#include <timsdata.h>

Public Member Functions
	TimsData (QDir timsDataDirectory)
	build using the tims data directory

	TimsData (const TimsData &other)

virtual	~TimsData ()

bool	isDdaRun () const
	tells if this MS run is a DDA run

bool	isDiaRun () const
	tells if this MS run is a DIA run

pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtrByRawIndex (std::size_t raw_index)
	get a mass spectrum given its spectrum index

pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtrByGlobalScanIndex (std::size_t index)

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

std::size_t	getTotalNumberOfFrames () const
	Get total number of frames.

std::size_t	getFrameCount () const

std::size_t	getTotalNumberOfScans () const
	get the total number of scans

std::size_t	getTotalScanCount () const

unsigned int	getMsLevelBySpectrumIndex (std::size_t index)

unsigned int	getMsLevelByGlobalScanIndex (std::size_t index)

void	getQualifiedMassSpectrumByRawIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_scan_index, bool want_binary_data)

void	getQualifiedMassSpectrumByGlobalScanIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_scan_index, bool want_binary_data)

Trace	getTicChromatogram () const

std::vector< std::size_t >	getTimsMS1FrameIdsInRtRange (double rt_begin, double rt_end) const

std::vector< std::size_t >	getTimsMS2FrameIdsInRtRange (double rt_begin, double rt_end) const

TimsFrameCstSPtr	getTimsFrameCstSPtrCached (std::size_t timsId)
	get a Tims frame with his database ID but look in the cache first

TimsFrameCstSPtr	getTimsFrameCstSPtr (std::size_t timsId)
	get a Tims frame with his database ID

TimsDataFastMap &	getRawMsBySpectrumIndex (std::size_t index)
	get raw signal for a spectrum index only to use to see the raw signal

TimsDataFastMap &	getScanByGlobalScanIndex (std::size_t index)

virtual std::vector< double >	getRetentionTimeLine () const
	retention timeline get retention times along the MSrun in seconds

virtual std::vector< double >	getRetentionTimeLineInSeconds () const

const std::vector< FrameIdDescr > &	getFrameIdDescrList () const

const std::vector< TimsFrameRecord > &	getTimsFrameRecordList () const

const QDir &	getTimsDataDirectory () const

TimsDdaPrecursors *	getTimsDdaPrecursorsPtr () const

TimsDiaSlices *	getTimsDiaSlicesPtr () const

const QVariant &	getGlobalMetadataValue (const QString &key) const

Protected Member Functions
QSqlDatabase	openDatabaseConnection () const

TimsBinDec *	getTimsBinDecPtr () const

Private Member Functions
std::pair< std::size_t, std::size_t >	getScanCoordinateFromRawIndex (std::size_t spectrum_index) const

std::pair< std::size_t, std::size_t >	getScanCoordinatesByGlobalScanIndex (std::size_t index) const

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

std::size_t	getGlobalScanIndexByScanCoordinates (std::size_t frame_id, std::size_t index) const

TimsFrameBaseCstSPtr	getTimsFrameBaseCstSPtr (std::size_t timsId)
	get a Tims frame base (no binary data file access) with his database ID

TimsFrameBaseCstSPtr	getTimsFrameBaseCstSPtrCached (std::size_t timsId)

void	fillFrameIdDescrList ()
	private function to fill m_frameIdDescrList

Private Attributes
friend	TimsDdaPrecursors

friend	TimsDiaSlices

QDir	m_timsDataDirectory

TimsBinDec *	mpa_timsBinDec = nullptr

TimsDdaPrecursors *	mpa_timsDdaPrecursors = nullptr

TimsDiaSlices *	mpa_timsDiaSlices = nullptr

std::size_t	m_totalScanCount

std::size_t	m_frameCount

std::size_t	m_cacheSize = 60

std::deque< TimsFrameCstSPtr >	m_timsFrameCache

std::deque< TimsFrameBaseCstSPtr >	m_timsFrameBaseCache

std::map< int, QSqlRecord >	m_mapMzCalibrationRecord

std::map< int, QSqlRecord >	m_mapTimsCalibrationRecord

std::vector< TimsFrameRecord >	m_mapFramesRecord

MzCalibrationStore *	mpa_mzCalibrationStore

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

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 @key thousands of TOF scans @value corresponding m_frameIdDescrList index

std::vector< std::size_t >	m_someoneIsLoadingFrameId
	tells if someone is loading a frame id

std::map< QString, QVariant >	m_mapGlobalMetadaTable

QMutex	m_mutex

Detailed Description

Todo:: write docs

Definition at line 67 of file timsdata.h.

Constructor & Destructor Documentation

◆ TimsData() [1/2]

pappso::TimsData::TimsData ( QDir timsDataDirectory )

build using the tims data directory

Definition at line 46 of file timsdata.cpp.

                                         : m_timsDataDirectory(timsDataDirectory)
{
 
  qDebug() << "Start of construction of TimsData";
  mpa_mzCalibrationStore = new MzCalibrationStore();
  if(!m_timsDataDirectory.exists())
    {
      qDebug();
      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 sql_query(qdb);
  if(!sql_query.exec("select Key, Value from GlobalMetadata;"))
    {
 
      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(sql_query.lastQuery())
                              .arg(sql_query.lastError().databaseText())
                              .arg(sql_query.lastError().driverText())
                              .arg(sql_query.lastError().nativeErrorCode()));
    }
 
  while(sql_query.next())
    {
      QSqlRecord record = sql_query.record();
      m_mapGlobalMetadaTable.insert(
        std::pair<QString, QVariant>(record.value(0).toString(), record.value(1)));
    }
 
  int compression_type = getGlobalMetadataValue("TimsCompressionType").toInt();
  qDebug() << " compression_type=" << compression_type;
  mpa_timsBinDec = new TimsBinDec(
    QFileInfo(m_timsDataDirectory.absoluteFilePath("analysis.tdf_bin")), compression_type);
 
  qDebug();
 
  try
    {
 
      qDebug();
      mpa_timsDdaPrecursors = new TimsDdaPrecursors(sql_query, this);
    }
  catch(pappso::ExceptionNotFound &not_found)
    {
 
      qDebug();
      mpa_timsDdaPrecursors = nullptr;
    }
 
 
  qDebug();
  try
    {
      qDebug();
      mpa_timsDiaSlices = new TimsDiaSlices(sql_query, this);
    }
  catch(pappso::ExceptionNotFound &not_found)
    {
      qDebug();
      mpa_timsDiaSlices = nullptr;
    }
 
  fillFrameIdDescrList();
 
  // get number of scans
  if(!sql_query.exec("SELECT SUM(NumScans),COUNT(Id) 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(sql_query.lastQuery())
                              .arg(qdb.lastError().databaseText())
                              .arg(qdb.lastError().driverText())
                              .arg(qdb.lastError().nativeErrorCode()));
    }
  if(sql_query.next())
    {
      qDebug();
      m_totalScanCount = sql_query.value(0).toLongLong();
      m_frameCount     = sql_query.value(1).toLongLong();
    }
 
  if(!sql_query.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(sql_query.lastQuery())
                              .arg(sql_query.lastError().databaseText())
                              .arg(sql_query.lastError().driverText())
                              .arg(sql_query.lastError().nativeErrorCode()));
    }
 
  while(sql_query.next())
    {
      QSqlRecord record = sql_query.record();
      m_mapMzCalibrationRecord.insert(std::pair<int, QSqlRecord>(record.value(0).toInt(), record));
    }
 
  // m_mapTimsCalibrationRecord
 
  if(!sql_query.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(sql_query.lastQuery())
                              .arg(sql_query.lastError().databaseText())
                              .arg(sql_query.lastError().driverText())
                              .arg(sql_query.lastError().nativeErrorCode()));
    }
  while(sql_query.next())
    {
      QSqlRecord record = sql_query.record();
      m_mapTimsCalibrationRecord.insert(
        std::pair<int, QSqlRecord>(record.value(0).toInt(), record));
    }
 
 
  // store frames
  if(!sql_query.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(sql_query.lastQuery())
                              .arg(sql_query.lastError().databaseText())
                              .arg(sql_query.lastError().driverText())
                              .arg(sql_query.lastError().nativeErrorCode()));
    }
 
  m_mapFramesRecord.resize(m_frameCount + 1);
  while(sql_query.next())
    {
      QSqlRecord record             = sql_query.record();
      TimsFrameRecord &frame_record = m_mapFramesRecord[record.value(8).toULongLong()];
 
      frame_record.frame_id            = record.value(8).toULongLong();
      frame_record.tims_offset         = record.value(0).toULongLong();
      frame_record.accumulation_time   = record.value(1).toDouble();
      frame_record.mz_calibration_id   = record.value(2).toULongLong();
      frame_record.frame_t1            = record.value(3).toDouble();
      frame_record.frame_t2            = record.value(4).toDouble();
      frame_record.frame_time          = record.value(5).toDouble();
      frame_record.msms_type           = record.value(6).toInt();
      frame_record.tims_calibration_id = record.value(7).toULongLong();
    }
 
  qDebug();
}

◆ TimsData() [2/2]

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

Copy constructor

Parameters

other TODO

Definition at line 251 of file timsdata.cpp.

{
  qDebug();
}

◆ ~TimsData()

pappso::TimsData::~TimsData ( )

virtual

Destructor

Definition at line 256 of file timsdata.cpp.

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

References mpa_mzCalibrationStore, mpa_timsBinDec, mpa_timsDdaPrecursors, and mpa_timsDiaSlices.

Member Function Documentation

◆ fillFrameIdDescrList()

void pappso::TimsData::fillFrameIdDescrList ( )

private

private function to fill m_frameIdDescrList

number of scans in mobility dimension (number of TOF scans)

Definition at line 278 of file timsdata.cpp.

{
  qDebug();
  QSqlDatabase qdb = openDatabaseConnection();
 
  QSqlQuery q(qdb);
  q.prepare(
    QString("SELECT Id, NumScans FROM "
            "Frames ORDER BY Id"));
  q.exec();
  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()));
    }
  TimsFrameSPtr tims_frame;
  bool index_found = false;
  std::size_t timsId;
  /** @brief number of scans in mobility dimension (number of TOF scans)
   */
  std::size_t numberScans;
  std::size_t cumulScans = 0;
  while(q.next() && (!index_found))
    {
      timsId      = q.value(0).toULongLong();
      numberScans = q.value(1).toULongLong();
 
      // qDebug() << timsId;
 
      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;
    }
  qDebug();
}

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

Referenced by TimsData().

◆ getFrameCount()

std::size_t pappso::TimsData::getFrameCount ( ) const

Definition at line 657 of file timsdata.cpp.

{
  return m_frameCount;
}

References m_frameCount.

◆ getFrameIdDescrList()

const std::vector< FrameIdDescr > & pappso::TimsData::getFrameIdDescrList ( ) const

Definition at line 1036 of file timsdata.cpp.

{
  return m_frameIdDescrList;
}

References m_frameIdDescrList.

Referenced by pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ getGlobalMetadataValue()

const QVariant & pappso::TimsData::getGlobalMetadataValue ( const QString & key ) const

Definition at line 1099 of file timsdata.cpp.

{
  auto it = m_mapGlobalMetadaTable.find(key);
  if(it == m_mapGlobalMetadaTable.end())
    {
      throw pappso::PappsoException(QString("TimsData GlobalMetadata key %1 not found").arg(key));
    }
  return it->second;
}

References m_mapGlobalMetadaTable.

Referenced by TimsData().

◆ getGlobalScanIndexByScanCoordinates()

std::size_t pappso::TimsData::getGlobalScanIndexByScanCoordinates	(	std::size_t	frame_id,
		std::size_t	index
	)		const

private

Definition at line 366 of file timsdata.cpp.

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

References m_frameIdDescrList.

Referenced by getQualifiedMassSpectrumByGlobalScanIndex(), getRawIndexFromCoordinate(), and pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ getMassSpectrumCstSPtr()

MassSpectrumCstSPtr pappso::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 640 of file timsdata.cpp.

{
  qDebug() << " timsId=" << timsId << " scanNum=" << scanNum;
  TimsFrameCstSPtr frame = getTimsFrameCstSPtrCached(timsId);
 
  return frame->getMassSpectrumCstSPtr(scanNum);
}

References getTimsFrameCstSPtrCached().

Referenced by getMassSpectrumCstSPtrByGlobalScanIndex().

◆ getMassSpectrumCstSPtrByGlobalScanIndex()

pappso::MassSpectrumCstSPtr pappso::TimsData::getMassSpectrumCstSPtrByGlobalScanIndex ( std::size_t index )

Definition at line 393 of file timsdata.cpp.

{
 
  qDebug() << " raw_index=" << raw_index;
  try
    {
      auto coordinate = getScanCoordinatesByGlobalScanIndex(raw_index);
      return getMassSpectrumCstSPtr(coordinate.first, coordinate.second);
    }
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("Error TimsData::getMassSpectrumCstSPtrByRawIndex "
                                        "raw_index=%1 :\n%2")
                              .arg(raw_index)
                              .arg(error.qwhat()));
    }
}

References getMassSpectrumCstSPtr(), getScanCoordinatesByGlobalScanIndex(), and pappso::PappsoException::qwhat().

Referenced by getMassSpectrumCstSPtrByRawIndex().

◆ getMassSpectrumCstSPtrByRawIndex()

MassSpectrumCstSPtr pappso::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 387 of file timsdata.cpp.

{
  return getMassSpectrumCstSPtrByGlobalScanIndex(raw_index);
}

References getMassSpectrumCstSPtrByGlobalScanIndex().

◆ getMsLevelByGlobalScanIndex()

unsigned int pappso::TimsData::getMsLevelByGlobalScanIndex ( std::size_t index )

Definition at line 684 of file timsdata.cpp.

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

References getScanCoordinatesByGlobalScanIndex(), and getTimsFrameCstSPtrCached().

Referenced by getMsLevelBySpectrumIndex().

◆ getMsLevelBySpectrumIndex()

unsigned int pappso::TimsData::getMsLevelBySpectrumIndex ( std::size_t index )

Definition at line 677 of file timsdata.cpp.

{
  return getMsLevelByGlobalScanIndex(index);
}

References getMsLevelByGlobalScanIndex().

◆ getQualifiedMassSpectrumByGlobalScanIndex()

void pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex	(	const MsRunIdCstSPtr &	msrun_id,
		QualifiedMassSpectrum &	mass_spectrum,
		std::size_t	global_scan_index,
		bool	want_binary_data
	)

Definition at line 704 of file timsdata.cpp.

{
 
 
  try
    {
      auto coordinate = getScanCoordinatesByGlobalScanIndex(global_scan_index);
      TimsFrameBaseCstSPtr tims_frame;
      if(want_binary_data)
        {
          tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
        }
      else
        {
          tims_frame = getTimsFrameBaseCstSPtrCached(coordinate.first);
        }
      MassSpectrumId spectrum_id;
 
      spectrum_id.setSpectrumIndex(global_scan_index);
      spectrum_id.setMsRunId(msrun_id);
      spectrum_id.setNativeId(QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
                                .arg(coordinate.first)
                                .arg(coordinate.second)
                                .arg(global_scan_index));
 
      mass_spectrum.setMassSpectrumId(spectrum_id);
 
      mass_spectrum.setMsLevel(tims_frame.get()->getMsLevel());
      mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
 
      mass_spectrum.setDtInMilliSeconds(
        tims_frame.get()->getDriftTimeInMilliseconds(coordinate.second));
      // 1/K0
      mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0,
        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)
        {
 
          if(mpa_timsDdaPrecursors != nullptr)
            {
              auto spectrum_descr =
                mpa_timsDdaPrecursors->getSpectrumDescrWithScanCoordinates(coordinate);
              if(spectrum_descr.precursor_id > 0)
                {
 
                  mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
 
 
                  MassSpectrumId spectrum_id;
                  std::size_t prec_spectrum_index = getGlobalScanIndexByScanCoordinates(
                    spectrum_descr.parent_frame, coordinate.second);
 
                  mass_spectrum.setPrecursorSpectrumIndex(prec_spectrum_index);
                  mass_spectrum.setPrecursorNativeId(
                    QString("frame_id=%1 scan_index=%2 global_scan_index=%3")
                      .arg(spectrum_descr.parent_frame)
                      .arg(coordinate.second)
                      .arg(prec_spectrum_index));
 
                  mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMz,
                                                  spectrum_descr.isolationMz);
                  mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationMzWidth,
                                                  spectrum_descr.isolationWidth);
 
                  mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::CollisionEnergy,
                                                  spectrum_descr.collisionEnergy);
                  mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::BrukerPrecursorIndex,
                    (quint64)spectrum_descr.precursor_id);
                }
            }
        }
    }
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("Error TimsData::getQualifiedMassSpectrumByRawIndex "
                                        "spectrum_index=%1 :\n%2")
                              .arg(global_scan_index)
                              .arg(error.qwhat()));
    }
}

Referenced by getQualifiedMassSpectrumByRawIndex().

◆ getQualifiedMassSpectrumByRawIndex()

void pappso::TimsData::getQualifiedMassSpectrumByRawIndex	(	const MsRunIdCstSPtr &	msrun_id,
		QualifiedMassSpectrum &	mass_spectrum,
		std::size_t	global_scan_index,
		bool	want_binary_data
	)

Definition at line 693 of file timsdata.cpp.

{
 
  return getQualifiedMassSpectrumByGlobalScanIndex(
    msrun_id, mass_spectrum, global_scan_index, want_binary_data);
}

References getQualifiedMassSpectrumByGlobalScanIndex().

◆ getRawIndexFromCoordinate()

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

private

Definition at line 359 of file timsdata.cpp.

{
 
  return getGlobalScanIndexByScanCoordinates(frame_id, index);
}

References getGlobalScanIndexByScanCoordinates().

◆ getRawMsBySpectrumIndex()

TimsDataFastMap & pappso::TimsData::getRawMsBySpectrumIndex ( std::size_t index )

get raw signal for a spectrum index only to use to see the raw signal

Parameters

spectrum_index spcetrum index

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

Definition at line 1015 of file timsdata.cpp.

{
  return getScanByGlobalScanIndex(index);
}

References getScanByGlobalScanIndex().

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsData::getRetentionTimeLine ( ) const

virtual

retention timeline get retention times along the MSrun in seconds

Returns: vector of retention times (seconds)

Definition at line 993 of file timsdata.cpp.

{
  return getRetentionTimeLineInSeconds();
}

References getRetentionTimeLineInSeconds().

◆ getRetentionTimeLineInSeconds()

std::vector< double > pappso::TimsData::getRetentionTimeLineInSeconds ( ) const

virtual

Definition at line 999 of file timsdata.cpp.

{
 
  std::vector<double> timeline;
  timeline.reserve(m_mapFramesRecord.size());
  for(const TimsFrameRecord &frame_record : m_mapFramesRecord)
    {
      if(frame_record.mz_calibration_id != 0)
        {
          timeline.push_back(frame_record.frame_time);
        }
    }
  return timeline;
}

References m_mapFramesRecord.

Referenced by getRetentionTimeLine().

◆ getScanByGlobalScanIndex()

TimsDataFastMap & pappso::TimsData::getScanByGlobalScanIndex ( std::size_t index )

Definition at line 1021 of file timsdata.cpp.

{
  qDebug() << " spectrum_index=" << index;
  auto coordinate = getScanCoordinatesByGlobalScanIndex(index);
  TimsFrameBaseCstSPtr tims_frame;
  tims_frame = getTimsFrameCstSPtrCached(coordinate.first);
 
  TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
  raw_spectrum.clear();
  tims_frame.get()->combineScansInTofIndexIntensityMap(
    raw_spectrum, coordinate.second, coordinate.second);
  return raw_spectrum;
}

References pappso::TimsDataFastMap::clear(), getScanCoordinatesByGlobalScanIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), and getTimsFrameCstSPtrCached().

Referenced by getRawMsBySpectrumIndex().

◆ getScanCoordinateFromRawIndex()

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

private

Definition at line 323 of file timsdata.cpp.

{
  return getScanCoordinatesByGlobalScanIndex(raw_index);
}

References getScanCoordinatesByGlobalScanIndex().

◆ getScanCoordinatesByGlobalScanIndex()

std::pair< std::size_t, std::size_t > pappso::TimsData::getScanCoordinatesByGlobalScanIndex ( std::size_t index ) const

private

Definition at line 329 of file timsdata.cpp.

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

References m_frameIdDescrList, and m_thousandIndexToFrameIdDescrListIndex.

Referenced by getMassSpectrumCstSPtrByGlobalScanIndex(), pappso::TimsDdaPrecursors::getMatchPrecursorIdByKo(), getMsLevelByGlobalScanIndex(), getQualifiedMassSpectrumByGlobalScanIndex(), getScanByGlobalScanIndex(), and getScanCoordinateFromRawIndex().

◆ getTicChromatogram()

Trace pappso::TimsData::getTicChromatogram ( ) const

Definition at line 809 of file timsdata.cpp.

{
  // In the Frames table, each frame has a record describing the
  // SummedIntensities for all the mobility spectra.
 
 
  MapTrace rt_tic_map_trace;
 
  using Pair     = std::pair<double, double>;
  using Map      = std::map<double, double>;
  using Iterator = Map::iterator;
 
 
  QSqlDatabase qdb = openDatabaseConnection();
  QSqlQuery q(qdb);
 
  q.prepare(
    QString("SELECT Time, SummedIntensities "
            "FROM Frames WHERE MsMsType = 0 "
            "ORDER BY Time;"));
  q.exec();
 
  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())
    {
 
      bool ok = false;
 
      int cumulated_results = 2;
 
      double rt = q.value(0).toDouble(&ok);
      cumulated_results -= ok;
 
      double sumY = q.value(1).toDouble(&ok);
      cumulated_results -= ok;
 
      if(cumulated_results)
        {
          throw PappsoException(
            QObject::tr("ERROR in TIMS sqlite database file: could not read either the "
                        "retention time or the summed intensities (%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()));
        }
 
      // Try to insert value sumY at key rt.
      std::pair<Iterator, bool> res = rt_tic_map_trace.insert(Pair(rt, sumY));
 
      if(!res.second)
        {
          // One other same rt value was seen already (like in ion mobility
          // mass spectrometry, for example). Only increment the y value.
 
          res.first->second += sumY;
        }
    }
 
  // qDebug().noquote() << "The TIC chromatogram:\n"
  //<< rt_tic_map_trace.toTrace().toString();
 
  return rt_tic_map_trace.toTrace();
}

References m_timsDataDirectory, openDatabaseConnection(), and pappso::MapTrace::toTrace().

◆ getTimsBinDecPtr()

TimsBinDec * pappso::TimsData::getTimsBinDecPtr ( ) const

protected

Definition at line 1064 of file timsdata.cpp.

{
  return mpa_timsBinDec;
}

References mpa_timsBinDec.

Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel().

◆ getTimsDataDirectory()

const QDir & pappso::TimsData::getTimsDataDirectory ( ) const

Definition at line 1048 of file timsdata.cpp.

{
  return m_timsDataDirectory;
}

References m_timsDataDirectory.

Referenced by pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId(), pappso::TimsDdaPrecursors::getPrecursorsByMzRtCharge(), pappso::TimsDdaPrecursors::getSpectrumDescrWithPrecursorId(), pappso::TimsDdaPrecursors::getSpectrumDescrWithScanCoordinates(), pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), and pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ getTimsDdaPrecursorsPtr()

TimsDdaPrecursors * pappso::TimsData::getTimsDdaPrecursorsPtr ( ) const

Definition at line 1054 of file timsdata.cpp.

{
  if(mpa_timsDdaPrecursors == nullptr)
    {
      throw pappso::PappsoException("TimsData does not contain DDA precursors");
    }
  return mpa_timsDdaPrecursors;
}

References mpa_timsDdaPrecursors.

◆ getTimsDiaSlicesPtr()

TimsDiaSlices * pappso::TimsData::getTimsDiaSlicesPtr ( ) const

Definition at line 1086 of file timsdata.cpp.

{
  qDebug();
  if(mpa_timsDiaSlices == nullptr)
    {
      throw pappso::PappsoException("TimsData does not contain DIA slices");
    }
  return mpa_timsDiaSlices;
}

References mpa_timsDiaSlices.

◆ getTimsFrameBaseCstSPtr()

TimsFrameBaseCstSPtr pappso::TimsData::getTimsFrameBaseCstSPtr ( std::size_t timsId )

private

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

Definition at line 412 of file timsdata.cpp.

{
 
  qDebug() << " timsId=" << timsId;
 
  const TimsFrameRecord &frame_record = m_mapFramesRecord[timsId];
  if(timsId > m_totalScanCount)
    {
      throw ExceptionNotFound(QObject::tr("ERROR Frames database id %1 not found").arg(timsId));
    }
  TimsFrameBaseSPtr tims_frame;
 
 
  tims_frame = std::make_shared<TimsFrameBase>(TimsFrameBase(timsId, frame_record.tims_offset));
 
  auto it_map_record = m_mapMzCalibrationRecord.find(frame_record.mz_calibration_id);
  if(it_map_record != m_mapMzCalibrationRecord.end())
    {
 
      double T1_frame = frame_record.frame_t1; // Frames.T1
      double T2_frame = frame_record.frame_t2; // 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(frame_record.mz_calibration_id));
    }
 
 
  tims_frame.get()->setAcqDurationInMilliseconds(frame_record.accumulation_time);
 
  tims_frame.get()->setRtInSeconds(frame_record.frame_time);
  tims_frame.get()->setMsMsType(frame_record.msms_type);
 
 
  auto it_map_record_tims_calibration =
    m_mapTimsCalibrationRecord.find(frame_record.tims_calibration_id);
  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(frame_record.tims_calibration_id));
    }
 
  return tims_frame;
}

References pappso::TimsFrameRecord::accumulation_time, pappso::TimsFrameRecord::frame_t1, pappso::TimsFrameRecord::frame_t2, pappso::TimsFrameRecord::frame_time, pappso::MzCalibrationStore::getInstance(), m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, m_totalScanCount, mpa_mzCalibrationStore, pappso::TimsFrameRecord::msms_type, pappso::TimsFrameRecord::mz_calibration_id, pappso::TimsFrameRecord::tims_calibration_id, and pappso::TimsFrameRecord::tims_offset.

Referenced by getTimsFrameBaseCstSPtrCached().

◆ getTimsFrameBaseCstSPtrCached()

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

private

Definition at line 894 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);
          if(m_timsFrameBaseCache.size() > m_cacheSize)
            m_timsFrameBaseCache.pop_front();
          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 pappso::TimsDdaPrecursors::getMatchPrecursorIdByKo(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), and pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ getTimsFrameCstSPtr()

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

get a Tims frame with his database ID

this function is not thread safe

Definition at line 558 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;
     }
     */
 
  const TimsFrameRecord &frame_record = m_mapFramesRecord[timsId];
  if(timsId > m_totalScanCount)
    {
      throw ExceptionNotFound(QObject::tr("ERROR Frames database id %1 not found").arg(timsId));
    }
 
  TimsFrameSPtr tims_frame;
 
 
  // QMutexLocker lock(&m_mutex);
  tims_frame = mpa_timsBinDec->getTimsFrameSPtrByOffset(timsId, m_mapFramesRecord);
  // lock.unlock();
 
  qDebug();
  auto it_map_record = m_mapMzCalibrationRecord.find(frame_record.mz_calibration_id);
  if(it_map_record != m_mapMzCalibrationRecord.end())
    {
 
      double T1_frame = frame_record.frame_t1; // Frames.T1
      double T2_frame = frame_record.frame_t2; // 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 for frame_id=%2")
          .arg(frame_record.mz_calibration_id)
          .arg(timsId));
    }
 
 
  tims_frame.get()->setAcqDurationInMilliseconds(frame_record.accumulation_time);
 
  tims_frame.get()->setRtInSeconds(frame_record.frame_time);
  tims_frame.get()->setMsMsType(frame_record.msms_type);
 
  qDebug();
  auto it_map_record_tims_calibration =
    m_mapTimsCalibrationRecord.find(frame_record.tims_calibration_id);
  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(frame_record.tims_calibration_id));
    }
  qDebug();
  return tims_frame;
}

References pappso::TimsFrameRecord::accumulation_time, pappso::TimsFrameRecord::frame_t1, pappso::TimsFrameRecord::frame_t2, pappso::TimsFrameRecord::frame_time, pappso::MzCalibrationStore::getInstance(), pappso::TimsBinDec::getTimsFrameSPtrByOffset(), m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, m_totalScanCount, mpa_mzCalibrationStore, mpa_timsBinDec, pappso::TimsFrameRecord::msms_type, pappso::TimsFrameRecord::mz_calibration_id, and pappso::TimsFrameRecord::tims_calibration_id.

Referenced by getTimsFrameCstSPtrCached().

◆ getTimsFrameCstSPtrCached()

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

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

thread safe

Definition at line 915 of file timsdata.cpp.

{
  qDebug();
  QMutexLocker locker(&m_mutex);
  for(auto &tims_frame : m_timsFrameCache)
    {
      if(tims_frame.get()->getId() == timsId)
        {
          m_timsFrameCache.push_back(tims_frame);
          if(m_timsFrameCache.size() > m_cacheSize)
            m_timsFrameCache.pop_front();
          return tims_frame;
        }
    }
  TimsFrameCstSPtr frame_sptr = getTimsFrameCstSPtr(timsId);
 
  // locker.relock();
  qDebug();
 
  m_timsFrameCache.push_back(frame_sptr);
  if(m_timsFrameCache.size() > m_cacheSize)
    m_timsFrameCache.pop_front();
  qDebug();
  return m_timsFrameCache.back();
 
 
  /*
// the frame is not in the cache
if(std::find(m_someoneIsLoadingFrameId.begin(),
             m_someoneIsLoadingFrameId.end(),
             timsId) == m_someoneIsLoadingFrameId.end())
  {
    // not found, we are alone on this frame
    m_someoneIsLoadingFrameId.push_back(timsId);
    qDebug();
    //locker.unlock();
    TimsFrameCstSPtr frame_sptr = getTimsFrameCstSPtr(timsId);
 
   // locker.relock();
    qDebug();
    m_someoneIsLoadingFrameId.erase(
      std::find(m_someoneIsLoadingFrameId.begin(),
                m_someoneIsLoadingFrameId.end(),
                timsId));
 
    m_timsFrameCache.push_back(frame_sptr);
    if(m_timsFrameCache.size() > m_cacheSize)
      m_timsFrameCache.pop_front();
    qDebug();
    return m_timsFrameCache.back();
  }
else
  {
    // this frame is loading by someone else, we have to wait
    qDebug();
    // locker.unlock();
    // std::size_t another_frame_id = timsId;
    while(true)
      {
        QThread::usleep(1);
  // locker.relock();
 
  for(auto &tims_frame : m_timsFrameCache)
    {
      if(tims_frame.get()->getId() == timsId)
        {
          m_timsFrameCache.push_back(tims_frame);
          return tims_frame;
        }
    }
  // locker.unlock();
}
} // namespace pappso
*/
}

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

Referenced by pappso::TimsDiaSlices::getCombinedMs2ScansByGlobalSliceIndex(), pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId(), getMassSpectrumCstSPtr(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), getMsLevelByGlobalScanIndex(), getQualifiedMassSpectrumByGlobalScanIndex(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), getScanByGlobalScanIndex(), and pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ getTimsFrameRecordList()

const std::vector< TimsFrameRecord > & pappso::TimsData::getTimsFrameRecordList ( ) const

Definition at line 1042 of file timsdata.cpp.

{
  return m_mapFramesRecord;
}

References m_mapFramesRecord.

◆ getTimsMS1FrameIdsInRtRange()

std::vector< std::size_t > pappso::TimsData::getTimsMS1FrameIdsInRtRange	(	double	rt_begin,
		double	rt_end
	)		const

Definition at line 479 of file timsdata.cpp.

{
 
  qDebug() << " rt_begin=" << rt_begin << " rt_end=" << rt_end;
  if(rt_begin < 0)
    rt_begin = 0;
  std::vector<std::size_t> tims_frameid_list;
  QSqlDatabase qdb = openDatabaseConnection();
  QSqlQuery q(qdb);
  q.prepare(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));
  q.exec();
  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\nrtbegin=%7 rtend=%8")
                              .arg(m_timsDataDirectory.absoluteFilePath("analysis.tdf"))
                              .arg(qdb.databaseName())
                              .arg(q.lastQuery())
                              .arg(qdb.lastError().databaseText())
                              .arg(qdb.lastError().driverText())
                              .arg(qdb.lastError().nativeErrorCode())
                              .arg(rt_begin)
                              .arg(rt_end));
    }
  while(q.next())
    {
 
      tims_frameid_list.push_back(q.value(0).toULongLong());
    }
  return tims_frameid_list;
}

References m_timsDataDirectory, and openDatabaseConnection().

◆ getTimsMS2FrameIdsInRtRange()

std::vector< std::size_t > pappso::TimsData::getTimsMS2FrameIdsInRtRange	(	double	rt_begin,
		double	rt_end
	)		const

Definition at line 519 of file timsdata.cpp.

{
 
  qDebug() << " rt_begin=" << rt_begin << " rt_end=" << rt_end;
  if(rt_begin < 0)
    rt_begin = 0;
  std::vector<std::size_t> tims_frameid_list;
  QSqlDatabase qdb = openDatabaseConnection();
 
  QSqlQuery q(qdb);
  q.prepare(QString("SELECT Frames.Id FROM Frames WHERE "
                    "Frames.MsMsType=8 AND "
                    "(Frames.Time>=%1) AND (Frames.Time<=%2) ORDER BY "
                    "Frames.Time;")
              .arg(rt_begin)
              .arg(rt_end));
  q.exec();
  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).toULongLong());
    }
  return tims_frameid_list;
}

References m_timsDataDirectory, and openDatabaseConnection().

◆ getTotalNumberOfFrames()

std::size_t pappso::TimsData::getTotalNumberOfFrames ( ) const

Get total number of frames.

Definition at line 650 of file timsdata.cpp.

{
  return m_frameCount;
}

References m_frameCount.

◆ getTotalNumberOfScans()

std::size_t pappso::TimsData::getTotalNumberOfScans ( ) const

get the total number of scans

Definition at line 664 of file timsdata.cpp.

{
  return m_totalScanCount;
}

References m_totalScanCount.

◆ getTotalScanCount()

std::size_t pappso::TimsData::getTotalScanCount ( ) const

Definition at line 671 of file timsdata.cpp.

{
  return m_totalScanCount;
}

References m_totalScanCount.

Referenced by pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().

◆ isDdaRun()

bool pappso::TimsData::isDdaRun ( ) const

tells if this MS run is a DDA run

Returns: true if it contains DDA precursors

Definition at line 1070 of file timsdata.cpp.

{
  if(mpa_timsDdaPrecursors == nullptr)
    return false;
  return true;
}

References mpa_timsDdaPrecursors.

◆ isDiaRun()

bool pappso::TimsData::isDiaRun ( ) const

tells if this MS run is a DIA run

Returns: true if it contains DIA slices

Definition at line 1078 of file timsdata.cpp.

{
  if(mpa_timsDiaSlices == nullptr)
    return false;
  return true;
}

◆ openDatabaseConnection()

QSqlDatabase pappso::TimsData::openDatabaseConnection ( ) const

protected

Definition at line 222 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.

Member Data Documentation

◆ m_cacheSize

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

private

Definition at line 247 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_frameCount

std::size_t pappso::TimsData::m_frameCount

private

Definition at line 246 of file timsdata.h.

Referenced by TimsData(), getFrameCount(), and getTotalNumberOfFrames().

◆ m_frameIdDescrList

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

private

store every frame id and corresponding sizes

Definition at line 261 of file timsdata.h.

Referenced by fillFrameIdDescrList(), getFrameIdDescrList(), getGlobalScanIndexByScanCoordinates(), and getScanCoordinatesByGlobalScanIndex().

◆ m_mapFramesRecord

std::vector<TimsFrameRecord> pappso::TimsData::m_mapFramesRecord

private

Definition at line 254 of file timsdata.h.

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

◆ m_mapGlobalMetadaTable

std::map<QString, QVariant> pappso::TimsData::m_mapGlobalMetadaTable

private

Definition at line 275 of file timsdata.h.

Referenced by TimsData(), and getGlobalMetadataValue().

◆ m_mapMzCalibrationRecord

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

private

Definition at line 252 of file timsdata.h.

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

◆ m_mapTimsCalibrationRecord

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

private

Definition at line 253 of file timsdata.h.

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

◆ m_mutex

QMutex pappso::TimsData::m_mutex

private

Definition at line 277 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().

◆ m_someoneIsLoadingFrameId

std::vector<std::size_t> pappso::TimsData::m_someoneIsLoadingFrameId

private

tells if someone is loading a frame id

Definition at line 273 of file timsdata.h.

◆ 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 @key thousands of TOF scans @value corresponding m_frameIdDescrList index

Definition at line 268 of file timsdata.h.

Referenced by fillFrameIdDescrList(), and getScanCoordinatesByGlobalScanIndex().

◆ m_timsDataDirectory

QDir pappso::TimsData::m_timsDataDirectory

private

Definition at line 239 of file timsdata.h.

Referenced by TimsData(), fillFrameIdDescrList(), pappso::TimsDdaPrecursors::getSpectrumDescrListByFrameId(), getTicChromatogram(), getTimsDataDirectory(), getTimsMS1FrameIdsInRtRange(), getTimsMS2FrameIdsInRtRange(), pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId(), and openDatabaseConnection().

◆ m_timsFrameBaseCache

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

private

Definition at line 249 of file timsdata.h.

Referenced by getTimsFrameBaseCstSPtrCached().

◆ m_timsFrameCache

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

private

Definition at line 248 of file timsdata.h.

Referenced by getTimsFrameCstSPtrCached().

◆ m_totalScanCount

std::size_t pappso::TimsData::m_totalScanCount

private

Definition at line 245 of file timsdata.h.

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

◆ mpa_mzCalibrationStore

MzCalibrationStore* pappso::TimsData::mpa_mzCalibrationStore

private

Definition at line 256 of file timsdata.h.

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

◆ mpa_timsBinDec

TimsBinDec* pappso::TimsData::mpa_timsBinDec = nullptr

private

Definition at line 240 of file timsdata.h.

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

◆ mpa_timsDdaPrecursors

TimsDdaPrecursors* pappso::TimsData::mpa_timsDdaPrecursors = nullptr

private

Definition at line 242 of file timsdata.h.

Referenced by TimsData(), ~TimsData(), getQualifiedMassSpectrumByGlobalScanIndex(), getTimsDdaPrecursorsPtr(), and isDdaRun().

◆ mpa_timsDiaSlices

TimsDiaSlices* pappso::TimsData::mpa_timsDiaSlices = nullptr

private

Definition at line 243 of file timsdata.h.

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

◆ TimsDdaPrecursors

friend pappso::TimsData::TimsDdaPrecursors

private

Definition at line 69 of file timsdata.h.

Referenced by TimsData().

◆ TimsDiaSlices

friend pappso::TimsData::TimsDiaSlices

private

Definition at line 70 of file timsdata.h.

Referenced by TimsData().

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

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TimsData() [1/2]

◆ TimsData() [2/2]

◆ ~TimsData()

Member Function Documentation

◆ fillFrameIdDescrList()

◆ getFrameCount()

◆ getFrameIdDescrList()

◆ getGlobalMetadataValue()

◆ getGlobalScanIndexByScanCoordinates()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumCstSPtrByGlobalScanIndex()

◆ getMassSpectrumCstSPtrByRawIndex()

◆ getMsLevelByGlobalScanIndex()

◆ getMsLevelBySpectrumIndex()

◆ getQualifiedMassSpectrumByGlobalScanIndex()

◆ getQualifiedMassSpectrumByRawIndex()

◆ getRawIndexFromCoordinate()

◆ getRawMsBySpectrumIndex()

◆ getRetentionTimeLine()

◆ getRetentionTimeLineInSeconds()

◆ getScanByGlobalScanIndex()

◆ getScanCoordinateFromRawIndex()

◆ getScanCoordinatesByGlobalScanIndex()

◆ getTicChromatogram()

◆ getTimsBinDecPtr()

◆ getTimsDataDirectory()

◆ getTimsDdaPrecursorsPtr()

◆ getTimsDiaSlicesPtr()

◆ getTimsFrameBaseCstSPtr()

◆ getTimsFrameBaseCstSPtrCached()

◆ getTimsFrameCstSPtr()

◆ getTimsFrameCstSPtrCached()

◆ getTimsFrameRecordList()

◆ getTimsMS1FrameIdsInRtRange()

◆ getTimsMS2FrameIdsInRtRange()

◆ getTotalNumberOfFrames()

◆ getTotalNumberOfScans()

◆ getTotalScanCount()

◆ isDdaRun()

◆ isDiaRun()

◆ openDatabaseConnection()

Member Data Documentation

◆ m_cacheSize

◆ m_frameCount

◆ m_frameIdDescrList

◆ m_mapFramesRecord

◆ m_mapGlobalMetadaTable

◆ m_mapMzCalibrationRecord

◆ m_mapTimsCalibrationRecord

◆ m_mutex

◆ m_someoneIsLoadingFrameId

◆ m_thousandIndexToFrameIdDescrListIndex

◆ m_timsDataDirectory

◆ m_timsFrameBaseCache

◆ m_timsFrameCache

◆ m_totalScanCount

◆ mpa_mzCalibrationStore

◆ mpa_timsBinDec

◆ mpa_timsDdaPrecursors

◆ mpa_timsDiaSlices

◆ TimsDdaPrecursors

◆ TimsDiaSlices