libpappsomspp
Library for mass spectrometry
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#include <timsdata.h>
Classes | |
struct | SpectrumDescr |
Public Member Functions | |
TimsData (QDir timsDataDirectory) | |
build using the tims data directory More... | |
TimsData (const TimsData &other) | |
virtual | ~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 | getTotalNumberOfFrames () const |
Get total number of frames. 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) |
void | getQualifiedMassSpectrumByRawIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t spectrum_index, bool want_binary_data) |
Trace | getTicChromatogram () const |
void | getQualifiedMs2MassSpectrumByPrecursorId (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data) |
void | getQualifiedMs1MassSpectrumByPrecursorId (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data) |
void | setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter) |
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters inside a FilterSuite object 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 | getTimsFrameCstSPtrCached (std::size_t timsId) |
get a Tims frame with his database ID but look in the cache first More... | |
TimsFrameCstSPtr | getTimsFrameCstSPtr (std::size_t timsId) |
get a Tims frame with his database ID More... | |
XicCoordTims | getXicCoordTimsFromPrecursorId (std::size_t precursor_id, PrecisionPtr precision_ptr) |
void | ms2ReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels More... | |
void | rawReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) |
function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels 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... | |
std::map< quint32, quint32 > | getRawMsBySpectrumIndex (std::size_t spectrum_index) |
get raw signal for a spectrum index only to use to see the raw signal More... | |
virtual std::vector< double > | getRetentionTimeLine () const |
retention timeline get retention times along the MSrun in seconds More... | |
SpectrumDescr | getSpectrumDescrWithPrecursorId (std::size_t precursor_id) |
get an intermediate structure describing a spectrum More... | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true More... | |
const std::vector< FrameIdDescr > & | getFrameIdDescrList () const |
Private Member Functions | |
SpectrumDescr | getSpectrumDescrWithScanCoordinate (const std::pair< std::size_t, std::size_t > &scan_coordinate) |
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) |
get a Tims frame base (no binary data file access) with his database ID 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... | |
void | ms2ReaderGenerateMS1MS2Spectrum (const MsRunIdCstSPtr &msrun_id, std::vector< QualifiedMassSpectrum > &qualified_mass_spectrum_list, SpectrumCollectionHandlerInterface &handler, const SpectrumDescr &spectrum_descr, unsigned int ms_level) |
void | fillSpectrumDescriptionWithSqlRecord (SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list) |
Private Attributes | |
QDir | m_timsDataDirectory |
TimsBinDec * | mpa_timsBinDec = nullptr |
std::size_t | m_totalNumberOfScans |
std::size_t | m_totalNumberOfPrecursors |
std::size_t | m_totalNumberOfFrames |
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::vector< TimsFrameRecord > | m_mapFramesRecord |
std::map< std::size_t, QSqlRecord > | m_mapXicCoordRecord |
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 @key thousands of TOF scans @value corresponding m_frameIdDescrList index More... | |
std::vector< std::size_t > | m_someoneIsLoadingFrameId |
tells if someone is loading a frame id More... | |
bool | m_isMonoThread = false |
bool | m_hasPrecursorTable |
QMutex | m_mutex |
Definition at line 63 of file timsdata.h.
pappso::TimsData::TimsData | ( | QDir | timsDataDirectory | ) |
build using the tims data directory
Definition at line 47 of file timsdata.cpp.
References pappso::TimsFrameRecord::accumulation_time, fillFrameIdDescrList(), pappso::TimsFrameRecord::frame_t1, pappso::TimsFrameRecord::frame_t2, pappso::TimsFrameRecord::frame_time, m_hasPrecursorTable, m_mapFramesRecord, m_mapMzCalibrationRecord, m_mapTimsCalibrationRecord, m_timsDataDirectory, m_totalNumberOfFrames, m_totalNumberOfPrecursors, m_totalNumberOfScans, mcsp_ms1Filter, mcsp_ms2Filter, mpa_mzCalibrationStore, mpa_timsBinDec, pappso::TimsFrameRecord::msms_type, pappso::TimsFrameRecord::mz_calibration_id, openDatabaseConnection(), pappso::TimsFrameRecord::tims_calibration_id, and pappso::TimsFrameRecord::tims_offset.
pappso::TimsData::TimsData | ( | const TimsData & | other | ) |
Copy constructor
other | TODO |
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Destructor
Definition at line 269 of file timsdata.cpp.
References mpa_mzCalibrationStore, and mpa_timsBinDec.
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private function to fill m_frameIdDescrList
number of scans in mobility dimension (number of TOF scans)
Definition at line 295 of file timsdata.cpp.
References m_frameIdDescrList, m_thousandIndexToFrameIdDescrListIndex, m_timsDataDirectory, and openDatabaseConnection().
Referenced by TimsData().
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Definition at line 2067 of file timsdata.cpp.
References pappso::TimsData::SpectrumDescr::collisionEnergy, pappso::TimsData::SpectrumDescr::isolationMz, pappso::TimsData::SpectrumDescr::isolationWidth, pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, and pappso::TimsData::SpectrumDescr::tims_frame_list.
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Definition at line 749 of file timsdata.cpp.
Referenced by getPrecursorsFromMzRtCharge().
const std::vector< FrameIdDescr > & pappso::TimsData::getFrameIdDescrList | ( | ) | const |
Definition at line 2361 of file timsdata.cpp.
References m_frameIdDescrList.
pappso::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 614 of file timsdata.cpp.
References getTimsFrameCstSPtrCached().
Referenced by getMassSpectrumCstSPtrByRawIndex().
pappso::MassSpectrumCstSPtr pappso::TimsData::getMassSpectrumCstSPtrByRawIndex | ( | std::size_t | raw_index | ) |
get a mass spectrum given its spectrum index
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 399 of file timsdata.cpp.
References getMassSpectrumCstSPtr(), getScanCoordinateFromRawIndex(), and pappso::PappsoException::qwhat().
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Definition at line 723 of file timsdata.cpp.
References getScanCoordinateFromRawIndex(), and getTimsFrameBaseCstSPtrCached().
bool pappso::TimsData::getMs2BuiltinCentroid | ( | ) | const |
tells if simple centroid filter on raw tims data for MS2 is enabled or not
Definition at line 289 of file timsdata.cpp.
References m_builtinMs2Centroid.
unsigned int pappso::TimsData::getMsLevelBySpectrumIndex | ( | std::size_t | spectrum_index | ) |
Definition at line 773 of file timsdata.cpp.
References getScanCoordinateFromRawIndex(), and getTimsFrameCstSPtrCached().
std::vector< std::size_t > pappso::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
Definition at line 644 of file timsdata.cpp.
References getClosestPrecursorIdByMz(), m_timsDataDirectory, and openDatabaseConnection().
void pappso::TimsData::getQualifiedMassSpectrumByRawIndex | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
std::size_t | spectrum_index, | ||
bool | want_binary_data | ||
) |
Definition at line 782 of file timsdata.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, getRawIndexFromCoordinate(), getScanCoordinateFromRawIndex(), getSpectrumDescrWithScanCoordinate(), getTimsFrameBaseCstSPtrCached(), getTimsFrameCstSPtrCached(), pappso::IsolationMz, pappso::IsolationWidth, pappso::OneOverK0, pappso::PappsoException::qwhat(), pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::QualifiedMassSpectrum::size().
void pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
const SpectrumDescr & | spectrum_descr, | ||
bool | want_binary_data | ||
) |
Definition at line 972 of file timsdata.cpp.
References pappso::TracePlusCombiner::combine(), getTimsFrameBaseCstSPtrCached(), getTimsFrameCstSPtrCached(), mcsp_ms1Filter, pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, pappso::OneOverK0begin, pappso::OneOverK0end, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::PappsoException::what().
Referenced by pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
void pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
const SpectrumDescr & | spectrum_descr, | ||
bool | want_binary_data | ||
) |
Definition at line 1416 of file timsdata.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, pappso::TimsData::SpectrumDescr::collisionEnergy, getTimsFrameBaseCstSPtrCached(), getTimsFrameCstSPtrCached(), pappso::IsolationMz, pappso::TimsData::SpectrumDescr::isolationMz, pappso::IsolationWidth, pappso::TimsData::SpectrumDescr::isolationWidth, m_builtinMs2Centroid, mcsp_ms2Filter, pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, pappso::OneOverK0begin, pappso::OneOverK0end, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsData::SpectrumDescr::tims_frame_list, and pappso::PappsoException::what().
Referenced by pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
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Definition at line 376 of file timsdata.cpp.
References m_frameIdDescrList.
Referenced by getQualifiedMassSpectrumByRawIndex().
std::map< quint32, quint32 > pappso::TimsData::getRawMs2ByPrecursorId | ( | std::size_t | precursor_index | ) |
get cumulated raw signal for a given precursor only to use to see the raw signal
precursor_index | precursor index to extract signal from |
Definition at line 1288 of file timsdata.cpp.
References getTimsFrameCstSPtrCached(), m_timsDataDirectory, openDatabaseConnection(), pappso::PappsoException::qwhat(), and pappso::PappsoException::what().
std::map< quint32, quint32 > pappso::TimsData::getRawMsBySpectrumIndex | ( | std::size_t | spectrum_index | ) |
get raw signal for a spectrum index only to use to see the raw signal
spectrum_index | spcetrum index |
Definition at line 2345 of file timsdata.cpp.
References getScanCoordinateFromRawIndex(), and getTimsFrameCstSPtrCached().
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retention timeline get retention times along the MSrun in seconds
Definition at line 1980 of file timsdata.cpp.
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Definition at line 340 of file timsdata.cpp.
References m_frameIdDescrList, and m_thousandIndexToFrameIdDescrListIndex.
Referenced by getMassSpectrumCstSPtrByRawIndex(), getMatchPrecursorIdByKo(), getMsLevelBySpectrumIndex(), getQualifiedMassSpectrumByRawIndex(), and getRawMsBySpectrumIndex().
pappso::TimsData::SpectrumDescr pappso::TimsData::getSpectrumDescrWithPrecursorId | ( | std::size_t | precursor_id | ) |
get an intermediate structure describing a spectrum
Definition at line 1897 of file timsdata.cpp.
References pappso::TimsData::SpectrumDescr::collisionEnergy, pappso::TimsData::SpectrumDescr::isolationMz, pappso::TimsData::SpectrumDescr::isolationWidth, pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, and pappso::TimsData::SpectrumDescr::tims_frame_list.
Referenced by pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
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Definition at line 1995 of file timsdata.cpp.
References pappso::TimsData::SpectrumDescr::collisionEnergy, pappso::TimsData::SpectrumDescr::isolationMz, pappso::TimsData::SpectrumDescr::isolationWidth, pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, and pappso::TimsData::SpectrumDescr::tims_frame_list.
Referenced by getQualifiedMassSpectrumByRawIndex().
Trace pappso::TimsData::getTicChromatogram | ( | ) | const |
Definition at line 888 of file timsdata.cpp.
References m_timsDataDirectory, openDatabaseConnection(), pappso::res, pappso::rt, and pappso::MapTrace::toTrace().
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get a Tims frame base (no binary data file access) with his database ID
Definition at line 420 of file timsdata.cpp.
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_totalNumberOfScans, mpa_mzCalibrationStore, pappso::TimsFrameRecord::msms_type, pappso::TimsFrameRecord::mz_calibration_id, pappso::TimsFrameRecord::tims_calibration_id, and pappso::TimsFrameRecord::tims_offset.
Referenced by getTimsFrameBaseCstSPtrCached().
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Definition at line 1073 of file timsdata.cpp.
References getTimsFrameBaseCstSPtr(), m_cacheSize, m_mutex, and m_timsFrameBaseCache.
Referenced by getMatchPrecursorIdByKo(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), and getQualifiedMs2MassSpectrumByPrecursorId().
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 528 of file timsdata.cpp.
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_totalNumberOfScans, mpa_mzCalibrationStore, mpa_timsBinDec, pappso::TimsFrameRecord::msms_type, pappso::TimsFrameRecord::mz_calibration_id, and pappso::TimsFrameRecord::tims_calibration_id.
Referenced by 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 1094 of file timsdata.cpp.
References getTimsFrameCstSPtr(), m_cacheSize, m_mutex, and m_timsFrameCache.
Referenced by getMassSpectrumCstSPtr(), getMsLevelBySpectrumIndex(), getQualifiedMassSpectrumByRawIndex(), getQualifiedMs1MassSpectrumByPrecursorId(), getQualifiedMs2MassSpectrumByPrecursorId(), getRawMs2ByPrecursorId(), and getRawMsBySpectrumIndex().
std::vector< std::size_t > pappso::TimsData::getTimsMS1FrameIdRange | ( | double | rt_begin, |
double | rt_end | ||
) | const |
Definition at line 492 of file timsdata.cpp.
References m_timsDataDirectory, and openDatabaseConnection().
std::size_t pappso::TimsData::getTotalNumberOfFrames | ( | ) | const |
Get total number of frames.
Definition at line 624 of file timsdata.cpp.
References m_totalNumberOfFrames.
std::size_t pappso::TimsData::getTotalNumberOfPrecursors | ( | ) | const |
get the number of precursors analyzes by PASEF
Definition at line 638 of file timsdata.cpp.
References m_totalNumberOfPrecursors.
Referenced by pappso::TimsMsRunReaderMs2Selected::spectrumListSize().
std::size_t pappso::TimsData::getTotalNumberOfScans | ( | ) | const |
get the total number of scans
Definition at line 631 of file timsdata.cpp.
References m_totalNumberOfScans.
pappso::XicCoordTims pappso::TimsData::getXicCoordTimsFromPrecursorId | ( | std::size_t | precursor_id, |
PrecisionPtr | precision_ptr | ||
) |
Definition at line 1182 of file timsdata.cpp.
References pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::XicCoordTims::scanNumBegin, pappso::XicCoordTims::scanNumEnd, pappso::PappsoException::what(), and pappso::XicCoord::xicSptr.
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Definition at line 1863 of file timsdata.cpp.
References pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList().
Referenced by ms2ReaderSpectrumCollectionByMsLevel().
void pappso::TimsData::ms2ReaderSpectrumCollectionByMsLevel | ( | const MsRunIdCstSPtr & | msrun_id, |
pappso::SpectrumCollectionHandlerInterface & | handler, | ||
unsigned int | ms_level | ||
) |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
this function will retrieve processed qualified spectrum depending on each Bruker precursors
Definition at line 1628 of file timsdata.cpp.
References pappso::TimsData::SpectrumDescr::collisionEnergy, pappso::TimsData::SpectrumDescr::isolationMz, pappso::TimsData::SpectrumDescr::isolationWidth, pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::TimsData::SpectrumDescr::ms1_index, pappso::TimsData::SpectrumDescr::ms2_index, ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::res, pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::TimsData::SpectrumDescr::tims_frame_list.
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Definition at line 234 of file timsdata.cpp.
References m_timsDataDirectory.
Referenced by TimsData(), fillFrameIdDescrList(), getPrecursorsFromMzRtCharge(), getRawMs2ByPrecursorId(), getTicChromatogram(), and getTimsMS1FrameIdRange().
void pappso::TimsData::rawReaderSpectrumCollectionByMsLevel | ( | const MsRunIdCstSPtr & | msrun_id, |
pappso::SpectrumCollectionHandlerInterface & | handler, | ||
unsigned int | ms_level | ||
) |
function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels
this function will retrieve every scans as a qualified mass spectrum
Definition at line 2097 of file timsdata.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, pappso::TimsData::SpectrumDescr::collisionEnergy, pappso::MassSpectrumId::getSpectrumIndex(), pappso::IsolationMz, pappso::TimsData::SpectrumDescr::isolationMz, pappso::IsolationWidth, pappso::TimsData::SpectrumDescr::isolationWidth, pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::OneOverK0, pappso::TimsData::SpectrumDescr::parent_frame, pappso::TimsData::SpectrumDescr::precursor_id, pappso::TimsData::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsData::SpectrumDescr::scan_mobility_end, pappso::TimsData::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::QualifiedMassSpectrum::size(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().
void pappso::TimsData::setMonoThread | ( | bool | is_mono_thread | ) |
set only one is_mono_thread to true
this avoid to use qtconcurrent
Definition at line 228 of file timsdata.cpp.
References m_isMonoThread.
void pappso::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 1176 of file timsdata.cpp.
References mcsp_ms1Filter.
Referenced by pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr().
void pappso::TimsData::setMs2BuiltinCentroid | ( | bool | centroid | ) |
enable or disable simple centroid filter on raw tims data for MS2
Definition at line 283 of file timsdata.cpp.
References m_builtinMs2Centroid.
void pappso::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 1171 of file timsdata.cpp.
References mcsp_ms2Filter.
Referenced by pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr().
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enable builtin centroid on raw tims integers by default
Definition at line 319 of file timsdata.h.
Referenced by getMs2BuiltinCentroid(), getQualifiedMs2MassSpectrumByPrecursorId(), and setMs2BuiltinCentroid().
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Definition at line 310 of file timsdata.h.
Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().
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store every frame id and corresponding sizes
Definition at line 332 of file timsdata.h.
Referenced by fillFrameIdDescrList(), getFrameIdDescrList(), getRawIndexFromCoordinate(), and getScanCoordinateFromRawIndex().
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Definition at line 348 of file timsdata.h.
Referenced by TimsData().
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Definition at line 346 of file timsdata.h.
Referenced by setMonoThread().
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Definition at line 324 of file timsdata.h.
Referenced by TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().
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Definition at line 322 of file timsdata.h.
Referenced by TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().
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Definition at line 323 of file timsdata.h.
Referenced by TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().
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Definition at line 325 of file timsdata.h.
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Definition at line 350 of file timsdata.h.
Referenced by getTimsFrameBaseCstSPtrCached(), and getTimsFrameCstSPtrCached().
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tells if someone is loading a frame id
Definition at line 344 of file timsdata.h.
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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 339 of file timsdata.h.
Referenced by fillFrameIdDescrList(), and getScanCoordinateFromRawIndex().
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Definition at line 304 of file timsdata.h.
Referenced by TimsData(), fillFrameIdDescrList(), getPrecursorsFromMzRtCharge(), getRawMs2ByPrecursorId(), getTicChromatogram(), getTimsMS1FrameIdRange(), and openDatabaseConnection().
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Definition at line 312 of file timsdata.h.
Referenced by getTimsFrameBaseCstSPtrCached().
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Definition at line 311 of file timsdata.h.
Referenced by getTimsFrameCstSPtrCached().
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Definition at line 309 of file timsdata.h.
Referenced by TimsData(), and getTotalNumberOfFrames().
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Definition at line 308 of file timsdata.h.
Referenced by TimsData(), and getTotalNumberOfPrecursors().
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Definition at line 307 of file timsdata.h.
Referenced by TimsData(), getTimsFrameBaseCstSPtr(), getTimsFrameCstSPtr(), and getTotalNumberOfScans().
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Definition at line 315 of file timsdata.h.
Referenced by TimsData(), getQualifiedMs1MassSpectrumByPrecursorId(), and setMs1FilterCstSPtr().
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Definition at line 314 of file timsdata.h.
Referenced by TimsData(), getQualifiedMs2MassSpectrumByPrecursorId(), and setMs2FilterCstSPtr().
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Definition at line 327 of file timsdata.h.
Referenced by TimsData(), ~TimsData(), getTimsFrameBaseCstSPtr(), and getTimsFrameCstSPtr().
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Definition at line 305 of file timsdata.h.
Referenced by TimsData(), ~TimsData(), and getTimsFrameCstSPtr().