_descr.precursor_id != (std::size_t)qprecursor_list.value(6).toLongLong())
962 {
963 // new precursor
964 if(spectrum_descr.precursor_id > 0)
965 {
966 spectrum_description_list.push_back(spectrum_descr);
967 }
968
969 spectrum_descr.tims_frame_list.clear();
970 first = true;
971 }
972 qDebug() << " qprecursor_list.value(6).toLongLong() ="
973 << qprecursor_list.value(6).toLongLong();
974 spectrum_descr.precursor_id = (std::size_t)qprecursor_list.value(6).toLongLong();
975 qDebug() << " spectrum_descr.precursor_id =" << spectrum_descr.precursor_id;
976 qDebug() << " cumul tims frame:" << qprecursor_list.value(0).toLongLong();
977 spectrum_descr.tims_frame_list.push_back(qprecursor_list.value(0).toLongLong());
978 qDebug() << " first =" << first;
979 if(first)
980 {
981 qDebug();
982 // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
983 // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
984 // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
985 spectrum_descr.precursor_ion_data =
986 PrecursorIonData(qprecursor_list.value(10).toDouble(),
987 qprecursor_list.value(11).toInt(),
988 qprecursor_list.value(13).toDouble());
989
990 // spectrum_descr.precursor_id = q.value(6).toLongLong();
991 spectrum_descr.ms2_index = (spectrum_descr.precursor_id * 2) - 1;
992 spectrum_descr.ms1_index = (spectrum_descr.precursor_id * 2) - 2;
993
994 spectrum_descr.scan_mobility_start = qprecursor_list.value(1).toLongLong();
995 spectrum_descr.scan_mobility_end = qprecursor_list.value(2).toLongLong();
996
997 spectrum_descr.isolationMz = qprecursor_list.value(3).toDouble();
998 spectrum_descr.isolationWidth = qprecursor_list.value(4).toDouble();
999 spectrum_descr.collisionEnergy = qprecursor_list.value(5).toFloat();
1000 spectrum_descr.parent_frame = qprecursor_list.value(14).toLongLong();
1001
1002
1003 first = false;
1004 }
1005 // qDebug() << "qprecursor_list.executedQuery()="
1006 // << qprecursor_list.executedQuery();
1007 // qDebug() << "qprecursor_list.last()=" << qprecursor_list.last();
1008 // i++;
1009 }
1010 while(qprecursor_list.next());
1011
1012 // last One
1013
1014 // new precursor
1015 if(spectrum_descr.precursor_id > 0)
1016 {
1017 spectrum_description_list.push_back(spectrum_descr);
1018 }
1019
1020
1021 QString local_filepath =
1022 mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf");
1023
1024 if(m_isMonoThread)
1025 {
1026 for(SpectrumDescr &spectrum_descr : spectrum_description_list)
1027 {
1028
1029 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1030 ms2ReaderGenerateMS1MS2Spectrum(
1031 msrun_id, mass_spectrum_list, handler, spectrum_descr, ms_level);
1032
1033 for(auto &qualified_spectrum : mass_spectrum_list)
1034 {
1035 handler.setQualifiedMassSpectrum(qualified_spectrum);
1036 }
1037
1038 if(handler.shouldStop())
1039 {
1040 qDebug() << "The operation was cancelled. Breaking the loop.";
1041 throw ExceptionInterrupted(
1042 QObject::tr("reading TimsTOF job cancelled by the user :\n%1").arg(local_filepath));
1043 }
1044 }
1045 }
1046 else
1047 {
1048
1049
1050 TimsDdaPrecursors *itself = this;
1051 SpectrumCollectionHandlerInterface *pointer_handler = &handler;
1052
1053
1054 std::function<std::vector<QualifiedMassSpectrum>(const TimsDdaPrecursors::SpectrumDescr &)>
1055 map_function_generate_spectrum = [itself, msrun_id, pointer_handler, ms_level](
1056 const TimsDdaPrecursors::SpectrumDescr &spectrum_descr)
1057 -> std::vector<QualifiedMassSpectrum> {
1058 std::vector<QualifiedMassSpectrum> mass_spectrum_list;
1059 itself->ms2ReaderGenerateMS1MS2Spectrum(
1060 msrun_id, mass_spectrum_list, *pointer_handler, spectrum_descr, ms_level);
1061
1062
1063 return mass_spectrum_list;
1064 };
1065
1066 std::function<void(std::size_t,
1067 const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list)>
1068 reduce_function_spectrum_list =
1069 [pointer_handler, local_filepath](
1070 std::size_t res, const std::vector<QualifiedMassSpectrum> &qualified_spectrum_list) {
1071 for(auto &qualified_spectrum : qualified_spectrum_list)
1072 {
1073 pointer_handler->setQualifiedMassSpectrum(qualified_spectrum);
1074 }
1075
1076 if(pointer_handler->shouldStop())
1077 {
1078 qDebug() << "The operation was cancelled. Breaking the loop.";
1079 throw ExceptionInterrupted(
1080 QObject::tr("reading TimsTOF job on %1 cancelled by the user")
1081 .arg(local_filepath));
1082 }
1083 res++;
1084 };
1085
1086
1087 QFuture<std::size_t> res;
1088 res = QtConcurrent::mappedReduced<std::size_t>(spectrum_description_list.begin(),
1089 spectrum_description_list.end(),
1090 map_function_generate_spectrum,
1091 reduce_function_spectrum_list,
1092 QtConcurrent::OrderedReduce);
1093 res.waitForFinished();
1094 }
1095 handler.loadingEnded();
1096 mp_timsDataOrigin->getTimsBinDecPtr()->closeLinearRead();
1097}
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:1106
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 1137 of file timsddaprecursors.cpp.

1140{
1141
1142
1143 // We'll need it to perform the looping in the spectrum list.
1144 std::size_t spectrum_list_size = mp_timsDataOrigin->getTotalScanCount();
1145
1146 // qDebug() << "The spectrum list has size:" << spectrum_list_size;
1147
1148 // Inform the handler of the spectrum list so that it can handle feedback to
1149 // the user.
1150 handler.spectrumListHasSize(spectrum_list_size);
1151
1152 QSqlDatabase qdb = mp_timsDataOrigin->openDatabaseConnection();
1153 QSqlQuery qprecursor_list =
1154 qdb.exec(QString("SELECT DISTINCT "
1155 "PasefFrameMsMsInfo.Frame, " // 0
1156 "PasefFrameMsMsInfo.ScanNumBegin, " // 1
1157 "PasefFrameMsMsInfo.ScanNumEnd, " // 2
1158 "PasefFrameMsMsInfo.IsolationMz, " // 3
1159 "PasefFrameMsMsInfo.IsolationWidth, " // 4
1160 "PasefFrameMsMsInfo.CollisionEnergy, " // 5
1161 "PasefFrameMsMsInfo.Precursor, " // 6
1162 "Precursors.Id, " // 7
1163 "Precursors.LargestPeakMz, " // 8
1164 "Precursors.AverageMz, " // 9
1165 "Precursors.MonoisotopicMz, " // 10
1166 "Precursors.Charge, " // 11
1167 "Precursors.ScanNumber, " // 12
1168 "Precursors.Intensity, " // 13
1169 "Precursors.Parent " // 14
1170 "FROM PasefFrameMsMsInfo "
1171 "INNER JOIN Precursors ON "
1172 "PasefFrameMsMsInfo.Precursor=Precursors.Id "
1173 "ORDER BY PasefFrameMsMsInfo.Frame, PasefFrameMsMsInfo.ScanNumBegin ;"));
1174 if(qprecursor_list.lastError().isValid())
1175 {
1176 throw PappsoException(
1177 QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
1178 "command %2:\n%3\n%4\n%5")
1179 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf"))
1180 .arg(qprecursor_list.lastQuery())
1181 .arg(qdb.lastError().databaseText())
1182 .arg(qdb.lastError().driverText())
1183 .arg(qdb.lastError().nativeErrorCode()));
1184 }
1185
1186
1187 std::size_t i = 0; // iterate on each Spectrum
1188
1189 qprecursor_list.last(); // strange bug : get the last sql record and get
1190 // back, unless it will not retrieve all records.
1191
1192 qDebug() << "qprecursor_list.at()=" << qprecursor_list.at();
1193 qprecursor_list.first();
1194
1195 TimsFrameBaseCstSPtr tims_frame;
1196 SpectrumDescr spectrum_descr;
1197
1198 for(const FrameIdDescr &current_frame : mp_timsDataOrigin->getFrameIdDescrList())
1199 {
1200
1201 // If the user of this reader instance wants to stop reading the
1202 // spectra, then break this loop.
1203 if(handler.shouldStop())
1204 {
1205 qDebug() << "The operation was cancelled. Breaking the loop.";
1206 throw ExceptionInterrupted(
1207 QObject::tr("reading TimsTOF job cancelled by the user :\n%1")
1208 .arg(mp_timsDataOrigin->getTimsDataDirectory().absoluteFilePath("analysis.tdf")));
1209 }
1210
1211 tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(current_frame.m_frameId);
1212 unsigned int tims_ms_level = tims_frame.get()->getMsLevel();
1213
1214 if((ms_level != 0) && (ms_level != tims_ms_level))
1215 { // bypass
1216 i += current_frame.m_scanCount;
1217 }
1218 else
1219 {
1220 bool want_binary_data = handler.needMsLevelPeakList(tims_ms_level);
1221 qDebug() << "want_binary_data=" << want_binary_data;
1222 if(want_binary_data)
1223 {
1224 qDebug() << "bindec";
1225 tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(current_frame.m_frameId);
1226 }
1227
1228 bool possible_precursor = false;
1229 if(tims_ms_level == 2)
1230 {
1231 // seek the precursor record:
1232 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1233 {
1234 qprecursor_list.next();
1235
1236 if(qprecursor_list.value(0).toULongLong() == current_frame.m_frameId)
1237 {
1238 possible_precursor = true;
1239 }
1240 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1241 }
1242 }
1243
1244 for(std::size_t scan_num = 0; scan_num < current_frame.m_scanCount; scan_num++)
1245 {
1246 bool has_a_precursor = false;
1247 if(possible_precursor)
1248 {
1249 if(spectrum_descr.scan_mobility_end < scan_num)
1250 {
1251 // seek the precursor record:
1252 while(qprecursor_list.value(0).toULongLong() < current_frame.m_frameId)
1253 {
1254 qprecursor_list.next();
1255
1256 if(qprecursor_list.value(0).toULongLong() != current_frame.m_frameId)
1257 {
1258 possible_precursor = false;
1259 }
1260 fillSpectrumDescriptionWithSqlRecord(spectrum_descr, qprecursor_list);
1261 }
1262 }
1263
1264 if(possible_precursor && (spectrum_descr.scan_mobility_start < scan_num))
1265 {
1266 // we are in
1267 has_a_precursor = true;
1268 }
1269 } // end to determine if we are in a precursor for this
1270 // spectrum
1271
1272 QualifiedMassSpectrum mass_spectrum;
1273
1274
1275 MassSpectrumId spectrum_id;
1276
1277 spectrum_id.setSpectrumIndex(i);
1278 spectrum_id.setMsRunId(msrun_id);
1279 spectrum_id.setNativeId(QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1280 .arg(current_frame.m_frameId)
1281 .arg(scan_num)
1282 .arg(i));
1283
1284 mass_spectrum.setMassSpectrumId(spectrum_id);
1285
1286 mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
1287 mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
1288
1289 mass_spectrum.setDtInMilliSeconds(
1290 tims_frame.get()->getDriftTimeInMilliseconds(scan_num));
1291 // 1/K0
1292 mass_spectrum.setParameterValue(
1293 QualifiedMassSpectrumParameter::IonMobOneOverK0,
1294 tims_frame.get()->getOneOverK0Transformation(scan_num));
1295
1296 mass_spectrum.setEmptyMassSpectrum(true);
1297 if(want_binary_data)
1298 {
1299 try
1300 {
1301 mass_spectrum.setMassSpectrumSPtr(
1302 tims_frame.get()->getMassSpectrumSPtr(scan_num));
1303 }
1304 catch(PappsoException &error)
1305 {
1306 throw PappsoException(
1307 QObject::tr("ERROR in %1 (scan_num=%2 spectrum_index=%3):\n%4")
1308 .arg(__FUNCTION__)
1309 .arg(scan_num)
1310 .arg(spectrum_id.getSpectrumIndex())
1311 .arg(error.qwhat()));
1312 }
1313 if(mass_spectrum.size() > 0)
1314 {
1315 mass_spectrum.setEmptyMassSpectrum(false);
1316 }
1317 }
1318 else
1319 {
1320 // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0)
1321 //{
1322 mass_spectrum.setEmptyMassSpectrum(false);
1323 // }
1324 }
1325 if(has_a_precursor)
1326 {
1327 if(spectrum_descr.precursor_id > 0)
1328 {
1329
1330 mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
1331
1332 std::size_t prec_spectrum_index =
1333 mp_timsDataOrigin->getGlobalScanIndexByScanCoordinates(
1334 spectrum_descr.parent_frame, scan_num);
1335
1336 mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
1337 mass_spectrum.setPrecursorNativeId(
1338 QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
1339 .arg(spectrum_descr.parent_frame)
1340 .arg(scan_num)
1341 .arg(prec_spectrum_index));
1342
1343 mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMz,
1344 spectrum_descr.isolationMz);
1345 mass_spectrum.setParameterValue(
1346 QualifiedMassSpectrumParameter::IsolationMzWidth,
1347 spectrum_descr.isolationWidth);
1348
1349 mass_spectrum.setParameterValue(
1350 QualifiedMassSpectrumParameter::CollisionEnergy,
1351 spectrum_descr.collisionEnergy);
1352 mass_spectrum.setParameterValue(
1353 QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
1354 (quint64)spectrum_descr.precursor_id);
1355 }
1356 }
1357
1358 handler.setQualifiedMassSpectrum(mass_spectrum);
1359 i++;
1360 }
1361 }
1362 }
1363}
pappso::TimsDdaPrecursors::fillSpectrumDescriptionWithSqlRecord
void fillSpectrumDescriptionWithSqlRecord(SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list)
Definition timsddaprecursors.cpp:547

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 1100 of file timsddaprecursors.cpp.

1101{
1102 m_isMonoThread = is_mono_thread;
1103}

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 675 of file timsddaprecursors.cpp.

676{
677 mcsp_ms1Filter = filter;
678}
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 873 of file timsddaprecursors.cpp.

874{
875 m_builtinMs2Centroid = centroid;
876}

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 670 of file timsddaprecursors.cpp.

671{
672 mcsp_ms2Filter = filter;
673}

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: