libpappsomspp
Library for mass spectrometry
Public Member Functions | Private Member Functions | Private Attributes | List of all members
pappso::TimsData Class Reference

#include <timsdata.h>

Public Member Functions

 TimsData (QDir timsDataDirectory)
 build using the tims data directory More...
 
 TimsData (const TimsData &other)
 
 ~TimsData ()
 
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtrByRawIndex (std::size_t raw_index)
 get a mass spectrum given its spectrum index More...
 
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr (std::size_t timsId, std::size_t scanNum)
 get a mass spectrum given the tims frame database id and scan number within tims frame More...
 
std::size_t getTotalNumberOfScans () const
 get the total number of scans More...
 
std::size_t getTotalNumberOfPrecursors () const
 get the number of precursors analyzes by PASEF More...
 
std::vector< std::size_t > getPrecursorsFromMzRtCharge (int charge, double mz_val, double rt_sec, double k0)
 guess possible precursor ids given a charge, m/z, retention time and k0 More...
 
unsigned int getMsLevelBySpectrumIndex (std::size_t spectrum_index)
 
QualifiedMassSpectrum getQualifiedMassSpectrumByRawIndex (std::size_t spectrum_index, bool want_binary_data)
 
void getQualifiedMs2MassSpectrumByPrecursorId (QualifiedMassSpectrum &mass_spectrum, std::size_t ms2_index, std::size_t precursor_index, bool want_binary_data)
 
QualifiedMassSpectrum getQualifiedMs1MassSpectrumByPrecursorId (std::size_t ms2_index, std::size_t precursor_index, 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 More...
 
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 More...
 
void setMs2BuiltinCentroid (bool centroid)
 enable or disable simple centroid filter on raw tims data for MS2 More...
 
bool getMs2BuiltinCentroid () const
 tells if simple centroid filter on raw tims data for MS2 is enabled or not More...
 
std::vector< std::size_t > getTimsMS1FrameIdRange (double rt_begin, double rt_end) const
 
TimsFrameCstSPtr getTimsFrameCstSPtr (std::size_t timsId) const
 get a Tims frame with his database ID More...
 

Private Member Functions

std::pair< std::size_t, std::size_t > getScanCoordinateFromRawIndex (std::size_t spectrum_index) const
 
std::size_t getRawIndexFromCoordinate (std::size_t frame_id, std::size_t scan_num) const
 
QSqlDatabase openDatabaseConnection () const
 
TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr (std::size_t timsId) const
 get a Tims frame base (no binary data file access) with his database ID More...
 
TimsFrameCstSPtr getTimsFrameCstSPtrCached (std::size_t timsId)
 get a Tims frame with his database ID but look in the cache first More...
 
TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtrCached (std::size_t timsId)
 
std::vector< TimsXicStructure > extractXicListByPrecursorIds (const std::vector< std::size_t > &precursor_id_list, PrecisionPtr precision_ptr, XicExtractMethod xicExtractMethod, double rtRange) const
 extract a list of XICs from Tims data More...
 
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)
 

Private Attributes

QDir m_timsDataDirectory
 
TimsBinDec * mpa_timsBinDec = nullptr
 
std::size_t m_totalNumberOfScans
 
std::size_t m_totalNumberOfPrecursors
 
std::size_t m_cacheSize = 60
 
std::deque< TimsFrameCstSPtr > m_timsFrameCache
 
std::deque< TimsFrameBaseCstSPtr > m_timsFrameBaseCache
 
pappso::FilterInterfaceCstSPtr mcsp_ms2Filter = nullptr
 
pappso::FilterInterfaceCstSPtr mcsp_ms1Filter = nullptr
 
bool m_builtinMs2Centroid = true
 enable builtin centroid on raw tims integers by default More...
 
std::map< int, QSqlRecord > m_mapMzCalibrationRecord
 
MzCalibrationStore * mpa_mzCalibrationStore
 
QMutex m_mutex
 

Detailed Description

Todo:
write docs

Definition at line 70 of file timsdata.h.

Constructor & Destructor Documentation

◆ TimsData() [1/2]

TimsData::TimsData ( QDir  timsDataDirectory)

build using the tims data directory

Definition at line 46 of file timsdata.cpp.

47  : m_timsDataDirectory(timsDataDirectory)
48 {
49 
50  qDebug();
51  mpa_mzCalibrationStore = new MzCalibrationStore();
52  if(!m_timsDataDirectory.exists())
53  {
54  throw PappsoException(
55  QObject::tr("ERROR TIMS data directory %1 not found")
56  .arg(m_timsDataDirectory.absolutePath()));
57  }
58 
59  if(!QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf")).exists())
60  {
61 
62  throw PappsoException(
63  QObject::tr("ERROR TIMS data directory, %1 sqlite file not found")
64  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")));
65  }
66 
67  // Open the database
68  QSqlDatabase qdb = openDatabaseConnection();
69 
70 
71  QSqlQuery q(qdb);
72  if(!q.exec("select Key, Value from GlobalMetadata where "
73  "Key='TimsCompressionType';"))
74  {
75 
76  qDebug();
77  throw PappsoException(
78  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
79  "command %2:\n%3\n%4\n%5")
80  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
81  .arg(q.lastQuery())
82  .arg(q.lastError().databaseText())
83  .arg(q.lastError().driverText())
84  .arg(q.lastError().nativeErrorCode()));
85  }
86 
87 
88  int compression_type = 0;
89  if(q.next())
90  {
91  compression_type = q.value(1).toInt();
92  }
93  qDebug() << " compression_type=" << compression_type;
94  mpa_timsBinDec = new TimsBinDec(
95  QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf_bin")),
96  compression_type);
97 
98 
99  // get number of precursors
100  if(!q.exec("SELECT COUNT( DISTINCT Id) FROM Precursors;"))
101  {
102  qDebug();
103  throw PappsoException(
104  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
105  "command %2:\n%3\n%4\n%5")
106  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
107  .arg(q.lastQuery())
108  .arg(qdb.lastError().databaseText())
109  .arg(qdb.lastError().driverText())
110  .arg(qdb.lastError().nativeErrorCode()));
111  }
112  if(q.next())
113  {
114  m_totalNumberOfPrecursors = q.value(0).toLongLong();
115  }
116 
117 
118  // get number of scans
119  if(!q.exec("SELECT SUM(NumScans) FROM Frames"))
120  {
121  qDebug();
122  throw PappsoException(
123  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
124  "command %2:\n%3\n%4\n%5")
125  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
126  .arg(q.lastQuery())
127  .arg(qdb.lastError().databaseText())
128  .arg(qdb.lastError().driverText())
129  .arg(qdb.lastError().nativeErrorCode()));
130  }
131  if(q.next())
132  {
133  m_totalNumberOfScans = q.value(0).toLongLong();
134  }
135 
136  if(!q.exec("select * from MzCalibration;"))
137  {
138  qDebug();
139  throw PappsoException(
140  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
141  "command %2:\n%3\n%4\n%5")
142  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
143  .arg(q.lastQuery())
144  .arg(q.lastError().databaseText())
145  .arg(q.lastError().driverText())
146  .arg(q.lastError().nativeErrorCode()));
147  }
148 
149  while(q.next())
150  {
151  QSqlRecord record = q.record();
152  m_mapMzCalibrationRecord.insert(
153  std::pair<int, QSqlRecord>(record.value(0).toInt(), record));
154  }
155 
156  std::shared_ptr<pappso::FilterPseudoCentroid> ms2filter =
157  std::make_shared<pappso::FilterPseudoCentroid>(35000, 5, 0.5, 0.1);
158  mcsp_ms2Filter = ms2filter;
159 
160 
161  std::shared_ptr<FilterTriangle> ms1filter =
162  std::make_shared<FilterTriangle>();
163  ms1filter.get()->setTriangleSlope(50, 0.01);
164  mcsp_ms1Filter = ms1filter;
165 }

References m_mapMzCalibrationRecord, m_timsDataDirectory, m_totalNumberOfPrecursors, m_totalNumberOfScans, mcsp_ms1Filter, mcsp_ms2Filter, mpa_mzCalibrationStore, mpa_timsBinDec, openDatabaseConnection(), and pappso::FilterTriangle::setTriangleSlope().

◆ TimsData() [2/2]

pappso::TimsData::TimsData ( const TimsData &  other)

Copy constructor

Parameters
otherTODO

◆ ~TimsData()

TimsData::~TimsData ( )

Destructor

Definition at line 203 of file timsdata.cpp.

204 {
205  // m_qdb.close();
206  if(mpa_timsBinDec != nullptr)
207  {
208  delete mpa_timsBinDec;
209  }
210 }

References mpa_timsBinDec.

Member Function Documentation

◆ extractXicListByPrecursorIds()

std::vector< TimsXicStructure > TimsData::extractXicListByPrecursorIds ( const std::vector< std::size_t > &  precursor_id_list,
PrecisionPtr  precision_ptr,
XicExtractMethod  xicExtractMethod,
double  rtRange 
) const
private

extract a list of XICs from Tims data

Parameters
precursor_id_listthe list of precursors to extract
precision_ptrprecision to compute the mz range to extract for each precursor mass
xicExtractMethodXIC extraction method (sum or max) to use
rtRangeretention time range in seconds to extract XIC from rtTarget
  • rtRange to rtTarget + rtRange
Returns
the corresponding XIC list as a specific structure

Definition at line 1277 of file timsdata.cpp.

1282 {
1283 
1284  qDebug();
1285  std::vector<TimsXicStructure> xic_list;
1286 
1287  try
1288  {
1289  QSqlDatabase qdb = openDatabaseConnection();
1290 
1291  for(auto precursor_id : precursor_id_list)
1292  {
1293  QSqlQuery q = qdb.exec(
1294  QString("SELECT Frames.Time, "
1295  "PasefFrameMsMsInfo.Frame,PasefFrameMsMsInfo.ScanNumBegin,"
1296  "PasefFrameMsMsInfo.ScanNumEnd, Precursors.MonoisotopicMz, "
1297  "Precursors.Charge FROM "
1298  "PasefFrameMsMsInfo INNER JOIN Precursors ON "
1299  "PasefFrameMsMsInfo.Precursor=Precursors.Id INNER JOIN "
1300  "Frames ON PasefFrameMsMsInfo.Frame=Frames.Id where "
1301  "Precursors.Id=%1;")
1302  .arg(precursor_id));
1303  if(q.lastError().isValid())
1304  {
1305  qDebug();
1306  throw PappsoException(
1307  QObject::tr(
1308  "ERROR in TIMS sqlite database file %1, executing SQL "
1309  "command %2:\n%3\n%4\n%5")
1310  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
1311  .arg(q.lastQuery())
1312  .arg(qdb.lastError().databaseText())
1313  .arg(qdb.lastError().driverText())
1314  .arg(qdb.lastError().nativeErrorCode()));
1315  }
1316 
1317  while(q.next())
1318  {
1319  // Frame, ScanNumBegin, ScanNumEnd, IsolationMz, ColliqionEnergy,
1320  // Precursor
1321  // Id, LargestPeakMz, AverageMz, MonoisotopicMz, Charge,
1322  // ScanNumber, Intensity, Parent
1323  TimsXicStructure xic_structure;
1324 
1325  xic_structure.precursorId = precursor_id;
1326  xic_structure.mzRange =
1327  MzRange(q.value(4).toDouble(), precision_ptr);
1328  xic_structure.scanNumBegin = q.value(2).toUInt();
1329  xic_structure.scanNumEnd = q.value(3).toUInt();
1330  xic_structure.rtTarget = q.value(0).toDouble();
1331  // xic_structure.charge = q.value(5).toUInt();
1332 
1333  xic_list.push_back(xic_structure);
1334  }
1335  }
1336  qDebug();
1337 
1338  TimsXicExtractorInterface *extractor_p = new TimsDirectXicExtractor(this);
1339  extractor_p->setXicExtractMethod(xicExtractMethod);
1340  extractor_p->extractTimsXicList(xic_list, rtRange);
1341  }
1342  catch(PappsoException &error)
1343  {
1344  throw error;
1345  }
1346  catch(std::exception &error)
1347  {
1348  qDebug() << QString("Failure %1 ").arg(error.what());
1349  }
1350 
1351  qDebug();
1352  return xic_list;
1353 }

References pappso::TimsXicExtractorInterface::extractTimsXicList(), m_timsDataDirectory, pappso::TimsXicStructure::mzRange, openDatabaseConnection(), pappso::TimsXicStructure::precursorId, pappso::TimsXicStructure::rtTarget, pappso::TimsXicStructure::scanNumBegin, pappso::TimsXicStructure::scanNumEnd, and pappso::TimsXicExtractorInterface::setXicExtractMethod().

◆ getClosestPrecursorIdByMz()

std::vector< std::size_t > TimsData::getClosestPrecursorIdByMz ( std::vector< std::vector< double >>  ids,
double  mz_value 
)
private
Todo:
documentation

Definition at line 658 of file timsdata.cpp.

660 {
661  std::vector<std::size_t> best_precursor;
662  double best_value = 1;
663  int count = 1;
664  int best_val_position = 0;
665 
666  for(std::vector<double> values : ids)
667  {
668  double new_val = abs(mz_value - values[4]);
669  if(new_val < best_value)
670  {
671  best_value = new_val;
672  best_val_position = count;
673  }
674  count++;
675  }
676  best_precursor.push_back(ids[best_val_position][1]);
677  return best_precursor;
678 }

Referenced by getPrecursorsFromMzRtCharge().

◆ getMassSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsData::getMassSpectrumCstSPtr ( std::size_t  timsId,
std::size_t  scanNum 
)

get a mass spectrum given the tims frame database id and scan number within tims frame

Definition at line 532 of file timsdata.cpp.

533 {
534  pappso::TimsFrameCstSPtr frame = getTimsFrameCstSPtrCached(timsId);
535 
536  return frame->getMassSpectrumCstSPtr(scanNum);
537 }

References getTimsFrameCstSPtrCached().

Referenced by getMassSpectrumCstSPtrByRawIndex().

◆ getMassSpectrumCstSPtrByRawIndex()

pappso::MassSpectrumCstSPtr TimsData::getMassSpectrumCstSPtrByRawIndex ( std::size_t  raw_index)

get a mass spectrum given its spectrum index

Parameters
raw_indexa number begining at 0, corresponding to a Tims Scan in the order they lies in the binary data file

Definition at line 319 of file timsdata.cpp.

320 {
321 
322  auto coordinate = getScanCoordinateFromRawIndex(raw_index);
323  return getMassSpectrumCstSPtr(coordinate.first, coordinate.second);
324 }

References getMassSpectrumCstSPtr(), and getScanCoordinateFromRawIndex().

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

◆ getMatchPrecursorIdByKo()

std::vector< std::size_t > TimsData::getMatchPrecursorIdByKo ( std::vector< std::vector< double >>  ids,
double  ko_value 
)
private

Definition at line 632 of file timsdata.cpp.

634 {
635  std::vector<std::size_t> precursor_id;
636  for(std::vector<double> index : ids)
637  {
638  auto coordinate = getScanCoordinateFromRawIndex(index[0]);
639 
640  TimsFrameBaseCstSPtr tims_frame;
641  tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first);
642 
643  double bko = tims_frame.get()->getOneOverK0Transformation(index[2]);
644  double eko = tims_frame.get()->getOneOverK0Transformation(index[3]);
645 
646  qInfo() << "diff" << (bko + eko) / 2;
647  double mean_ko = (bko + eko) / 2;
648 
649  if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1)
650  {
651  precursor_id.push_back(index[1]);
652  }
653  }
654  return precursor_id;
655 }

References getScanCoordinateFromRawIndex(), and getTimsFrameBaseCstSPtrCached().

◆ getMs2BuiltinCentroid()

bool TimsData::getMs2BuiltinCentroid ( ) const

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

Definition at line 219 of file timsdata.cpp.

220 {
221  return m_builtinMs2Centroid;
222 }

References m_builtinMs2Centroid.

◆ getMsLevelBySpectrumIndex()

unsigned int TimsData::getMsLevelBySpectrumIndex ( std::size_t  spectrum_index)

Definition at line 682 of file timsdata.cpp.

683 {
684  auto coordinate = getScanCoordinateFromRawIndex(spectrum_index);
685  auto tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
686  return tims_frame.get()->getMsLevel();
687 }

References getScanCoordinateFromRawIndex(), and getTimsFrameCstSPtrCached().

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

◆ getPrecursorsFromMzRtCharge()

std::vector< std::size_t > TimsData::getPrecursorsFromMzRtCharge ( 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 553 of file timsdata.cpp.

557 {
558  std::vector<std::size_t> precursor_ids;
559  std::vector<std::vector<double>> ids;
560 
561  QSqlDatabase qdb = openDatabaseConnection();
562  QSqlQuery q = qdb.exec(
563  QString(
564  "SELECT Frames.time, Precursors.MonoisotopicMz, Precursors.Charge, "
565  "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
566  "PasefFrameMsMsInfo.scanNumEnd "
567  "FROM Frames "
568  "INNER JOIN PasefFrameMsMsInfo ON Frames.Id = PasefFrameMsMsInfo.Frame "
569  "INNER JOIN Precursors ON PasefFrameMsMsInfo.Precursor = Precursors.Id "
570  "WHERE Precursors.Charge == %1 "
571  "AND Precursors.MonoisotopicMz > %2 -0.01 "
572  "AND Precursors.MonoisotopicMz < %2 +0.01 "
573  "AND Frames.Time >= %3 "
574  "AND Frames.Time < %3 +1; ")
575  .arg(charge)
576  .arg(mz_val)
577  .arg(rt_sec));
578  if(q.lastError().isValid())
579  {
580 
581  throw PappsoException(
582  QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
583  "executing SQL "
584  "command %3:\n%4\n%5\n%6")
585  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
586  .arg(qdb.databaseName())
587  .arg(q.lastQuery())
588  .arg(qdb.lastError().databaseText())
589  .arg(qdb.lastError().driverText())
590  .arg(qdb.lastError().nativeErrorCode()));
591  }
592  while(q.next())
593  {
594  qInfo() << q.value(0).toDouble() << q.value(1).toDouble()
595  << q.value(2).toDouble() << q.value(3).toDouble();
596 
597  std::vector<double> sql_values;
598  sql_values.push_back(q.value(4).toDouble()); // frame id
599  sql_values.push_back(q.value(3).toDouble()); // precursor id
600  sql_values.push_back(q.value(5).toDouble()); // scan num begin
601  sql_values.push_back(q.value(6).toDouble()); // scan num end
602  sql_values.push_back(q.value(1).toDouble()); // mz_value
603 
604  ids.push_back(sql_values);
605 
606 
607  if(std::find(precursor_ids.begin(),
608  precursor_ids.end(),
609  q.value(3).toDouble()) == precursor_ids.end())
610  {
611  precursor_ids.push_back(q.value(3).toDouble());
612  }
613  }
614 
615  if(precursor_ids.size() > 1)
616  {
617  // std::vector<std::size_t> precursor_ids_ko =
618  // getMatchPrecursorIdByKo(ids, values[3]);
619  if(precursor_ids.size() > 1)
620  {
621  precursor_ids = getClosestPrecursorIdByMz(ids, k0);
622  }
623  return precursor_ids;
624  }
625  else
626  {
627  return precursor_ids;
628  }
629 }

References getClosestPrecursorIdByMz(), m_timsDataDirectory, and openDatabaseConnection().

◆ getQualifiedMassSpectrumByRawIndex()

QualifiedMassSpectrum TimsData::getQualifiedMassSpectrumByRawIndex ( std::size_t  spectrum_index,
bool  want_binary_data 
)

Definition at line 691 of file timsdata.cpp.

693 {
694  auto coordinate = getScanCoordinateFromRawIndex(spectrum_index);
695  TimsFrameBaseCstSPtr tims_frame;
696  if(want_binary_data)
697  {
698  tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
699  }
700  else
701  {
702  tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first);
703  }
704  QualifiedMassSpectrum mass_spectrum;
705  MassSpectrumId spectrum_id;
706 
707  spectrum_id.setSpectrumIndex(spectrum_index);
708  spectrum_id.setNativeId(QString("frame=%1 scan=%2 index=%3")
709  .arg(coordinate.first)
710  .arg(coordinate.second)
711  .arg(spectrum_index));
712 
713  mass_spectrum.setMassSpectrumId(spectrum_id);
714 
715  mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
716  mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
717 
718  mass_spectrum.setDtInMilliSeconds(
719  tims_frame.get()->getDriftTime(coordinate.second));
720  // 1/K0
721  mass_spectrum.setParameterValue(
722  QualifiedMassSpectrumParameter::OneOverK0,
723  tims_frame.get()->getOneOverK0Transformation(coordinate.second));
724 
725  mass_spectrum.setEmptyMassSpectrum(true);
726  if(want_binary_data)
727  {
728  mass_spectrum.setMassSpectrumSPtr(
729  tims_frame.get()->getMassSpectrumSPtr(coordinate.second));
730  if(mass_spectrum.size() > 0)
731  {
732  mass_spectrum.setEmptyMassSpectrum(false);
733  }
734  }
735  else
736  {
737  // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0)
738  //{
739  mass_spectrum.setEmptyMassSpectrum(false);
740  // }
741  }
742  if(tims_frame.get()->getMsLevel() > 1)
743  {
744 
745  QSqlDatabase qdb = openDatabaseConnection();
746  QSqlQuery q = qdb.exec(
747  QString(
748  "SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
749  "PasefFrameMsMsInfo INNER JOIN Precursors ON "
750  "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
751  "PasefFrameMsMsInfo.Frame=%1 and (PasefFrameMsMsInfo.ScanNumBegin "
752  "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);")
753  .arg(coordinate.first)
754  .arg(coordinate.second));
755  if(q.lastError().isValid())
756  {
757  throw PappsoException(
758  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
759  "command %2:\n%3\n%4\n%5")
760  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
761  .arg(q.lastQuery())
762  .arg(qdb.lastError().databaseText())
763  .arg(qdb.lastError().driverText())
764  .arg(qdb.lastError().nativeErrorCode()));
765  }
766  if(q.next())
767  {
768  // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
769  // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
770  // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
771  // mass_spectrum.setPrecursorSpectrumIndex();
772 
773  mass_spectrum.appendPrecursorIonData(
774  PrecursorIonData(q.value(10).toDouble(),
775  q.value(11).toInt(),
776  q.value(13).toDouble()));
777 
778 
779  MassSpectrumId spectrum_id;
780  std::size_t prec_spectrum_index = getRawIndexFromCoordinate(
781  q.value(14).toDouble(), coordinate.second);
782 
783  mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
784  mass_spectrum.setPrecursorNativeId(
785  QString("frame=%1 scan=%2 index=%3")
786  .arg(q.value(14).toDouble())
787  .arg(coordinate.second)
788  .arg(prec_spectrum_index));
789 
790  mass_spectrum.setParameterValue(
791  QualifiedMassSpectrumParameter::IsolationMz, q.value(3).toDouble());
792  mass_spectrum.setParameterValue(
793  QualifiedMassSpectrumParameter::IsolationWidth,
794  q.value(4).toDouble());
795 
796  mass_spectrum.setParameterValue(
797  QualifiedMassSpectrumParameter::CollisionEnergy,
798  q.value(5).toFloat());
799  mass_spectrum.setParameterValue(
800  QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
801  q.value(6).toInt());
802  }
803  }
804 
805  return mass_spectrum;
806 }

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), getRawIndexFromCoordinate(), getScanCoordinateFromRawIndex(), getTimsFrameBaseCstSPtrCached(), getTimsFrameCstSPtrCached(), m_timsDataDirectory, openDatabaseConnection(), pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::QualifiedMassSpectrum::size().

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

◆ getQualifiedMs1MassSpectrumByPrecursorId()

QualifiedMassSpectrum TimsData::getQualifiedMs1MassSpectrumByPrecursorId ( std::size_t  ms2_index,
std::size_t  precursor_index,
bool  want_binary_data 
)

Definition at line 810 of file timsdata.cpp.

813 {
814  QualifiedMassSpectrum mass_spectrum;
815 
816  try
817  {
818  QSqlDatabase qdb = openDatabaseConnection();
819  mass_spectrum.setMsLevel(1);
820  mass_spectrum.setPrecursorSpectrumIndex(0);
821  mass_spectrum.setEmptyMassSpectrum(true);
822  QSqlQuery q =
823  qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
824  "PasefFrameMsMsInfo INNER JOIN Precursors ON "
825  "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
826  "Precursors.Id=%1;")
827  .arg(precursor_index));
828  if(q.lastError().isValid())
829  {
830 
831  throw PappsoException(
832  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
833  "command %2:\n%3\n%4\n%5")
834  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
835  .arg(q.lastQuery())
836  .arg(qdb.lastError().databaseText())
837  .arg(qdb.lastError().driverText())
838  .arg(qdb.lastError().nativeErrorCode()));
839  }
840  if(q.size() == 0)
841  {
842 
843  throw ExceptionNotFound(
844  QObject::tr(
845  "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
846  "id=%1 not found")
847  .arg(precursor_index));
848  }
849  else
850  {
851  TracePlusCombiner combiner;
852  MapTrace combiner_result;
853 
854 
855  bool first = true;
856  std::size_t scan_mobility_start = 0;
857  std::size_t scan_mobility_end = 0;
858  std::set<std::size_t> tims_frame_list;
859  while(q.next())
860  {
861  // get MS1 frame
862  tims_frame_list.insert(q.value(14).toLongLong());
863  if(first)
864  {
865 
866 
867  MassSpectrumId spectrum_id;
868 
869  spectrum_id.setSpectrumIndex(precursor_index);
870  spectrum_id.setNativeId(
871  QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5")
872  .arg(q.value(0).toLongLong())
873  .arg(q.value(1).toLongLong())
874  .arg(q.value(2).toLongLong())
875  .arg(precursor_index)
876  .arg(ms2_index));
877 
878 
879  mass_spectrum.setMassSpectrumId(spectrum_id);
880 
881 
882  scan_mobility_start = q.value(1).toLongLong();
883  scan_mobility_end = q.value(2).toLongLong();
884 
885  first = false;
886  }
887  }
888 
889  first = true;
890  for(std::size_t tims_id : tims_frame_list)
891  {
892  TimsFrameBaseCstSPtr tims_frame =
893  getTimsFrameCstSPtrCached(tims_id);
894  if(first)
895  {
896  mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
897 
898  mass_spectrum.setParameterValue(
899  QualifiedMassSpectrumParameter::OneOverK0begin,
900  tims_frame.get()->getOneOverK0Transformation(
901  scan_mobility_start));
902 
903  mass_spectrum.setParameterValue(
904  QualifiedMassSpectrumParameter::OneOverK0end,
905  tims_frame.get()->getOneOverK0Transformation(
906  scan_mobility_end));
907 
908  first = false;
909  }
910 
911 
912  if(want_binary_data)
913  {
914  combiner.combine(combiner_result,
915  tims_frame.get()->cumulateScanToTrace(
916  scan_mobility_start, scan_mobility_end));
917  }
918  else
919  {
920  break;
921  }
922  }
923 
924 
925  if(first == true)
926  {
927  throw ExceptionNotFound(
928  QObject::tr(
929  "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
930  "id=%1 not found")
931  .arg(precursor_index));
932  }
933 
934 
935  if(want_binary_data)
936  {
937 
938  pappso::Trace trace(combiner_result);
939  qDebug();
940 
941  if(trace.size() > 0)
942  {
943  if(mcsp_ms1Filter != nullptr)
944  {
945  mcsp_ms1Filter->filter(trace);
946  }
947 
948  qDebug();
949  mass_spectrum.setMassSpectrumSPtr(
950  MassSpectrum(trace).makeMassSpectrumSPtr());
951  mass_spectrum.setEmptyMassSpectrum(false);
952  }
953  else
954  {
955  mass_spectrum.setMassSpectrumSPtr(nullptr);
956  mass_spectrum.setEmptyMassSpectrum(true);
957  }
958  }
959  }
960  }
961 
962  catch(PappsoException &error)
963  {
964  throw error;
965  }
966  catch(std::exception &error)
967  {
968  qDebug() << QString("Failure %1 ").arg(error.what());
969  }
970  return mass_spectrum;
971 }

References pappso::TracePlusCombiner::combine(), getTimsFrameCstSPtrCached(), m_timsDataDirectory, mcsp_ms1Filter, openDatabaseConnection(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().

◆ getQualifiedMs2MassSpectrumByPrecursorId()

void TimsData::getQualifiedMs2MassSpectrumByPrecursorId ( QualifiedMassSpectrum &  mass_spectrum,
std::size_t  ms2_index,
std::size_t  precursor_index,
bool  want_binary_data 
)

Definition at line 975 of file timsdata.cpp.

980 {
981  qDebug();
982  try
983  {
984  QSqlDatabase qdb = openDatabaseConnection();
985  MassSpectrumId spectrum_id;
986 
987  spectrum_id.setSpectrumIndex(precursor_index);
988  spectrum_id.setNativeId(
989  QString("precursor=%1 idxms2=%2").arg(precursor_index).arg(ms2_index));
990 
991  mass_spectrum.setMassSpectrumId(spectrum_id);
992 
993  mass_spectrum.setMsLevel(2);
994  mass_spectrum.setPrecursorSpectrumIndex(ms2_index - 1);
995 
996  mass_spectrum.setEmptyMassSpectrum(true);
997 
998  qdb = openDatabaseConnection();
999  // m_mutex.lock();
1000  // if(m_query != nullptr)
1001  // {
1002  // *m_query =
1003  // qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.*
1004  // FROM "
1005  // "PasefFrameMsMsInfo INNER JOIN Precursors ON "
1006  // "PasefFrameMsMsInfo.Precursor=Precursors.Id
1007  // where " "Precursors.Id=%1;")
1008  // .arg(precursor_index));
1009  // }
1010  QSqlQuery q =
1011  qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
1012  "PasefFrameMsMsInfo INNER JOIN Precursors ON "
1013  "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
1014  "Precursors.Id=%1;")
1015  .arg(precursor_index));
1016  if(q.lastError().isValid())
1017  {
1018  qDebug();
1019  throw PappsoException(
1020  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
1021  "command %2:\n%3\n%4\n%5")
1022  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
1023  .arg(q.lastQuery())
1024  .arg(qdb.lastError().databaseText())
1025  .arg(qdb.lastError().driverText())
1026  .arg(qdb.lastError().nativeErrorCode()));
1027  }
1028  qDebug();
1029  // m_mutex.unlock();
1030  if(q.size() == 0)
1031  {
1032 
1033  throw ExceptionNotFound(
1034  QObject::tr(
1035  "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
1036  "id=%1 not found")
1037  .arg(precursor_index));
1038  }
1039  else
1040  {
1041  // qDebug() << " q.size()="<< q.size();
1042  qDebug();
1043  bool first = true;
1044  std::size_t scan_mobility_start = 0;
1045  std::size_t scan_mobility_end = 0;
1046  std::vector<std::size_t> tims_frame_list;
1047 
1048  while(q.next())
1049  {
1050  tims_frame_list.push_back(q.value(0).toLongLong());
1051  if(first)
1052  {
1053  // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
1054  // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
1055  // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
1056 
1057  mass_spectrum.appendPrecursorIonData(
1058  PrecursorIonData(q.value(10).toDouble(),
1059  q.value(11).toInt(),
1060  q.value(13).toDouble()));
1061 
1062  mass_spectrum.setPrecursorNativeId(
1063  QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5")
1064  .arg(q.value(14).toLongLong())
1065  .arg(q.value(1).toLongLong())
1066  .arg(q.value(2).toLongLong())
1067  .arg(precursor_index)
1068  .arg(ms2_index - 1));
1069  // mass_spectrum.setPrecursorSpectrumIndex();
1070 
1071  scan_mobility_start = q.value(1).toLongLong();
1072  scan_mobility_end = q.value(2).toLongLong();
1073 
1074  mass_spectrum.setParameterValue(
1075  QualifiedMassSpectrumParameter::IsolationMz,
1076  q.value(3).toDouble());
1077  mass_spectrum.setParameterValue(
1078  QualifiedMassSpectrumParameter::IsolationWidth,
1079  q.value(4).toDouble());
1080 
1081  mass_spectrum.setParameterValue(
1082  QualifiedMassSpectrumParameter::CollisionEnergy,
1083  q.value(5).toFloat());
1084  mass_spectrum.setParameterValue(
1085  QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
1086  q.value(6).toInt());
1087 
1088  first = false;
1089  }
1090  }
1091  // QMutexLocker locker(&m_mutex_spectrum);
1092  qDebug();
1093  pappso::TimsFrameCstSPtr tims_frame, previous_frame;
1094  // TracePlusCombiner combiner;
1095  // MapTrace combiner_result;
1096  std::map<quint32, quint32> raw_spectrum;
1097  first = true;
1098  for(std::size_t tims_id : tims_frame_list)
1099  {
1100 
1101  tims_frame = getTimsFrameCstSPtrCached(tims_id);
1102  if(first)
1103  {
1104  mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
1105 
1106  mass_spectrum.setParameterValue(
1107  QualifiedMassSpectrumParameter::OneOverK0begin,
1108  tims_frame.get()->getOneOverK0Transformation(
1109  scan_mobility_start));
1110 
1111  mass_spectrum.setParameterValue(
1112  QualifiedMassSpectrumParameter::OneOverK0end,
1113  tims_frame.get()->getOneOverK0Transformation(
1114  scan_mobility_end));
1115 
1116  first = false;
1117  }
1118 
1119 
1120  if(want_binary_data)
1121  {
1122  qDebug();
1123  /*combiner.combine(combiner_result,
1124  tims_frame.get()->cumulateScanToTrace(
1125  scan_mobility_start, scan_mobility_end));*/
1126  if(previous_frame.get() != nullptr)
1127  {
1128  if(previous_frame.get()->hasSameCalibrationData(
1129  *tims_frame.get()))
1130  {
1131  }
1132  else
1133  {
1134  throw ExceptionNotFound(
1135  QObject::tr(
1136  "ERROR in %1 %2, different calibration data "
1137  "between frame id %3 and frame id %4")
1138  .arg(__FILE__)
1139  .arg(__FUNCTION__)
1140  .arg(previous_frame.get()->getId())
1141  .arg(tims_frame.get()->getId()));
1142  }
1143  }
1144  tims_frame.get()->cumulateScansInRawMap(
1145  raw_spectrum, scan_mobility_start, scan_mobility_end);
1146  qDebug();
1147  }
1148  previous_frame = tims_frame;
1149  }
1150  qDebug() << " precursor_index=" << precursor_index
1151  << " num_rows=" << tims_frame_list.size()
1152  << " sql=" << q.lastQuery() << " "
1153  << (std::size_t)QThread::currentThreadId();
1154  if(first == true)
1155  {
1156  throw ExceptionNotFound(
1157  QObject::tr(
1158  "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
1159  "id=%1 not found")
1160  .arg(precursor_index));
1161  }
1162  if(want_binary_data)
1163  {
1164  qDebug();
1165  // peak_pick.filter(trace);
1166  pappso::Trace trace;
1167  if(m_builtinMs2Centroid)
1168  {
1169  trace =
1170  tims_frame.get()->getTraceFromCumulatedScansBuiltinCentroid(
1171  raw_spectrum);
1172  }
1173  else
1174  {
1175  // no builtin centroid:
1176 
1177  trace =
1178  tims_frame.get()->getTraceFromCumulatedScans(raw_spectrum);
1179  }
1180 
1181  if(trace.size() > 0)
1182  {
1183  qDebug() << trace.size() << " "
1184  << (std::size_t)QThread::currentThreadId();
1185 
1186  if(mcsp_ms2Filter != nullptr)
1187  {
1188  // FilterTriangle filter;
1189  // filter.setTriangleSlope(50, 0.02);
1190  // filter.filter(trace);
1191  // trace.filter(pappso::FilterHighPass(10));
1192  mcsp_ms2Filter->filter(trace);
1193  }
1194 
1195  // FilterScaleFactorY filter_scale((double)1 /
1196  // (double)tims_frame_list.size());
1197  // filter_scale.filter(trace);
1198  qDebug();
1199  mass_spectrum.setMassSpectrumSPtr(
1200  MassSpectrum(trace).makeMassSpectrumSPtr());
1201  mass_spectrum.setEmptyMassSpectrum(false);
1202  }
1203  else
1204  {
1205  mass_spectrum.setMassSpectrumSPtr(nullptr);
1206  mass_spectrum.setEmptyMassSpectrum(true);
1207  }
1208 
1209  qDebug();
1210  }
1211  qDebug();
1212  }
1213  }
1214 
1215  catch(PappsoException &error)
1216  {
1217  throw error;
1218  }
1219  catch(std::exception &error)
1220  {
1221  qDebug() << QString("Failure %1 ").arg(error.what());
1222  }
1223  qDebug();
1224 }

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), getTimsFrameCstSPtrCached(), m_builtinMs2Centroid, m_timsDataDirectory, mcsp_ms2Filter, openDatabaseConnection(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().

◆ getRawIndexFromCoordinate()

std::size_t TimsData::getRawIndexFromCoordinate ( std::size_t  frame_id,
std::size_t  scan_num 
) const
private

Definition at line 270 of file timsdata.cpp.

272 {
273 
274 
275  QSqlDatabase qdb = openDatabaseConnection();
276  QSqlQuery q =
277  qdb.exec(QString("SELECT Id, NumScans FROM "
278  "Frames ORDER BY Id"));
279  if(q.lastError().isValid())
280  {
281 
282  throw PappsoException(
283  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
284  "command %2:\n%3\n%4\n%5")
285  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
286  .arg(q.lastQuery())
287  .arg(qdb.lastError().databaseText())
288  .arg(qdb.lastError().driverText())
289  .arg(qdb.lastError().nativeErrorCode()));
290  }
291  bool index_found = false;
292  std::size_t timsId;
293  std::size_t numberScans;
294  std::size_t offset = 0;
295  while(q.next() && (!index_found))
296  {
297  timsId = q.value(0).toUInt();
298  numberScans = q.value(1).toUInt();
299 
300  if(timsId == frame_id)
301  {
302  return offset + scan_num;
303  }
304 
305  offset += numberScans;
306  }
307 
308  throw ExceptionNotFound(
309  QObject::tr("ERROR raw index with frame=%1 scan=%2 not found")
310  .arg(frame_id)
311  .arg(scan_num));
312 }

References m_timsDataDirectory, and openDatabaseConnection().

Referenced by getQualifiedMassSpectrumByRawIndex().

◆ getScanCoordinateFromRawIndex()

std::pair< std::size_t, std::size_t > TimsData::getScanCoordinateFromRawIndex ( std::size_t  spectrum_index) const
private

Definition at line 225 of file timsdata.cpp.

226 {
227 
228  QSqlDatabase qdb = openDatabaseConnection();
229 
230  QSqlQuery q =
231  qdb.exec(QString("SELECT Id, NumScans FROM "
232  "Frames ORDER BY Id"));
233  if(q.lastError().isValid())
234  {
235 
236  throw PappsoException(
237  QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
238  "command %2:\n%3\n%4\n%5")
239  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
240  .arg(q.lastQuery())
241  .arg(qdb.lastError().databaseText())
242  .arg(qdb.lastError().driverText())
243  .arg(qdb.lastError().nativeErrorCode()));
244  }
245  pappso::TimsFrameSPtr tims_frame;
246  bool index_found = false;
247  std::size_t timsId;
248  std::size_t numberScans;
249  std::size_t offset = 0;
250  while(q.next() && (!index_found))
251  {
252  timsId = q.value(0).toUInt();
253  numberScans = q.value(1).toUInt();
254 
255  if(raw_index < (offset + numberScans))
256  {
257  return std::pair<std::size_t, std::size_t>(timsId,
258  raw_index - offset);
259  }
260 
261  offset += numberScans;
262  }
263 
264  throw ExceptionNotFound(
265  QObject::tr("ERROR raw index %1 not found").arg(raw_index));
266 }

References m_timsDataDirectory, and openDatabaseConnection().

Referenced by getMassSpectrumCstSPtrByRawIndex(), getMatchPrecursorIdByKo(), getMsLevelBySpectrumIndex(), and getQualifiedMassSpectrumByRawIndex().

◆ getTimsFrameBaseCstSPtr()

TimsFrameBaseCstSPtr TimsData::getTimsFrameBaseCstSPtr ( std::size_t  timsId) const
private

get a Tims frame base (no binary data file access) with his database ID

Definition at line 328 of file timsdata.cpp.

329 {
330 
331  qDebug() << " timsId=" << timsId;
332 
333  QSqlDatabase qdb = openDatabaseConnection();
334  QSqlQuery q = qdb.exec(
335  QString("SELECT Frames.TimsId, Frames.AccumulationTime, " // 1
336  "Frames.MzCalibration, " // 2
337  "Frames.T1, Frames.T2, " // 4
338  "Frames.Time, Frames.MsMsType, TimsCalibration.ModelType, " // 7
339  "TimsCalibration.C0, TimsCalibration.C1, TimsCalibration.C2, " // 10
340  "TimsCalibration.C3, TimsCalibration.C4, TimsCalibration.C5, " // 13
341  "TimsCalibration.C6, TimsCalibration.C7, TimsCalibration.C8, " // 16
342  "TimsCalibration.C9 FROM Frames" // 17
343  " INNER JOIN TimsCalibration "
344  "ON Frames.TimsCalibration=TimsCalibration.Id where "
345  "Frames.Id=%1;")
346  .arg(timsId));
347  if(q.lastError().isValid())
348  {
349 
350  throw PappsoException(
351  QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
352  "executing SQL "
353  "command %3:\n%4\n%5\n%6")
354  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
355  .arg(qdb.databaseName())
356  .arg(q.lastQuery())
357  .arg(qdb.lastError().databaseText())
358  .arg(qdb.lastError().driverText())
359  .arg(qdb.lastError().nativeErrorCode()));
360  }
361  pappso::TimsFrameBaseSPtr tims_frame;
362  if(q.next())
363  {
364 
365 
366  tims_frame = std::make_shared<TimsFrameBase>(
367  TimsFrameBase(timsId, q.value(0).toUInt()));
368 
369  auto it_map_record = m_mapMzCalibrationRecord.find(q.value(2).toInt());
370  if(it_map_record != m_mapMzCalibrationRecord.end())
371  {
372 
373  double T1_frame = q.value(3).toDouble(); // Frames.T1
374  double T2_frame = q.value(4).toDouble(); // Frames.T2
375 
376 
377  tims_frame.get()->setMzCalibrationInterfaceSPtr(
378  mpa_mzCalibrationStore->getInstance(
379  T1_frame, T2_frame, it_map_record->second));
380  }
381  else
382  {
383  throw ExceptionNotFound(
384  QObject::tr("ERROR MzCalibration database id %1 not found")
385  .arg(q.value(2).toInt()));
386  }
387 
388  tims_frame.get()->setAccumulationTime(q.value(1).toDouble());
389 
390  tims_frame.get()->setTime(q.value(5).toDouble());
391  tims_frame.get()->setMsMsType(q.value(6).toUInt());
392 
393  tims_frame.get()->setTimsCalibration(q.value(7).toInt(),
394  q.value(8).toDouble(),
395  q.value(9).toDouble(),
396  q.value(10).toDouble(),
397  q.value(11).toDouble(),
398  q.value(12).toDouble(),
399  q.value(13).toDouble(),
400  q.value(14).toDouble(),
401  q.value(15).toDouble(),
402  q.value(16).toDouble(),
403  q.value(17).toDouble());
404  return tims_frame;
405  }
406 
407  throw ExceptionNotFound(QObject::tr("ERROR timsId %1 not found").arg(timsId));
408  // return TimsFrameCstSPtr;
409 }

References pappso::MzCalibrationStore::getInstance(), m_mapMzCalibrationRecord, m_timsDataDirectory, mpa_mzCalibrationStore, and openDatabaseConnection().

Referenced by getTimsFrameBaseCstSPtrCached().

◆ getTimsFrameBaseCstSPtrCached()

TimsFrameBaseCstSPtr TimsData::getTimsFrameBaseCstSPtrCached ( std::size_t  timsId)
private

Definition at line 1228 of file timsdata.cpp.

1229 {
1230  QMutexLocker locker(&m_mutex);
1231  for(auto &tims_frame : m_timsFrameBaseCache)
1232  {
1233  if(tims_frame.get()->getId() == timsId)
1234  {
1235  m_timsFrameBaseCache.push_back(tims_frame);
1236  return tims_frame;
1237  }
1238  }
1239 
1240  m_timsFrameBaseCache.push_back(getTimsFrameBaseCstSPtr(timsId));
1241  if(m_timsFrameBaseCache.size() > m_cacheSize)
1242  m_timsFrameBaseCache.pop_front();
1243  return m_timsFrameBaseCache.back();
1244 }

References getTimsFrameBaseCstSPtr(), m_cacheSize, m_mutex, and m_timsFrameBaseCache.

Referenced by getMatchPrecursorIdByKo(), and getQualifiedMassSpectrumByRawIndex().

◆ getTimsFrameCstSPtr()

TimsFrameCstSPtr TimsData::getTimsFrameCstSPtr ( std::size_t  timsId) const

get a Tims frame with his database ID

Definition at line 446 of file timsdata.cpp.

447 {
448 
449  qDebug() << " timsId=" << timsId;
450 
451  QSqlDatabase qdb = openDatabaseConnection();
452  QSqlQuery q = qdb.exec(
453  QString("SELECT Frames.TimsId, Frames.AccumulationTime, " // 1
454  "Frames.MzCalibration, " // 2
455  "Frames.T1, Frames.T2, " // 4
456  "Frames.Time, Frames.MsMsType, TimsCalibration.ModelType, " // 7
457  "TimsCalibration.C0, TimsCalibration.C1, TimsCalibration.C2, " // 10
458  "TimsCalibration.C3, TimsCalibration.C4, TimsCalibration.C5, " // 13
459  "TimsCalibration.C6, TimsCalibration.C7, TimsCalibration.C8, " // 16
460  "TimsCalibration.C9 FROM Frames" // 17
461  " INNER JOIN TimsCalibration "
462  "ON Frames.TimsCalibration=TimsCalibration.Id where "
463  "Frames.Id=%1;")
464  .arg(timsId));
465  if(q.lastError().isValid())
466  {
467 
468  throw PappsoException(
469  QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
470  "executing SQL "
471  "command %3:\n%4\n%5\n%6")
472  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
473  .arg(qdb.databaseName())
474  .arg(q.lastQuery())
475  .arg(qdb.lastError().databaseText())
476  .arg(qdb.lastError().driverText())
477  .arg(qdb.lastError().nativeErrorCode()));
478  }
479  pappso::TimsFrameSPtr tims_frame;
480  if(q.next())
481  {
482 
483 
484  tims_frame =
485  mpa_timsBinDec->getTimsFrameSPtrByOffset(timsId, q.value(0).toUInt());
486 
487 
488  auto it_map_record = m_mapMzCalibrationRecord.find(q.value(2).toInt());
489  if(it_map_record != m_mapMzCalibrationRecord.end())
490  {
491 
492  double T1_frame = q.value(3).toDouble(); // Frames.T1
493  double T2_frame = q.value(4).toDouble(); // Frames.T2
494 
495 
496  tims_frame.get()->setMzCalibrationInterfaceSPtr(
497  mpa_mzCalibrationStore->getInstance(
498  T1_frame, T2_frame, it_map_record->second));
499  }
500  else
501  {
502  throw ExceptionNotFound(
503  QObject::tr("ERROR MzCalibration database id %1 not found")
504  .arg(q.value(2).toInt()));
505  }
506 
507  tims_frame.get()->setAccumulationTime(q.value(1).toDouble());
508 
509  tims_frame.get()->setTime(q.value(5).toDouble());
510  tims_frame.get()->setMsMsType(q.value(6).toUInt());
511 
512  tims_frame.get()->setTimsCalibration(q.value(7).toInt(),
513  q.value(8).toDouble(),
514  q.value(9).toDouble(),
515  q.value(10).toDouble(),
516  q.value(11).toDouble(),
517  q.value(12).toDouble(),
518  q.value(13).toDouble(),
519  q.value(14).toDouble(),
520  q.value(15).toDouble(),
521  q.value(16).toDouble(),
522  q.value(17).toDouble());
523  return tims_frame;
524  }
525 
526  throw ExceptionNotFound(QObject::tr("ERROR timsId %1 not found").arg(timsId));
527  // return TimsFrameCstSPtr;
528 }

References pappso::MzCalibrationStore::getInstance(), pappso::TimsBinDec::getTimsFrameSPtrByOffset(), m_mapMzCalibrationRecord, m_timsDataDirectory, mpa_mzCalibrationStore, mpa_timsBinDec, and openDatabaseConnection().

Referenced by pappso::TimsDirectXicExtractor::extractTimsXicList(), and getTimsFrameCstSPtrCached().

◆ getTimsFrameCstSPtrCached()

TimsFrameCstSPtr TimsData::getTimsFrameCstSPtrCached ( std::size_t  timsId)
private

get a Tims frame with his database ID but look in the cache first

Definition at line 1247 of file timsdata.cpp.

1248 {
1249  QMutexLocker locker(&m_mutex);
1250  for(auto &tims_frame : m_timsFrameCache)
1251  {
1252  if(tims_frame.get()->getId() == timsId)
1253  {
1254  m_timsFrameCache.push_back(tims_frame);
1255  return tims_frame;
1256  }
1257  }
1258 
1259  m_timsFrameCache.push_back(getTimsFrameCstSPtr(timsId));
1260  if(m_timsFrameCache.size() > m_cacheSize)
1261  m_timsFrameCache.pop_front();
1262  return m_timsFrameCache.back();
1263 }

References getTimsFrameCstSPtr(), m_cacheSize, m_mutex, and m_timsFrameCache.

Referenced by getMassSpectrumCstSPtr(), getMsLevelBySpectrumIndex(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), and getQualifiedMs2MassSpectrumByPrecursorId().

◆ getTimsMS1FrameIdRange()

std::vector< std::size_t > TimsData::getTimsMS1FrameIdRange ( double  rt_begin,
double  rt_end 
) const

Definition at line 412 of file timsdata.cpp.

413 {
414 
415  qDebug() << " rt_begin=" << rt_begin << " rt_end=" << rt_end;
416  std::vector<std::size_t> tims_frameid_list;
417  QSqlDatabase qdb = openDatabaseConnection();
418  QSqlQuery q = qdb.exec(QString("SELECT Frames.TimsId FROM Frames WHERE "
419  "Frames.MsMsType=0 AND (Frames.Time=>%1) AND "
420  "(Frames.Time<=%2) SORT BY Frames.Time;")
421  .arg(rt_begin)
422  .arg(rt_end));
423  if(q.lastError().isValid())
424  {
425 
426  throw PappsoException(
427  QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
428  "executing SQL "
429  "command %3:\n%4\n%5\n%6")
430  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
431  .arg(qdb.databaseName())
432  .arg(q.lastQuery())
433  .arg(qdb.lastError().databaseText())
434  .arg(qdb.lastError().driverText())
435  .arg(qdb.lastError().nativeErrorCode()));
436  }
437  while(q.next())
438  {
439 
440  tims_frameid_list.push_back(q.value(0).toUInt());
441  }
442  return tims_frameid_list;
443 }

References m_timsDataDirectory, and openDatabaseConnection().

Referenced by pappso::TimsDirectXicExtractor::extractTimsXicList().

◆ getTotalNumberOfPrecursors()

std::size_t TimsData::getTotalNumberOfPrecursors ( ) const

get the number of precursors analyzes by PASEF

Definition at line 547 of file timsdata.cpp.

548 {
549  return m_totalNumberOfPrecursors;
550 }

References m_totalNumberOfPrecursors.

Referenced by pappso::TimsMsRunReaderMs2Selected::spectrumListSize().

◆ getTotalNumberOfScans()

std::size_t TimsData::getTotalNumberOfScans ( ) const

get the total number of scans

Definition at line 540 of file timsdata.cpp.

541 {
542  return m_totalNumberOfScans;
543 }

References m_totalNumberOfScans.

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

◆ openDatabaseConnection()

QSqlDatabase TimsData::openDatabaseConnection ( ) const
private

Definition at line 168 of file timsdata.cpp.

169 {
170  QString database_connection_name = QString("%1_%2")
171  .arg(m_timsDataDirectory.absolutePath())
172  .arg((quintptr)QThread::currentThread());
173  // Open the database
174  QSqlDatabase qdb = QSqlDatabase::database(database_connection_name);
175  if(!qdb.isValid())
176  {
177  qDebug() << database_connection_name;
178  qdb = QSqlDatabase::addDatabase("QSQLITE", database_connection_name);
179  qdb.setDatabaseName(m_timsDataDirectory.absoluteFilePath("analysis.tdf"));
180  }
181 
182 
183  if(!qdb.open())
184  {
185  qDebug();
186  throw PappsoException(
187  QObject::tr("ERROR opening TIMS sqlite database file %1, database name "
188  "%2 :\n%3\n%4\n%5")
189  .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
190  .arg(database_connection_name)
191  .arg(qdb.lastError().databaseText())
192  .arg(qdb.lastError().driverText())
193  .arg(qdb.lastError().nativeErrorCode()));
194  }
195  return qdb;
196 }

References m_timsDataDirectory.

Referenced by TimsData(), extractXicListByPrecursorIds(), getPrecursorsFromMzRtCharge(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), getRawIndexFromCoordinate(), getScanCoordinateFromRawIndex(), getTimsFrameBaseCstSPtr(), getTimsFrameCstSPtr(), and getTimsMS1FrameIdRange().

◆ setMs1FilterCstSPtr()

void TimsData::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 1271 of file timsdata.cpp.

1272 {
1273  mcsp_ms1Filter = filter;
1274 }

References mcsp_ms1Filter.

Referenced by pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr().

◆ setMs2BuiltinCentroid()

void TimsData::setMs2BuiltinCentroid ( bool  centroid)

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

Definition at line 213 of file timsdata.cpp.

214 {
215  m_builtinMs2Centroid = centroid;
216 }

References m_builtinMs2Centroid.

◆ setMs2FilterCstSPtr()

void TimsData::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 1266 of file timsdata.cpp.

1267 {
1268  mcsp_ms2Filter = filter;
1269 }

References mcsp_ms2Filter.

Referenced by pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr().

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsData::m_builtinMs2Centroid = true
private

enable builtin centroid on raw tims integers by default

Definition at line 228 of file timsdata.h.

Referenced by getMs2BuiltinCentroid(), getQualifiedMs2MassSpectrumByPrecursorId(), and setMs2BuiltinCentroid().

◆ m_cacheSize

std::size_t pappso::TimsData::m_cacheSize = 60
private

Definition at line 219 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_mapMzCalibrationRecord

std::map<int, QSqlRecord> pappso::TimsData::m_mapMzCalibrationRecord
private

Definition at line 231 of file timsdata.h.

Referenced by TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().

◆ m_mutex

QMutex pappso::TimsData::m_mutex
private

Definition at line 235 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_timsDataDirectory

QDir pappso::TimsData::m_timsDataDirectory
private

Definition at line 214 of file timsdata.h.

Referenced by TimsData(), extractXicListByPrecursorIds(), getPrecursorsFromMzRtCharge(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), getRawIndexFromCoordinate(), getScanCoordinateFromRawIndex(), getTimsFrameBaseCstSPtr(), getTimsFrameCstSPtr(), getTimsMS1FrameIdRange(), and openDatabaseConnection().

◆ m_timsFrameBaseCache

std::deque<TimsFrameBaseCstSPtr> pappso::TimsData::m_timsFrameBaseCache
private

Definition at line 221 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached().

◆ m_timsFrameCache

std::deque<TimsFrameCstSPtr> pappso::TimsData::m_timsFrameCache
private

Definition at line 220 of file timsdata.h.

Referenced by getTimsFrameCstSPtrCached().

◆ m_totalNumberOfPrecursors

std::size_t pappso::TimsData::m_totalNumberOfPrecursors
private

Definition at line 218 of file timsdata.h.

Referenced by TimsData(), and getTotalNumberOfPrecursors().

◆ m_totalNumberOfScans

std::size_t pappso::TimsData::m_totalNumberOfScans
private

Definition at line 217 of file timsdata.h.

Referenced by TimsData(), and getTotalNumberOfScans().

◆ mcsp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsData::mcsp_ms1Filter = nullptr
private

Definition at line 224 of file timsdata.h.

Referenced by TimsData(), getQualifiedMs1MassSpectrumByPrecursorId(), and setMs1FilterCstSPtr().

◆ mcsp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsData::mcsp_ms2Filter = nullptr
private

Definition at line 223 of file timsdata.h.

Referenced by TimsData(), getQualifiedMs2MassSpectrumByPrecursorId(), and setMs2FilterCstSPtr().

◆ mpa_mzCalibrationStore

MzCalibrationStore* pappso::TimsData::mpa_mzCalibrationStore
private

Definition at line 233 of file timsdata.h.

Referenced by TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().

◆ mpa_timsBinDec

TimsBinDec* pappso::TimsData::mpa_timsBinDec = nullptr
private

Definition at line 215 of file timsdata.h.

Referenced by TimsData(), ~TimsData(), and getTimsFrameCstSPtr().

The documentation for this class was generated from the following files:
pappso::TimsData::m_mapMzCalibrationRecord
std::map< int, QSqlRecord > m_mapMzCalibrationRecord
Definition: timsdata.h:231
pappso::TimsData::mcsp_ms2Filter
pappso::FilterInterfaceCstSPtr mcsp_ms2Filter
Definition: timsdata.h:223
pappso::TimsData::m_totalNumberOfPrecursors
std::size_t m_totalNumberOfPrecursors
Definition: timsdata.h:218
pappso::TimsXicStructure::precursorId
std::size_t precursorId
Definition: timsdata.h:51
pappso::TimsData::mcsp_ms1Filter
pappso::FilterInterfaceCstSPtr mcsp_ms1Filter
Definition: timsdata.h:224
pappso::TimsData::m_timsFrameBaseCache
std::deque< TimsFrameBaseCstSPtr > m_timsFrameBaseCache
Definition: timsdata.h:221
pappso::TimsData::getTimsFrameBaseCstSPtrCached
TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtrCached(std::size_t timsId)
Definition: timsdata.cpp:1228
pappso::TimsFrameSPtr
std::shared_ptr< TimsFrame > TimsFrameSPtr
Definition: timsframe.h:40
pappso::TracePlusCombiner::combine
virtual MapTrace & combine(MapTrace &map_trace, const Trace &trace) const override
Definition: tracepluscombiner.cpp:52
pappso::MzCalibrationStore
Definition: mzcalibrationstore.h:40
pappso::TimsFrameBase
Definition: timsframebase.h:48
pappso::TimsBinDec
Definition: timsbindec.h:41
pappso::TimsXicExtractorInterface
Definition: timsxicextractorinterface.h:42
pappso::TimsBinDec::getTimsFrameSPtrByOffset
TimsFrameSPtr getTimsFrameSPtrByOffset(std::size_t timsId, std::size_t timsOffset) const
Definition: timsbindec.cpp:143
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition: massspectrum.h:71
pappso::TimsData::m_cacheSize
std::size_t m_cacheSize
Definition: timsdata.h:219
pappso::TimsFrameBaseCstSPtr
std::shared_ptr< const TimsFrameBase > TimsFrameBaseCstSPtr
Definition: timsframebase.h:41
pappso::QualifiedMassSpectrum::setParameterValue
void setParameterValue(QualifiedMassSpectrumParameter parameter, const QVariant &value)
Definition: qualifiedmassspectrum.cpp:461
pappso::MapTrace
Definition: maptrace.h:33
pappso::TimsXicStructure::scanNumBegin
std::size_t scanNumBegin
Definition: timsdata.h:54
pappso::QualifiedMassSpectrum::setMassSpectrumSPtr
void setMassSpectrumSPtr(MassSpectrumSPtr massSpectrum)
Set the MassSpectrumSPtr.
Definition: qualifiedmassspectrum.cpp:125
pappso::TimsData::getTimsFrameBaseCstSPtr
TimsFrameBaseCstSPtr getTimsFrameBaseCstSPtr(std::size_t timsId) const
get a Tims frame base (no binary data file access) with his database ID
Definition: timsdata.cpp:328
pappso::TimsDirectXicExtractor
Definition: timsdirectxicextractor.h:38
pappso::TimsData::getClosestPrecursorIdByMz
std::vector< std::size_t > getClosestPrecursorIdByMz(std::vector< std::vector< double >> ids, double mz_value)
Definition: timsdata.cpp:658
pappso::QualifiedMassSpectrum::setMsLevel
void setMsLevel(uint ms_level)
Set the mass spectrum level.
Definition: qualifiedmassspectrum.cpp:179
pappso::TimsData::getTimsFrameCstSPtrCached
TimsFrameCstSPtr getTimsFrameCstSPtrCached(std::size_t timsId)
get a Tims frame with his database ID but look in the cache first
Definition: timsdata.cpp:1247
pappso::QualifiedMassSpectrum::size
std::size_t size() const
Definition: qualifiedmassspectrum.cpp:492
pappso::QualifiedMassSpectrum::setRtInSeconds
void setRtInSeconds(pappso_double rt)
Set the retention time in seconds.
Definition: qualifiedmassspectrum.cpp:195
pappso::TimsData::m_mutex
QMutex m_mutex
Definition: timsdata.h:235
pappso::MzRange
Definition: mzrange.h:46
pappso::Trace
A simple container of DataPoint instances.
Definition: trace.h:132
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::TimsData::getScanCoordinateFromRawIndex
std::pair< std::size_t, std::size_t > getScanCoordinateFromRawIndex(std::size_t spectrum_index) const
Definition: timsdata.cpp:225
pappso::TimsData::m_timsDataDirectory
QDir m_timsDataDirectory
Definition: timsdata.h:214
pappso::TimsData::getMassSpectrumCstSPtr
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t timsId, std::size_t scanNum)
get a mass spectrum given the tims frame database id and scan number within tims frame
Definition: timsdata.cpp:532
pappso::QualifiedMassSpectrum::setPrecursorNativeId
void setPrecursorNativeId(const QString &native_id)
Set the scan native id of the precursor ion.
Definition: qualifiedmassspectrum.cpp:417
pappso::QualifiedMassSpectrum::appendPrecursorIonData
void appendPrecursorIonData(const PrecursorIonData &precursor_ion_data)
Definition: qualifiedmassspectrum.cpp:430
pappso::QualifiedMassSpectrum::setMassSpectrumId
void setMassSpectrumId(const MassSpectrumId &iD)
Set the MassSpectrumId.
Definition: qualifiedmassspectrum.cpp:149
pappso::MzCalibrationStore::getInstance
MzCalibrationInterfaceSPtr getInstance(double T1_frame, double T2_frame, const QSqlRecord &mzcalibration_record)
Definition: mzcalibrationstore.cpp:46
pappso::TimsFrameBaseSPtr
std::shared_ptr< TimsFrameBase > TimsFrameBaseSPtr
Definition: timsframebase.h:39
pappso::TimsData::m_totalNumberOfScans
std::size_t m_totalNumberOfScans
Definition: timsdata.h:217
pappso::TimsData::mpa_timsBinDec
TimsBinDec * mpa_timsBinDec
Definition: timsdata.h:215
pappso::TimsXicExtractorInterface::setXicExtractMethod
void setXicExtractMethod(XicExtractMethod method)
set the XIC extraction method
Definition: timsxicextractorinterface.cpp:43
pappso::TimsData::m_timsFrameCache
std::deque< TimsFrameCstSPtr > m_timsFrameCache
Definition: timsdata.h:220
pappso::ExceptionNotFound
Definition: exceptionnotfound.h:32
pappso::TimsXicStructure
structure needed to extract XIC from Tims data
Definition: timsdata.h:49
pappso::MassSpectrumId
Definition: massspectrumid.h:38
pappso::QualifiedMassSpectrum::setEmptyMassSpectrum
void setEmptyMassSpectrum(bool is_empty_mass_spectrum)
Definition: qualifiedmassspectrum.cpp:164
pappso::TimsXicStructure::mzRange
MzRange mzRange
Definition: timsdata.h:53
pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex
void setPrecursorSpectrumIndex(std::size_t precursor_scan_num)
Set the scan number of the precursor ion.
Definition: qualifiedmassspectrum.cpp:400
pappso::TimsData::getTimsFrameCstSPtr
TimsFrameCstSPtr getTimsFrameCstSPtr(std::size_t timsId) const
get a Tims frame with his database ID
Definition: timsdata.cpp:446
pappso::TimsXicStructure::scanNumEnd
std::size_t scanNumEnd
Definition: timsdata.h:55
pappso::TimsData::mpa_mzCalibrationStore
MzCalibrationStore * mpa_mzCalibrationStore
Definition: timsdata.h:233
pappso::MassSpectrumId::setSpectrumIndex
void setSpectrumIndex(std::size_t index)
Definition: massspectrumid.cpp:103
pappso::QualifiedMassSpectrum::setDtInMilliSeconds
void setDtInMilliSeconds(pappso_double rt)
Set the drift time in milliseconds.
Definition: qualifiedmassspectrum.cpp:219
pappso::MassSpectrumId::setNativeId
void setNativeId(const QString &native_id)
Definition: massspectrumid.cpp:89
pappso::TimsData::getRawIndexFromCoordinate
std::size_t getRawIndexFromCoordinate(std::size_t frame_id, std::size_t scan_num) const
Definition: timsdata.cpp:270
pappso::TimsXicExtractorInterface::extractTimsXicList
virtual void extractTimsXicList(std::vector< TimsXicStructure > &timsXicList, double rtRange) const =0
extract XICs for given coordinates XICs are extracted given their coordinates : retention time target...
pappso::TimsFrameCstSPtr
std::shared_ptr< const TimsFrame > TimsFrameCstSPtr
Definition: timsframe.h:42
pappso::TimsData::openDatabaseConnection
QSqlDatabase openDatabaseConnection() const
Definition: timsdata.cpp:168
pappso::TimsXicStructure::rtTarget
pappso::pappso_double rtTarget
Definition: timsdata.h:56
pappso::PrecursorIonData
Definition: qualifiedmassspectrum.h:62
pappso::TracePlusCombiner
Definition: tracepluscombiner.h:27
pappso::TimsData::m_builtinMs2Centroid
bool m_builtinMs2Centroid
enable builtin centroid on raw tims integers by default
Definition: timsdata.h:228
pappso::PappsoException
Definition: pappsoexception.h:42
pappso::FilterTriangle::setTriangleSlope
double setTriangleSlope(double intensity, double mz)
Definition: filtertriangle.cpp:47