#include <timsdata.h>

Classes
struct	FrameIdDescr

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...

TimsXicStructure	getTimsXicStructureFromPrecursorId (std::size_t precursor_id, PrecisionPtr precision_ptr) const

void	extractXicListByTimsXicStructureList (std::vector< TimsXicStructure > &tims_xic_structure_list, XicExtractMethod xicExtractMethod, double rtRange) const
	extract a list of XICs from Tims data More...

std::map< quint32, quint32 >	getRawMs2ByPrecursorId (std::size_t precursor_index)
	get cumulated raw signal for a given precursor only to use to see the raw signal More...

Private Member Functions
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::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< 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)

void	fillFrameIdDescrList ()
	private function to fill m_frameIdDescrList More...

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

std::map< int, QSqlRecord >	m_mapTimsCalibrationRecord

std::map< std::size_t, QSqlRecord >	m_mapFramesRecord

MzCalibrationStore *	mpa_mzCalibrationStore

std::vector< FrameIdDescr >	m_frameIdDescrList
	store every frame id and corresponding sizes More...

std::map< std::size_t, std::size_t >	m_thousandIndexToFrameIdDescrListIndex
	index to find quickly a frameId in the description list with the raw index of spectrum modulo 1000 More...

QMutex	m_mutex

Detailed Description

Todo:: write docs

Definition at line 90 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.

   : m_timsDataDirectory(timsDataDirectory)
 {
  
   qDebug();
   mpa_mzCalibrationStore = new MzCalibrationStore();
   if(!m_timsDataDirectory.exists())
     {
       throw PappsoException(
         QObject::tr("ERROR TIMS data directory %1 not found")
           .arg(m_timsDataDirectory.absolutePath()));
     }
  
   if(!QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf")).exists())
     {
  
       throw PappsoException(
         QObject::tr("ERROR TIMS data directory, %1 sqlite file not found")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf")));
     }
  
   // Open the database
   QSqlDatabase qdb = openDatabaseConnection();
  
  
   QSqlQuery q(qdb);
   if(!q.exec("select Key, Value from GlobalMetadata where "
              "Key='TimsCompressionType';"))
     {
  
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(q.lastError().databaseText())
           .arg(q.lastError().driverText())
           .arg(q.lastError().nativeErrorCode()));
     }
  
  
   int compression_type = 0;
   if(q.next())
     {
       compression_type = q.value(1).toInt();
     }
   qDebug() << " compression_type=" << compression_type;
   mpa_timsBinDec = new TimsBinDec(
     QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf_bin")),
     compression_type);
  
  
   // get number of precursors
   if(!q.exec("SELECT COUNT( DISTINCT Id) FROM Precursors;"))
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   if(q.next())
     {
       m_totalNumberOfPrecursors = q.value(0).toLongLong();
     }
  
  
   fillFrameIdDescrList();
  
   // get number of scans
   if(!q.exec("SELECT SUM(NumScans) FROM Frames"))
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   if(q.next())
     {
       m_totalNumberOfScans = q.value(0).toLongLong();
     }
  
   if(!q.exec("select * from MzCalibration;"))
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(q.lastError().databaseText())
           .arg(q.lastError().driverText())
           .arg(q.lastError().nativeErrorCode()));
     }
  
   while(q.next())
     {
       QSqlRecord record = q.record();
       m_mapMzCalibrationRecord.insert(
         std::pair<int, QSqlRecord>(record.value(0).toInt(), record));
     }
  
   // m_mapTimsCalibrationRecord
  
   if(!q.exec("select * from TimsCalibration;"))
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(q.lastError().databaseText())
           .arg(q.lastError().driverText())
           .arg(q.lastError().nativeErrorCode()));
     }
   while(q.next())
     {
       QSqlRecord record = q.record();
       m_mapTimsCalibrationRecord.insert(
         std::pair<int, QSqlRecord>(record.value(0).toInt(), record));
     }
  
  
   // store frames
   if(!q.exec("select Frames.TimsId, Frames.AccumulationTime, "        // 1
              "Frames.MzCalibration, "                                 // 2
              "Frames.T1, Frames.T2, "                                 // 4
              "Frames.Time, Frames.MsMsType, Frames.TimsCalibration, " // 7
              "Frames.Id "                                             // 8
              " FROM Frames;"))
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(q.lastError().databaseText())
           .arg(q.lastError().driverText())
           .arg(q.lastError().nativeErrorCode()));
     }
   while(q.next())
     {
       QSqlRecord record = q.record();
       m_mapFramesRecord.insert(
         std::pair<std::size_t, QSqlRecord>(record.value(8).toUInt(), record));
     }
  
  
   std::shared_ptr<pappso::FilterPseudoCentroid> ms2filter =
     std::make_shared<pappso::FilterPseudoCentroid>(35000, 5, 0.5, 0.1);
   mcsp_ms2Filter = ms2filter;
  
  
   std::shared_ptr<FilterTriangle> ms1filter =
     std::make_shared<FilterTriangle>();
   ms1filter.get()->setTriangleSlope(50, 0.01);
   mcsp_ms1Filter = ms1filter;
 }

References fillFrameIdDescrList(), m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, m_timsDataDirectory, m_totalNumberOfPrecursors, m_totalNumberOfScans, mcsp_ms1Filter, mcsp_ms2Filter, mpa_mzCalibrationStore, mpa_timsBinDec, and openDatabaseConnection().

◆ TimsData() [2/2]

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

Copy constructor

Parameters

other TODO

◆ ~TimsData()

TimsData::~TimsData ( )

Destructor

Definition at line 253 of file timsdata.cpp.

 {
   // m_qdb.close();
   if(mpa_timsBinDec != nullptr)
     {
       delete mpa_timsBinDec;
     }
   if(mpa_mzCalibrationStore != nullptr)
     {
       delete mpa_mzCalibrationStore;
     }
 }

References mpa_mzCalibrationStore, and 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_list	the list of precursors to extract
precision_ptr	precision to compute the mz range to extract for each precursor mass
xicExtractMethod	XIC extraction method (sum or max) to use
rtRange	retention 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 1327 of file timsdata.cpp.

 {
  
   qDebug();
   std::vector<TimsXicStructure> xic_list;
  
   try
     {
       QSqlDatabase qdb = openDatabaseConnection();
  
       for(auto precursor_id : precursor_id_list)
         {
           QSqlQuery q = qdb.exec(
             QString("SELECT Frames.Time, "
                     "PasefFrameMsMsInfo.Frame,PasefFrameMsMsInfo.ScanNumBegin,"
                     "PasefFrameMsMsInfo.ScanNumEnd, Precursors.MonoisotopicMz, "
                     "Precursors.Charge  FROM "
                     "PasefFrameMsMsInfo INNER JOIN Precursors ON "
                     "PasefFrameMsMsInfo.Precursor=Precursors.Id INNER JOIN "
                     "Frames ON PasefFrameMsMsInfo.Frame=Frames.Id where "
                     "Precursors.Id=%1;")
               .arg(precursor_id));
           if(q.lastError().isValid())
             {
               qDebug();
               throw PappsoException(
                 QObject::tr(
                   "ERROR in TIMS sqlite database file %1, executing SQL "
                   "command %2:\n%3\n%4\n%5")
                   .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
                   .arg(q.lastQuery())
                   .arg(qdb.lastError().databaseText())
                   .arg(qdb.lastError().driverText())
                   .arg(qdb.lastError().nativeErrorCode()));
             }
  
           while(q.next())
             {
               // Frame, ScanNumBegin, ScanNumEnd, IsolationMz, ColliqionEnergy,
               // Precursor
               // Id, LargestPeakMz, AverageMz, MonoisotopicMz, Charge,
               // ScanNumber, Intensity, Parent
               TimsXicStructure xic_structure;
  
               xic_structure.precursorId = precursor_id;
               xic_structure.mzRange =
                 MzRange(q.value(4).toDouble(), precision_ptr);
               xic_structure.scanNumBegin = q.value(2).toUInt();
               xic_structure.scanNumEnd   = q.value(3).toUInt();
               xic_structure.rtTarget     = q.value(0).toDouble();
               // xic_structure.charge       = q.value(5).toUInt();
               xic_structure.xicSptr = std::make_shared<Xic>();
  
               xic_list.push_back(xic_structure);
             }
         }
       qDebug();
  
       TimsXicExtractorInterface *extractor_p = new TimsDirectXicExtractor(this);
       extractor_p->setXicExtractMethod(xicExtractMethod);
       extractor_p->extractTimsXicList(xic_list, rtRange);
     }
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
  
   qDebug();
   return xic_list;
 }

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

◆ extractXicListByTimsXicStructureList()

void pappso::TimsData::extractXicListByTimsXicStructureList	(	std::vector< TimsXicStructure > &	tims_xic_structure_list,
		pappso::XicExtractMethod	xicExtractMethod,
		double	rtRange
	)		const

extract a list of XICs from Tims data

Parameters

tims_xic_structure_list	the list of tims XIC structure to extract
xicExtractMethod	XIC extraction method (sum or max) to use
rtRange	retention time range in seconds to extract XIC from rtTarget rtRange to rtTarget + rtRange

Definition at line 1407 of file timsdata.cpp.

 {
   try
     {
  
       TimsXicExtractorInterface *extractor_p = new TimsDirectXicExtractor(this);
       extractor_p->setXicExtractMethod(xicExtractMethod);
       extractor_p->extractTimsXicList(tims_xic_structure_list, rtRange);
     }
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
  
   qDebug();
 }

References pappso::TimsXicExtractorInterface::extractTimsXicList(), pappso::TimsXicExtractorInterface::setXicExtractMethod(), and pappso::PappsoException::what().

◆ fillFrameIdDescrList()

void TimsData::fillFrameIdDescrList ( )

private

private function to fill m_frameIdDescrList

Definition at line 279 of file timsdata.cpp.

 {
  
   QSqlDatabase qdb = openDatabaseConnection();
  
   QSqlQuery q =
     qdb.exec(QString("SELECT Id, NumScans FROM "
                      "Frames ORDER BY Id"));
   if(q.lastError().isValid())
     {
  
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                     "command %2:\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(q.lastQuery())
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   pappso::TimsFrameSPtr tims_frame;
   bool index_found = false;
   std::size_t timsId;
   std::size_t numberScans;
   std::size_t cumulScans = 0;
   while(q.next() && (!index_found))
     {
       timsId      = q.value(0).toUInt();
       numberScans = q.value(1).toUInt();
  
       m_thousandIndexToFrameIdDescrListIndex.insert(
         std::pair<std::size_t, std::size_t>((cumulScans % 1000),
                                             m_frameIdDescrList.size()));
  
       m_frameIdDescrList.push_back({timsId, numberScans, cumulScans});
       cumulScans += numberScans;
     }
 }

References m_frameIdDescrList, m_thousandIndexToFrameIdDescrListIndex, m_timsDataDirectory, and openDatabaseConnection().

Referenced by TimsData().

◆ getClosestPrecursorIdByMz()

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

private

Todo:: documentation

Definition at line 708 of file timsdata.cpp.

 {
   std::vector<std::size_t> best_precursor;
   double best_value     = 1;
   int count             = 1;
   int best_val_position = 0;
  
   for(std::vector<double> values : ids)
     {
       double new_val = abs(mz_value - values[4]);
       if(new_val < best_value)
         {
           best_value        = new_val;
           best_val_position = count;
         }
       count++;
     }
   best_precursor.push_back(ids[best_val_position][1]);
   return best_precursor;
 }

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 582 of file timsdata.cpp.

 {
   pappso::TimsFrameCstSPtr frame = getTimsFrameCstSPtrCached(timsId);
  
   return frame->getMassSpectrumCstSPtr(scanNum);
 }

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

Definition at line 376 of file timsdata.cpp.

 {
  
   auto coordinate = getScanCoordinateFromRawIndex(raw_index);
   return getMassSpectrumCstSPtr(coordinate.first, coordinate.second);
 }

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 682 of file timsdata.cpp.

 {
   std::vector<std::size_t> precursor_id;
   for(std::vector<double> index : ids)
     {
       auto coordinate = getScanCoordinateFromRawIndex(index[0]);
  
       TimsFrameBaseCstSPtr tims_frame;
       tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first);
  
       double bko = tims_frame.get()->getOneOverK0Transformation(index[2]);
       double eko = tims_frame.get()->getOneOverK0Transformation(index[3]);
  
       // qInfo() << "diff" << (bko + eko) / 2;
       double mean_ko = (bko + eko) / 2;
  
       if(mean_ko > ko_value - 0.1 && mean_ko < ko_value + 0.1)
         {
           precursor_id.push_back(index[1]);
         }
     }
   return precursor_id;
 }

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 273 of file timsdata.cpp.

 {
   return m_builtinMs2Centroid;
 }

References m_builtinMs2Centroid.

◆ getMsLevelBySpectrumIndex()

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

Definition at line 732 of file timsdata.cpp.

 {
   auto coordinate = getScanCoordinateFromRawIndex(spectrum_index);
   auto tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
   return tims_frame.get()->getMsLevel();
 }

References getScanCoordinateFromRawIndex(), and getTimsFrameCstSPtrCached().

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

◆ 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 603 of file timsdata.cpp.

 {
   std::vector<std::size_t> precursor_ids;
   std::vector<std::vector<double>> ids;
  
   QSqlDatabase qdb = openDatabaseConnection();
   QSqlQuery q      = qdb.exec(
     QString(
       "SELECT Frames.time, Precursors.MonoisotopicMz, Precursors.Charge, "
       "Precursors.Id, Frames.Id, PasefFrameMsMsInfo.ScanNumBegin, "
       "PasefFrameMsMsInfo.scanNumEnd "
       "FROM Frames "
       "INNER JOIN PasefFrameMsMsInfo ON Frames.Id = PasefFrameMsMsInfo.Frame "
       "INNER JOIN Precursors ON PasefFrameMsMsInfo.Precursor = Precursors.Id "
       "WHERE Precursors.Charge == %1 "
       "AND Precursors.MonoisotopicMz > %2 -0.01 "
       "AND Precursors.MonoisotopicMz < %2 +0.01 "
       "AND Frames.Time >= %3 "
       "AND Frames.Time < %3 +1; ")
       .arg(charge)
       .arg(mz_val)
       .arg(rt_sec));
   if(q.lastError().isValid())
     {
  
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
                     "executing SQL "
                     "command %3:\n%4\n%5\n%6")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(qdb.databaseName())
           .arg(q.lastQuery())
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   while(q.next())
     {
       // qInfo() << q.value(0).toDouble() << q.value(1).toDouble()
       //       << q.value(2).toDouble() << q.value(3).toDouble();
  
       std::vector<double> sql_values;
       sql_values.push_back(q.value(4).toDouble()); // frame id
       sql_values.push_back(q.value(3).toDouble()); // precursor id
       sql_values.push_back(q.value(5).toDouble()); // scan num begin
       sql_values.push_back(q.value(6).toDouble()); // scan num end
       sql_values.push_back(q.value(1).toDouble()); // mz_value
  
       ids.push_back(sql_values);
  
  
       if(std::find(precursor_ids.begin(),
                    precursor_ids.end(),
                    q.value(3).toDouble()) == precursor_ids.end())
         {
           precursor_ids.push_back(q.value(3).toDouble());
         }
     }
  
   if(precursor_ids.size() > 1)
     {
       // std::vector<std::size_t> precursor_ids_ko =
       // getMatchPrecursorIdByKo(ids, values[3]);
       if(precursor_ids.size() > 1)
         {
           precursor_ids = getClosestPrecursorIdByMz(ids, k0);
         }
       return precursor_ids;
     }
   else
     {
       return precursor_ids;
     }
 }

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

◆ getQualifiedMassSpectrumByRawIndex()

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

Definition at line 741 of file timsdata.cpp.

 {
   auto coordinate = getScanCoordinateFromRawIndex(spectrum_index);
   TimsFrameBaseCstSPtr tims_frame;
   if(want_binary_data)
     {
       tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
     }
   else
     {
       tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first);
     }
   QualifiedMassSpectrum mass_spectrum;
   MassSpectrumId spectrum_id;
  
   spectrum_id.setSpectrumIndex(spectrum_index);
   spectrum_id.setNativeId(QString("frame=%1 scan=%2 index=%3")
                             .arg(coordinate.first)
                             .arg(coordinate.second)
                             .arg(spectrum_index));
  
   mass_spectrum.setMassSpectrumId(spectrum_id);
  
   mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
   mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
  
   mass_spectrum.setDtInMilliSeconds(
     tims_frame.get()->getDriftTime(coordinate.second));
   // 1/K0
   mass_spectrum.setParameterValue(
     QualifiedMassSpectrumParameter::OneOverK0,
     tims_frame.get()->getOneOverK0Transformation(coordinate.second));
  
   mass_spectrum.setEmptyMassSpectrum(true);
   if(want_binary_data)
     {
       mass_spectrum.setMassSpectrumSPtr(
         tims_frame.get()->getMassSpectrumSPtr(coordinate.second));
       if(mass_spectrum.size() > 0)
         {
           mass_spectrum.setEmptyMassSpectrum(false);
         }
     }
   else
     {
       // if(tims_frame.get()->getNbrPeaks(coordinate.second) > 0)
       //{
       mass_spectrum.setEmptyMassSpectrum(false);
       // }
     }
   if(tims_frame.get()->getMsLevel() > 1)
     {
  
       QSqlDatabase qdb = openDatabaseConnection();
       QSqlQuery q      = qdb.exec(
         QString(
           "SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
           "PasefFrameMsMsInfo INNER JOIN Precursors ON "
           "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
           "PasefFrameMsMsInfo.Frame=%1 and (PasefFrameMsMsInfo.ScanNumBegin "
           "<= %2 and PasefFrameMsMsInfo.ScanNumEnd >= %2);")
           .arg(coordinate.first)
           .arg(coordinate.second));
       if(q.lastError().isValid())
         {
           throw PappsoException(
             QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                         "command %2:\n%3\n%4\n%5")
               .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
               .arg(q.lastQuery())
               .arg(qdb.lastError().databaseText())
               .arg(qdb.lastError().driverText())
               .arg(qdb.lastError().nativeErrorCode()));
         }
       if(q.next())
         {
           // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
           // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
           // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
           // mass_spectrum.setPrecursorSpectrumIndex();
  
           mass_spectrum.appendPrecursorIonData(
             PrecursorIonData(q.value(10).toDouble(),
                              q.value(11).toInt(),
                              q.value(13).toDouble()));
  
  
           MassSpectrumId spectrum_id;
           std::size_t prec_spectrum_index = getRawIndexFromCoordinate(
             q.value(14).toDouble(), coordinate.second);
  
           mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
           mass_spectrum.setPrecursorNativeId(
             QString("frame=%1 scan=%2 index=%3")
               .arg(q.value(14).toDouble())
               .arg(coordinate.second)
               .arg(prec_spectrum_index));
  
           mass_spectrum.setParameterValue(
             QualifiedMassSpectrumParameter::IsolationMz, q.value(3).toDouble());
           mass_spectrum.setParameterValue(
             QualifiedMassSpectrumParameter::IsolationWidth,
             q.value(4).toDouble());
  
           mass_spectrum.setParameterValue(
             QualifiedMassSpectrumParameter::CollisionEnergy,
             q.value(5).toFloat());
           mass_spectrum.setParameterValue(
             QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
             q.value(6).toInt());
         }
     }
  
   return mass_spectrum;
 }

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 860 of file timsdata.cpp.

 {
   QualifiedMassSpectrum mass_spectrum;
  
   try
     {
       QSqlDatabase qdb = openDatabaseConnection();
       mass_spectrum.setMsLevel(1);
       mass_spectrum.setPrecursorSpectrumIndex(0);
       mass_spectrum.setEmptyMassSpectrum(true);
       QSqlQuery q =
         qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
                          "PasefFrameMsMsInfo INNER JOIN Precursors ON "
                          "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
                          "Precursors.Id=%1;")
                    .arg(precursor_index));
       if(q.lastError().isValid())
         {
  
           throw PappsoException(
             QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                         "command %2:\n%3\n%4\n%5")
               .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
               .arg(q.lastQuery())
               .arg(qdb.lastError().databaseText())
               .arg(qdb.lastError().driverText())
               .arg(qdb.lastError().nativeErrorCode()));
         }
       if(q.size() == 0)
         {
  
           throw ExceptionNotFound(
             QObject::tr(
               "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
               "id=%1 not found")
               .arg(precursor_index));
         }
       else
         {
           TracePlusCombiner combiner;
           MapTrace combiner_result;
  
  
           bool first                      = true;
           std::size_t scan_mobility_start = 0;
           std::size_t scan_mobility_end   = 0;
           std::set<std::size_t> tims_frame_list;
           while(q.next())
             {
               // get MS1 frame
               tims_frame_list.insert(q.value(14).toLongLong());
               if(first)
                 {
  
  
                   MassSpectrumId spectrum_id;
  
                   spectrum_id.setSpectrumIndex(precursor_index);
                   spectrum_id.setNativeId(
                     QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5")
                       .arg(q.value(0).toLongLong())
                       .arg(q.value(1).toLongLong())
                       .arg(q.value(2).toLongLong())
                       .arg(precursor_index)
                       .arg(ms2_index));
  
  
                   mass_spectrum.setMassSpectrumId(spectrum_id);
  
  
                   scan_mobility_start = q.value(1).toLongLong();
                   scan_mobility_end   = q.value(2).toLongLong();
  
                   first = false;
                 }
             }
  
           first = true;
           for(std::size_t tims_id : tims_frame_list)
             {
               TimsFrameBaseCstSPtr tims_frame =
                 getTimsFrameCstSPtrCached(tims_id);
               if(first)
                 {
                   mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::OneOverK0begin,
                     tims_frame.get()->getOneOverK0Transformation(
                       scan_mobility_start));
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::OneOverK0end,
                     tims_frame.get()->getOneOverK0Transformation(
                       scan_mobility_end));
  
                   first = false;
                 }
  
  
               if(want_binary_data)
                 {
                   combiner.combine(combiner_result,
                                    tims_frame.get()->cumulateScanToTrace(
                                      scan_mobility_start, scan_mobility_end));
                 }
               else
                 {
                   break;
                 }
             }
  
  
           if(first == true)
             {
               throw ExceptionNotFound(
                 QObject::tr(
                   "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
                   "id=%1 not found")
                   .arg(precursor_index));
             }
  
  
           if(want_binary_data)
             {
  
               pappso::Trace trace(combiner_result);
               qDebug();
  
               if(trace.size() > 0)
                 {
                   if(mcsp_ms1Filter != nullptr)
                     {
                       mcsp_ms1Filter->filter(trace);
                     }
  
                   qDebug();
                   mass_spectrum.setMassSpectrumSPtr(
                     MassSpectrum(trace).makeMassSpectrumSPtr());
                   mass_spectrum.setEmptyMassSpectrum(false);
                 }
               else
                 {
                   mass_spectrum.setMassSpectrumSPtr(nullptr);
                   mass_spectrum.setEmptyMassSpectrum(true);
                 }
             }
         }
     }
  
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
   return mass_spectrum;
 }

References pappso::TracePlusCombiner::combine(), getTimsFrameCstSPtrCached(), m_timsDataDirectory, mcsp_ms1Filter, pappso::OneOverK0begin, pappso::OneOverK0end, 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(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::PappsoException::what().

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 1025 of file timsdata.cpp.

 {
   qDebug();
   try
     {
       QSqlDatabase qdb = openDatabaseConnection();
       MassSpectrumId spectrum_id;
  
       spectrum_id.setSpectrumIndex(precursor_index);
       spectrum_id.setNativeId(
         QString("precursor=%1 idxms2=%2").arg(precursor_index).arg(ms2_index));
  
       mass_spectrum.setMassSpectrumId(spectrum_id);
  
       mass_spectrum.setMsLevel(2);
       mass_spectrum.setPrecursorSpectrumIndex(ms2_index - 1);
  
       mass_spectrum.setEmptyMassSpectrum(true);
  
       qdb = openDatabaseConnection();
       // m_mutex.lock();
       //       if(m_query != nullptr)
       //       {
       //         *m_query =
       //         qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.*
       //         FROM "
       //                          "PasefFrameMsMsInfo INNER JOIN Precursors ON "
       //                          "PasefFrameMsMsInfo.Precursor=Precursors.Id
       //                          where " "Precursors.Id=%1;")
       //                    .arg(precursor_index));
       //       }
       QSqlQuery q =
         qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
                          "PasefFrameMsMsInfo INNER JOIN Precursors ON "
                          "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
                          "Precursors.Id=%1;")
                    .arg(precursor_index));
       if(q.lastError().isValid())
         {
           qDebug();
           throw PappsoException(
             QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                         "command %2:\n%3\n%4\n%5")
               .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
               .arg(q.lastQuery())
               .arg(qdb.lastError().databaseText())
               .arg(qdb.lastError().driverText())
               .arg(qdb.lastError().nativeErrorCode()));
         }
       qDebug();
       // m_mutex.unlock();
       if(q.size() == 0)
         {
  
           throw ExceptionNotFound(
             QObject::tr(
               "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
               "id=%1 not found")
               .arg(precursor_index));
         }
       else
         {
           //  qDebug() << " q.size()="<< q.size();
           qDebug();
           bool first                      = true;
           std::size_t scan_mobility_start = 0;
           std::size_t scan_mobility_end   = 0;
           std::vector<std::size_t> tims_frame_list;
  
           while(q.next())
             {
               tims_frame_list.push_back(q.value(0).toLongLong());
               if(first)
                 {
                   // mass_spectrum.setPrecursorCharge(q.value(11).toInt());
                   // mass_spectrum.setPrecursorMz(q.value(10).toDouble());
                   // mass_spectrum.setPrecursorIntensity(q.value(13).toDouble());
  
                   mass_spectrum.appendPrecursorIonData(
                     PrecursorIonData(q.value(10).toDouble(),
                                      q.value(11).toInt(),
                                      q.value(13).toDouble()));
  
                   mass_spectrum.setPrecursorNativeId(
                     QString("frame=%1 begin=%2 end=%3 precursor=%4 idxms2=%5")
                       .arg(q.value(14).toLongLong())
                       .arg(q.value(1).toLongLong())
                       .arg(q.value(2).toLongLong())
                       .arg(precursor_index)
                       .arg(ms2_index - 1));
                   // mass_spectrum.setPrecursorSpectrumIndex();
  
                   scan_mobility_start = q.value(1).toLongLong();
                   scan_mobility_end   = q.value(2).toLongLong();
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::IsolationMz,
                     q.value(3).toDouble());
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::IsolationWidth,
                     q.value(4).toDouble());
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::CollisionEnergy,
                     q.value(5).toFloat());
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
                     q.value(6).toInt());
  
                   first = false;
                 }
             }
           // QMutexLocker locker(&m_mutex_spectrum);
           qDebug();
           pappso::TimsFrameCstSPtr tims_frame, previous_frame;
           // TracePlusCombiner combiner;
           // MapTrace combiner_result;
           std::map<quint32, quint32> raw_spectrum;
           first = true;
           for(std::size_t tims_id : tims_frame_list)
             {
  
               tims_frame = getTimsFrameCstSPtrCached(tims_id);
               if(first)
                 {
                   mass_spectrum.setRtInSeconds(tims_frame.get()->getTime());
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::OneOverK0begin,
                     tims_frame.get()->getOneOverK0Transformation(
                       scan_mobility_start));
  
                   mass_spectrum.setParameterValue(
                     QualifiedMassSpectrumParameter::OneOverK0end,
                     tims_frame.get()->getOneOverK0Transformation(
                       scan_mobility_end));
  
                   first = false;
                 }
  
  
               if(want_binary_data)
                 {
                   qDebug();
                   /*combiner.combine(combiner_result,
                                    tims_frame.get()->cumulateScanToTrace(
                                      scan_mobility_start, scan_mobility_end));*/
                   if(previous_frame.get() != nullptr)
                     {
                       if(previous_frame.get()->hasSameCalibrationData(
                            *tims_frame.get()))
                         {
                         }
                       else
                         {
                           throw ExceptionNotFound(
                             QObject::tr(
                               "ERROR in %1 %2, different calibration data "
                               "between frame id %3 and frame id %4")
                               .arg(__FILE__)
                               .arg(__FUNCTION__)
                               .arg(previous_frame.get()->getId())
                               .arg(tims_frame.get()->getId()));
                         }
                     }
                   tims_frame.get()->cumulateScansInRawMap(
                     raw_spectrum, scan_mobility_start, scan_mobility_end);
                   qDebug();
                 }
               previous_frame = tims_frame;
             }
           qDebug() << " precursor_index=" << precursor_index
                    << " num_rows=" << tims_frame_list.size()
                    << " sql=" << q.lastQuery() << " "
                    << (std::size_t)QThread::currentThreadId();
           if(first == true)
             {
               throw ExceptionNotFound(
                 QObject::tr(
                   "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
                   "id=%1 not found")
                   .arg(precursor_index));
             }
           if(want_binary_data)
             {
               qDebug();
               // peak_pick.filter(trace);
               pappso::Trace trace;
               if(m_builtinMs2Centroid)
                 {
                   trace =
                     tims_frame.get()->getTraceFromCumulatedScansBuiltinCentroid(
                       raw_spectrum);
                 }
               else
                 {
                   // no builtin centroid:
  
                   trace =
                     tims_frame.get()->getTraceFromCumulatedScans(raw_spectrum);
                 }
  
               if(trace.size() > 0)
                 {
                   qDebug() << trace.size() << " "
                            << (std::size_t)QThread::currentThreadId();
  
                   if(mcsp_ms2Filter != nullptr)
                     {
                       // FilterTriangle filter;
                       // filter.setTriangleSlope(50, 0.02);
                       // filter.filter(trace);
                       // trace.filter(pappso::FilterHighPass(10));
                       mcsp_ms2Filter->filter(trace);
                     }
  
                   // FilterScaleFactorY filter_scale((double)1 /
                   //                                 (double)tims_frame_list.size());
                   // filter_scale.filter(trace);
                   qDebug();
                   mass_spectrum.setMassSpectrumSPtr(
                     MassSpectrum(trace).makeMassSpectrumSPtr());
                   mass_spectrum.setEmptyMassSpectrum(false);
                 }
               else
                 {
                   mass_spectrum.setMassSpectrumSPtr(nullptr);
                   mass_spectrum.setEmptyMassSpectrum(true);
                 }
  
               qDebug();
             }
           qDebug();
         }
     }
  
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
   qDebug();
 }

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 353 of file timsdata.cpp.

 {
  
   for(auto frameDescr : m_frameIdDescrList)
     {
       if(frameDescr.m_frameId == frame_id)
         {
           return frameDescr.m_cumulSize + scan_num;
         }
     }
  
   throw ExceptionNotFound(
     QObject::tr("ERROR raw index with frame=%1 scan=%2 not found")
       .arg(frame_id)
       .arg(scan_num));
 }

References m_frameIdDescrList.

Referenced by getQualifiedMassSpectrumByRawIndex().

◆ getRawMs2ByPrecursorId()

std::map< quint32, quint32 > TimsData::getRawMs2ByPrecursorId ( std::size_t precursor_index )

get cumulated raw signal for a given precursor only to use to see the raw signal

Parameters

precursor_index precursor index to extract signal from

Returns: a map of integers, x=time of flights, y= intensities

Definition at line 1496 of file timsdata.cpp.

 {
   qDebug();
   try
     {
       QSqlDatabase qdb = openDatabaseConnection();
  
       qdb = openDatabaseConnection();
       QSqlQuery q =
         qdb.exec(QString("SELECT PasefFrameMsMsInfo.*, Precursors.* FROM "
                          "PasefFrameMsMsInfo INNER JOIN Precursors ON "
                          "PasefFrameMsMsInfo.Precursor=Precursors.Id where "
                          "Precursors.Id=%1;")
                    .arg(precursor_index));
       if(q.lastError().isValid())
         {
           qDebug();
           throw PappsoException(
             QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                         "command %2:\n%3\n%4\n%5")
               .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
               .arg(q.lastQuery())
               .arg(qdb.lastError().databaseText())
               .arg(qdb.lastError().driverText())
               .arg(qdb.lastError().nativeErrorCode()));
         }
       qDebug();
       // m_mutex.unlock();
       if(q.size() == 0)
         {
  
           throw ExceptionNotFound(
             QObject::tr(
               "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
               "id=%1 not found")
               .arg(precursor_index));
         }
       else
         {
           //  qDebug() << " q.size()="<< q.size();
           qDebug();
           bool first                      = true;
           std::size_t scan_mobility_start = 0;
           std::size_t scan_mobility_end   = 0;
           std::vector<std::size_t> tims_frame_list;
  
           while(q.next())
             {
               tims_frame_list.push_back(q.value(0).toLongLong());
               if(first)
                 {
  
                   scan_mobility_start = q.value(1).toLongLong();
                   scan_mobility_end   = q.value(2).toLongLong();
  
                   first = false;
                 }
             }
           // QMutexLocker locker(&m_mutex_spectrum);
           qDebug();
           pappso::TimsFrameCstSPtr tims_frame, previous_frame;
           // TracePlusCombiner combiner;
           // MapTrace combiner_result;
           std::map<quint32, quint32> raw_spectrum;
           for(std::size_t tims_id : tims_frame_list)
             {
               tims_frame = getTimsFrameCstSPtrCached(tims_id);
               qDebug();
               /*combiner.combine(combiner_result,
                                tims_frame.get()->cumulateScanToTrace(
                                  scan_mobility_start, scan_mobility_end));*/
               if(previous_frame.get() != nullptr)
                 {
                   if(previous_frame.get()->hasSameCalibrationData(
                        *tims_frame.get()))
                     {
                     }
                   else
                     {
                       throw ExceptionNotFound(
                         QObject::tr(
                           "ERROR in %1 %2, different calibration data "
                           "between frame id %3 and frame id %4")
                           .arg(__FILE__)
                           .arg(__FUNCTION__)
                           .arg(previous_frame.get()->getId())
                           .arg(tims_frame.get()->getId()));
                     }
                 }
               tims_frame.get()->cumulateScansInRawMap(
                 raw_spectrum, scan_mobility_start, scan_mobility_end);
               qDebug();
  
               previous_frame = tims_frame;
             }
           qDebug() << " precursor_index=" << precursor_index
                    << " num_rows=" << tims_frame_list.size()
                    << " sql=" << q.lastQuery() << " "
                    << (std::size_t)QThread::currentThreadId();
           if(first == true)
             {
               throw ExceptionNotFound(
                 QObject::tr(
                   "ERROR in getQualifiedMassSpectrumByPrecursorId, precursor "
                   "id=%1 not found")
                   .arg(precursor_index));
             }
           qDebug();
         }
     }
  
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
   qDebug();
 }

References getTimsFrameCstSPtrCached(), m_timsDataDirectory, openDatabaseConnection(), and pappso::PappsoException::what().

◆ getScanCoordinateFromRawIndex()

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

private

Definition at line 319 of file timsdata.cpp.

 {
  
   std::size_t modulo = raw_index % 1000;
   auto map_it        = m_thousandIndexToFrameIdDescrListIndex.find(modulo);
   if(map_it == m_thousandIndexToFrameIdDescrListIndex.end())
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR raw index %1 not found (modulo)").arg(raw_index));
     }
   std::size_t start_point_index = map_it->second;
   while((start_point_index > 0) &&
         (m_frameIdDescrList[start_point_index].m_cumulSize > raw_index))
     {
       start_point_index--;
     }
   for(std::size_t i = start_point_index; i < m_frameIdDescrList.size(); i++)
     {
  
       if(raw_index <
          (m_frameIdDescrList[i].m_cumulSize + m_frameIdDescrList[i].m_size))
         {
           return std::pair<std::size_t, std::size_t>(
             m_frameIdDescrList[i].m_frameId,
             raw_index - m_frameIdDescrList[i].m_cumulSize);
         }
     }
  
   throw ExceptionNotFound(
     QObject::tr("ERROR raw index %1 not found").arg(raw_index));
 }

References m_frameIdDescrList, and m_thousandIndexToFrameIdDescrListIndex.

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 385 of file timsdata.cpp.

 {
  
   qDebug() << " timsId=" << timsId;
  
   auto it_map_record_frames = m_mapFramesRecord.find(timsId);
   if(it_map_record_frames == m_mapFramesRecord.end())
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR Frames database id %1 not found").arg(timsId));
     }
   pappso::TimsFrameBaseSPtr tims_frame;
  
  
   tims_frame = std::make_shared<TimsFrameBase>(
     TimsFrameBase(timsId, it_map_record_frames->second.value(0).toUInt()));
  
   auto it_map_record = m_mapMzCalibrationRecord.find(
     it_map_record_frames->second.value(2).toInt());
   if(it_map_record != m_mapMzCalibrationRecord.end())
     {
  
       double T1_frame =
         it_map_record_frames->second.value(3).toDouble(); // Frames.T1
       double T2_frame =
         it_map_record_frames->second.value(4).toDouble(); // Frames.T2
  
  
       tims_frame.get()->setMzCalibrationInterfaceSPtr(
         mpa_mzCalibrationStore->getInstance(
           T1_frame, T2_frame, it_map_record->second));
     }
   else
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR MzCalibration database id %1 not found")
           .arg(it_map_record_frames->second.value(2).toInt()));
     }
  
   tims_frame.get()->setAccumulationTime(
     it_map_record_frames->second.value(1).toDouble());
  
   tims_frame.get()->setTime(it_map_record_frames->second.value(5).toDouble());
   tims_frame.get()->setMsMsType(it_map_record_frames->second.value(6).toUInt());
  
  
   auto it_map_record_tims_calibration = m_mapTimsCalibrationRecord.find(
     it_map_record_frames->second.value(7).toInt());
   if(it_map_record_tims_calibration != m_mapTimsCalibrationRecord.end())
     {
  
       tims_frame.get()->setTimsCalibration(
         it_map_record_tims_calibration->second.value(1).toInt(),
         it_map_record_tims_calibration->second.value(2).toDouble(),
         it_map_record_tims_calibration->second.value(3).toDouble(),
         it_map_record_tims_calibration->second.value(4).toDouble(),
         it_map_record_tims_calibration->second.value(5).toDouble(),
         it_map_record_tims_calibration->second.value(6).toDouble(),
         it_map_record_tims_calibration->second.value(7).toDouble(),
         it_map_record_tims_calibration->second.value(8).toDouble(),
         it_map_record_tims_calibration->second.value(9).toDouble(),
         it_map_record_tims_calibration->second.value(10).toDouble(),
         it_map_record_tims_calibration->second.value(11).toDouble());
     }
   else
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR TimsCalibration database id %1 not found")
           .arg(it_map_record_frames->second.value(7).toInt()));
     }
  
   return tims_frame;
 }

References pappso::MzCalibrationStore::getInstance(), m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, and mpa_mzCalibrationStore.

Referenced by getTimsFrameBaseCstSPtrCached().

◆ getTimsFrameBaseCstSPtrCached()

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

private

Definition at line 1278 of file timsdata.cpp.

 {
   QMutexLocker locker(&m_mutex);
   for(auto &tims_frame : m_timsFrameBaseCache)
     {
       if(tims_frame.get()->getId() == timsId)
         {
           m_timsFrameBaseCache.push_back(tims_frame);
           return tims_frame;
         }
     }
  
   m_timsFrameBaseCache.push_back(getTimsFrameBaseCstSPtr(timsId));
   if(m_timsFrameBaseCache.size() > m_cacheSize)
     m_timsFrameBaseCache.pop_front();
   return m_timsFrameBaseCache.back();
 }

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 494 of file timsdata.cpp.

 {
  
   qDebug() << " timsId=" << timsId
            << " m_mapFramesRecord.size()=" << m_mapFramesRecord.size();
   /*
     for(auto pair_i : m_mapFramesRecord)
       {
  
         qDebug() << " pair_i=" << pair_i.first;
       }
       */
  
   auto it_map_record_frames = m_mapFramesRecord.find(timsId);
   if(it_map_record_frames == m_mapFramesRecord.end())
     {
  
       throw ExceptionNotFound(
         QObject::tr("ERROR Frames database id %1 not found").arg(timsId));
     }
  
  
   pappso::TimsFrameSPtr tims_frame;
  
  
   tims_frame = mpa_timsBinDec->getTimsFrameSPtrByOffset(
     timsId, it_map_record_frames->second.value(0).toUInt());
  
   qDebug();
   auto it_map_record = m_mapMzCalibrationRecord.find(
     it_map_record_frames->second.value(2).toInt());
   if(it_map_record != m_mapMzCalibrationRecord.end())
     {
  
       double T1_frame =
         it_map_record_frames->second.value(3).toDouble(); // Frames.T1
       double T2_frame =
         it_map_record_frames->second.value(4).toDouble(); // Frames.T2
  
  
       tims_frame.get()->setMzCalibrationInterfaceSPtr(
         mpa_mzCalibrationStore->getInstance(
           T1_frame, T2_frame, it_map_record->second));
     }
   else
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR MzCalibration database id %1 not found")
           .arg(it_map_record_frames->second.value(2).toInt()));
     }
  
   tims_frame.get()->setAccumulationTime(
     it_map_record_frames->second.value(1).toDouble());
  
   tims_frame.get()->setTime(it_map_record_frames->second.value(5).toDouble());
   tims_frame.get()->setMsMsType(it_map_record_frames->second.value(6).toUInt());
  
   qDebug();
   auto it_map_record_tims_calibration = m_mapTimsCalibrationRecord.find(
     it_map_record_frames->second.value(7).toInt());
   if(it_map_record_tims_calibration != m_mapTimsCalibrationRecord.end())
     {
  
       tims_frame.get()->setTimsCalibration(
         it_map_record_tims_calibration->second.value(1).toInt(),
         it_map_record_tims_calibration->second.value(2).toDouble(),
         it_map_record_tims_calibration->second.value(3).toDouble(),
         it_map_record_tims_calibration->second.value(4).toDouble(),
         it_map_record_tims_calibration->second.value(5).toDouble(),
         it_map_record_tims_calibration->second.value(6).toDouble(),
         it_map_record_tims_calibration->second.value(7).toDouble(),
         it_map_record_tims_calibration->second.value(8).toDouble(),
         it_map_record_tims_calibration->second.value(9).toDouble(),
         it_map_record_tims_calibration->second.value(10).toDouble(),
         it_map_record_tims_calibration->second.value(11).toDouble());
     }
   else
     {
       throw ExceptionNotFound(
         QObject::tr("ERROR TimsCalibration database id %1 not found")
           .arg(it_map_record_frames->second.value(7).toInt()));
     }
   qDebug();
   return tims_frame;
 }

References pappso::MzCalibrationStore::getInstance(), pappso::TimsBinDec::getTimsFrameSPtrByOffset(), m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, mpa_mzCalibrationStore, and mpa_timsBinDec.

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 1297 of file timsdata.cpp.

 {
   QMutexLocker locker(&m_mutex);
   for(auto &tims_frame : m_timsFrameCache)
     {
       if(tims_frame.get()->getId() == timsId)
         {
           m_timsFrameCache.push_back(tims_frame);
           return tims_frame;
         }
     }
  
   m_timsFrameCache.push_back(getTimsFrameCstSPtr(timsId));
   if(m_timsFrameCache.size() > m_cacheSize)
     m_timsFrameCache.pop_front();
   return m_timsFrameCache.back();
 }

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

Referenced by getMassSpectrumCstSPtr(), getMsLevelBySpectrumIndex(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), and getRawMs2ByPrecursorId().

◆ getTimsMS1FrameIdRange()

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

Definition at line 460 of file timsdata.cpp.

 {
  
   qDebug() << " rt_begin=" << rt_begin << " rt_end=" << rt_end;
   std::vector<std::size_t> tims_frameid_list;
   QSqlDatabase qdb = openDatabaseConnection();
   QSqlQuery q      = qdb.exec(QString("SELECT Frames.Id FROM Frames WHERE "
                                  "Frames.MsMsType=0 AND (Frames.Time>=%1) AND "
                                  "(Frames.Time<=%2) ORDER BY Frames.Time;")
                            .arg(rt_begin)
                            .arg(rt_end));
   if(q.lastError().isValid())
     {
  
       throw PappsoException(
         QObject::tr("ERROR in TIMS sqlite database file %1, database name %2, "
                     "executing SQL "
                     "command %3:\n%4\n%5\n%6")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(qdb.databaseName())
           .arg(q.lastQuery())
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   while(q.next())
     {
  
       tims_frameid_list.push_back(q.value(0).toUInt());
     }
   return tims_frameid_list;
 }

References m_timsDataDirectory, and openDatabaseConnection().

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

◆ getTimsXicStructureFromPrecursorId()

pappso::TimsXicStructure pappso::TimsData::getTimsXicStructureFromPrecursorId	(	std::size_t	precursor_id,
		PrecisionPtr	precision_ptr
	)		const

Definition at line 1433 of file timsdata.cpp.

 {
  
   qDebug();
   TimsXicStructure tims_xic_structure;
  
   try
     {
       QSqlDatabase qdb = openDatabaseConnection();
       QSqlQuery q      = qdb.exec(
         QString("SELECT Frames.Time, "
                 "PasefFrameMsMsInfo.Frame,PasefFrameMsMsInfo.ScanNumBegin,"
                 "PasefFrameMsMsInfo.ScanNumEnd, Precursors.MonoisotopicMz, "
                 "Precursors.Charge  FROM "
                 "PasefFrameMsMsInfo INNER JOIN Precursors ON "
                 "PasefFrameMsMsInfo.Precursor=Precursors.Id INNER JOIN "
                 "Frames ON PasefFrameMsMsInfo.Frame=Frames.Id where "
                 "Precursors.Id=%1;")
           .arg(precursor_id));
       if(q.lastError().isValid())
         {
           qDebug();
           throw PappsoException(
             QObject::tr("ERROR in TIMS sqlite database file %1, executing SQL "
                         "command %2:\n%3\n%4\n%5")
               .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
               .arg(q.lastQuery())
               .arg(qdb.lastError().databaseText())
               .arg(qdb.lastError().driverText())
               .arg(qdb.lastError().nativeErrorCode()));
         }
  
       while(q.next())
         {
           // Frame, ScanNumBegin, ScanNumEnd, IsolationMz, ColliqionEnergy,
           // Precursor
           // Id, LargestPeakMz, AverageMz, MonoisotopicMz, Charge,
           // ScanNumber, Intensity, Parent
  
           tims_xic_structure.precursorId = precursor_id;
           tims_xic_structure.mzRange =
             MzRange(q.value(4).toDouble(), precision_ptr);
           tims_xic_structure.scanNumBegin = q.value(2).toUInt();
           tims_xic_structure.scanNumEnd   = q.value(3).toUInt();
           tims_xic_structure.rtTarget     = q.value(0).toDouble();
           // xic_structure.charge       = q.value(5).toUInt();
           tims_xic_structure.xicSptr = std::make_shared<Xic>();
         }
     }
   catch(PappsoException &error)
     {
       throw error;
     }
   catch(std::exception &error)
     {
       qDebug() << QString("Failure %1 ").arg(error.what());
     }
   return tims_xic_structure;
 }

References pappso::TimsXicStructure::mzRange, pappso::TimsXicStructure::precursorId, pappso::TimsXicStructure::rtTarget, pappso::TimsXicStructure::scanNumBegin, pappso::TimsXicStructure::scanNumEnd, pappso::PappsoException::what(), and pappso::TimsXicStructure::xicSptr.

◆ getTotalNumberOfPrecursors()

std::size_t TimsData::getTotalNumberOfPrecursors ( ) const

get the number of precursors analyzes by PASEF

Definition at line 597 of file timsdata.cpp.

 {
   return m_totalNumberOfPrecursors;
 }

References m_totalNumberOfPrecursors.

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

◆ getTotalNumberOfScans()

std::size_t TimsData::getTotalNumberOfScans ( ) const

get the total number of scans

Definition at line 590 of file timsdata.cpp.

 {
   return m_totalNumberOfScans;
 }

References m_totalNumberOfScans.

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

◆ openDatabaseConnection()

QSqlDatabase TimsData::openDatabaseConnection ( ) const

private

Definition at line 218 of file timsdata.cpp.

 {
   QString database_connection_name = QString("%1_%2")
                                        .arg(m_timsDataDirectory.absolutePath())
                                        .arg((quintptr)QThread::currentThread());
   // Open the database
   QSqlDatabase qdb = QSqlDatabase::database(database_connection_name);
   if(!qdb.isValid())
     {
       qDebug() << database_connection_name;
       qdb = QSqlDatabase::addDatabase("QSQLITE", database_connection_name);
       qdb.setDatabaseName(m_timsDataDirectory.absoluteFilePath("analysis.tdf"));
     }
  
  
   if(!qdb.open())
     {
       qDebug();
       throw PappsoException(
         QObject::tr("ERROR opening TIMS sqlite database file %1, database name "
                     "%2 :\n%3\n%4\n%5")
           .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
           .arg(database_connection_name)
           .arg(qdb.lastError().databaseText())
           .arg(qdb.lastError().driverText())
           .arg(qdb.lastError().nativeErrorCode()));
     }
   return qdb;
 }

References m_timsDataDirectory.

Referenced by TimsData(), extractXicListByPrecursorIds(), fillFrameIdDescrList(), getPrecursorsFromMzRtCharge(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), getRawMs2ByPrecursorId(), 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 1321 of file timsdata.cpp.

 {
   mcsp_ms1Filter = filter;
 }

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 267 of file timsdata.cpp.

 {
   m_builtinMs2Centroid = centroid;
 }

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 1316 of file timsdata.cpp.

 {
   mcsp_ms2Filter = filter;
 }

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 283 of file timsdata.h.

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

◆ m_cacheSize

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

private

Definition at line 274 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_frameIdDescrList

std::vector<FrameIdDescr> pappso::TimsData::m_frameIdDescrList

private

store every frame id and corresponding sizes

Definition at line 302 of file timsdata.h.

Referenced by fillFrameIdDescrList(), getRawIndexFromCoordinate(), and getScanCoordinateFromRawIndex().

◆ m_mapFramesRecord

std::map<std::size_t, QSqlRecord> pappso::TimsData::m_mapFramesRecord

private

Definition at line 288 of file timsdata.h.

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

◆ m_mapMzCalibrationRecord

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

private

Definition at line 286 of file timsdata.h.

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

◆ m_mapTimsCalibrationRecord

std::map<int, QSqlRecord> pappso::TimsData::m_mapTimsCalibrationRecord

private

Definition at line 287 of file timsdata.h.

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

◆ m_mutex

QMutex pappso::TimsData::m_mutex

private

Definition at line 309 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_thousandIndexToFrameIdDescrListIndex

std::map<std::size_t, std::size_t> pappso::TimsData::m_thousandIndexToFrameIdDescrListIndex

private

index to find quickly a frameId in the description list with the raw index of spectrum modulo 1000

Definition at line 307 of file timsdata.h.

Referenced by fillFrameIdDescrList(), and getScanCoordinateFromRawIndex().

◆ m_timsDataDirectory

QDir pappso::TimsData::m_timsDataDirectory

private

Definition at line 269 of file timsdata.h.

Referenced by TimsData(), extractXicListByPrecursorIds(), fillFrameIdDescrList(), getPrecursorsFromMzRtCharge(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), getRawMs2ByPrecursorId(), getTimsMS1FrameIdRange(), and openDatabaseConnection().

◆ m_timsFrameBaseCache

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

private

Definition at line 276 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached().

◆ m_timsFrameCache

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

private

Definition at line 275 of file timsdata.h.

Referenced by getTimsFrameCstSPtrCached().

◆ m_totalNumberOfPrecursors

std::size_t pappso::TimsData::m_totalNumberOfPrecursors

private

Definition at line 273 of file timsdata.h.

Referenced by TimsData(), and getTotalNumberOfPrecursors().

◆ m_totalNumberOfScans

std::size_t pappso::TimsData::m_totalNumberOfScans

private

Definition at line 272 of file timsdata.h.

Referenced by TimsData(), and getTotalNumberOfScans().

◆ mcsp_ms1Filter

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

private

Definition at line 279 of file timsdata.h.

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

◆ mcsp_ms2Filter

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

private

Definition at line 278 of file timsdata.h.

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

◆ mpa_mzCalibrationStore

MzCalibrationStore* pappso::TimsData::mpa_mzCalibrationStore

private

Definition at line 290 of file timsdata.h.

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

◆ mpa_timsBinDec

TimsBinDec* pappso::TimsData::mpa_timsBinDec = nullptr

private

Definition at line 270 of file timsdata.h.

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

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

pappsomspp/vendors/tims/timsdata.h
pappsomspp/vendors/tims/timsdata.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TimsData() [1/2]

◆ TimsData() [2/2]

◆ ~TimsData()

Member Function Documentation

◆ extractXicListByPrecursorIds()

◆ extractXicListByTimsXicStructureList()

◆ fillFrameIdDescrList()

◆ getClosestPrecursorIdByMz()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumCstSPtrByRawIndex()

◆ getMatchPrecursorIdByKo()

◆ getMs2BuiltinCentroid()

◆ getMsLevelBySpectrumIndex()

◆ getPrecursorsFromMzRtCharge()

◆ getQualifiedMassSpectrumByRawIndex()

◆ getQualifiedMs1MassSpectrumByPrecursorId()

◆ getQualifiedMs2MassSpectrumByPrecursorId()

◆ getRawIndexFromCoordinate()

◆ getRawMs2ByPrecursorId()

◆ getScanCoordinateFromRawIndex()

◆ getTimsFrameBaseCstSPtr()

◆ getTimsFrameBaseCstSPtrCached()

◆ getTimsFrameCstSPtr()

◆ getTimsFrameCstSPtrCached()

◆ getTimsMS1FrameIdRange()

◆ getTimsXicStructureFromPrecursorId()

◆ getTotalNumberOfPrecursors()

◆ getTotalNumberOfScans()

◆ openDatabaseConnection()

◆ setMs1FilterCstSPtr()

◆ setMs2BuiltinCentroid()

◆ setMs2FilterCstSPtr()

Member Data Documentation

◆ m_builtinMs2Centroid

◆ m_cacheSize

◆ m_frameIdDescrList

◆ m_mapFramesRecord

◆ m_mapMzCalibrationRecord

◆ m_mapTimsCalibrationRecord

◆ m_mutex

◆ m_thousandIndexToFrameIdDescrListIndex

◆ m_timsDataDirectory

◆ m_timsFrameBaseCache

◆ m_timsFrameCache

◆ m_totalNumberOfPrecursors

◆ m_totalNumberOfScans

◆ mcsp_ms1Filter

◆ mcsp_ms2Filter

◆ mpa_mzCalibrationStore

◆ mpa_timsBinDec