libpappsomspp
Library for mass spectrometry
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#include <timsddaprecursors.h>
Classes | |
struct | SpectrumDescr |
Public Member Functions | |
TimsDdaPrecursors (QSqlQuery &query, TimsData *tims_data_origin) | |
~TimsDdaPrecursors () | |
std::size_t | getTotalPrecursorCount () const |
get the number of precursors analyzed by PASEF | |
XicCoordTims | getXicCoordTimsFromPrecursorId (std::size_t precursor_id, PrecisionPtr precision_ptr) |
TimsDdaPrecursors::SpectrumDescr | getSpectrumDescrWithPrecursorId (std::size_t precursor_id) const |
get an intermediate structure describing a spectrum | |
std::vector< TimsDdaPrecursors::SpectrumDescr > | getSpectrumDescrListByFrameId (std::size_t frame_id) const |
get a list of TimsDdaPrecursors::SpectrumDescr for a frame | |
void | getQualifiedMs2MassSpectrumBySpectrumDescr (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data) |
void | getQualifiedMs1MassSpectrumBySpectrumDescr (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, const SpectrumDescr &spectrum_descr, bool want_binary_data) |
void | setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter) |
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters inside a FilterSuite object | |
void | setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter) |
filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters inside a FilterSuite object | |
void | setMs2BuiltinCentroid (bool centroid) |
enable or disable simple centroid filter on raw tims data for MS2 | |
bool | getMs2BuiltinCentroid () const |
tells if simple centroid filter on raw tims data for MS2 is enabled or not | |
void | ms2ReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true | |
void | rawReaderSpectrumCollectionByMsLevel (const MsRunIdCstSPtr &msrun_id, SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) |
function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels | |
std::vector< std::size_t > | getPrecursorsByMzRtCharge (int charge, double mz_val, double rt_sec, double k0) |
guess possible precursor ids given a charge, m/z, retention time and k0 | |
std::vector< std::size_t > | getMatchPrecursorIdByKo (std::vector< std::vector< double > > ids, double ko_value) |
std::vector< std::size_t > | getClosestPrecursorIdByMz (std::vector< std::vector< double > > ids, double mz_value) |
TimsDataFastMap & | getCombinedMs2ScansByPrecursorId (std::size_t precursor_id) |
get cumulated raw signal for a given precursorCMakeLists.txt.userCMakeLists.txt.userCMakeLists.txt.user only to use to see the raw signal | |
Protected Member Functions | |
SpectrumDescr | getSpectrumDescrWithScanCoordinates (const std::pair< std::size_t, std::size_t > &scan_coordinates) |
Private Member Functions | |
void | ms2ReaderGenerateMS1MS2Spectrum (const MsRunIdCstSPtr &msrun_id, std::vector< QualifiedMassSpectrum > &qualified_mass_spectrum_list, SpectrumCollectionHandlerInterface &handler, const SpectrumDescr &spectrum_descr, unsigned int ms_level) |
void | fillSpectrumDescriptionWithSqlRecord (SpectrumDescr &spectrum_descr, QSqlQuery &qprecursor_list) |
Private Attributes | |
friend | TimsData |
TimsData * | mp_timsDataOrigin |
std::size_t | m_totalPrecursorCount |
std::map< std::size_t, QSqlRecord > | m_mapXicCoordRecord |
pappso::FilterInterfaceCstSPtr | mcsp_ms2Filter = nullptr |
pappso::FilterInterfaceCstSPtr | mcsp_ms1Filter = nullptr |
bool | m_builtinMs2Centroid = true |
enable builtin centroid on raw tims integers by default | |
bool | m_isMonoThread = false |
QMutex | m_mutex |
Definition at line 35 of file timsddaprecursors.h.
pappso::TimsDdaPrecursors::TimsDdaPrecursors | ( | QSqlQuery & | query, |
TimsData * | tims_data_origin ) |
Default constructor
Definition at line 38 of file timsddaprecursors.cpp.
References m_totalPrecursorCount, mcsp_ms1Filter, and mcsp_ms2Filter.
pappso::TimsDdaPrecursors::~TimsDdaPrecursors | ( | ) |
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Definition at line 574 of file timsddaprecursors.cpp.
References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.
Referenced by rawReaderSpectrumCollectionByMsLevel().
std::vector< std::size_t > pappso::TimsDdaPrecursors::getClosestPrecursorIdByMz | ( | std::vector< std::vector< double > > | ids, |
double | mz_value ) |
Definition at line 1573 of file timsddaprecursors.cpp.
Referenced by getPrecursorsByMzRtCharge().
TimsDataFastMap & pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId | ( | std::size_t | precursor_id | ) |
get cumulated raw signal for a given precursorCMakeLists.txt.userCMakeLists.txt.userCMakeLists.txt.user only to use to see the raw signal
precursor_index | precursor index to extract signal from |
Definition at line 170 of file timsddaprecursors.cpp.
References pappso::TimsDataFastMap::clear(), pappso::TimsData::getTimsDataDirectory(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsData::getTimsFrameCstSPtrCached(), mp_timsDataOrigin, pappso::TimsData::openDatabaseConnection(), pappso::PappsoException::qwhat(), and pappso::PappsoException::what().
std::vector< std::size_t > pappso::TimsDdaPrecursors::getMatchPrecursorIdByKo | ( | std::vector< std::vector< double > > | ids, |
double | ko_value ) |
Definition at line 1545 of file timsddaprecursors.cpp.
References pappso::TimsData::getScanCoordinatesByGlobalScanIndex(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), and mp_timsDataOrigin.
bool pappso::TimsDdaPrecursors::getMs2BuiltinCentroid | ( | ) | const |
tells if simple centroid filter on raw tims data for MS2 is enabled or not
Definition at line 935 of file timsddaprecursors.cpp.
References m_builtinMs2Centroid.
std::vector< std::size_t > pappso::TimsDdaPrecursors::getPrecursorsByMzRtCharge | ( | int | charge, |
double | mz_val, | ||
double | rt_sec, | ||
double | k0 ) |
guess possible precursor ids given a charge, m/z, retention time and k0
Definition at line 1463 of file timsddaprecursors.cpp.
References getClosestPrecursorIdByMz(), pappso::TimsData::getTimsDataDirectory(), mp_timsDataOrigin, and pappso::TimsData::openDatabaseConnection().
void pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
const SpectrumDescr & | spectrum_descr, | ||
bool | want_binary_data ) |
Definition at line 603 of file timsddaprecursors.cpp.
References pappso::TracePlusCombiner::combine(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, mcsp_ms1Filter, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), and pappso::PappsoException::what().
Referenced by ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
void pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr | ( | const MsRunIdCstSPtr & | msrun_id, |
QualifiedMassSpectrum & | mass_spectrum, | ||
const SpectrumDescr & | spectrum_descr, | ||
bool | want_binary_data ) |
Definition at line 717 of file timsddaprecursors.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::CollisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::IsolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::IsolationMzWidth, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, m_builtinMs2Centroid, mcsp_ms2Filter, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list, and pappso::PappsoException::what().
Referenced by ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
std::vector< TimsDdaPrecursors::SpectrumDescr > pappso::TimsDdaPrecursors::getSpectrumDescrListByFrameId | ( | std::size_t | frame_id | ) | const |
get a list of TimsDdaPrecursors::SpectrumDescr for a frame
frame_id | the frame_id |
Definition at line 77 of file timsddaprecursors.cpp.
References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::TimsData::m_timsDataDirectory, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsData::openDatabaseConnection(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list, and pappso::PappsoException::what().
Referenced by pappso::TimsMsRunReader::readSpectrumCollection2().
TimsDdaPrecursors::SpectrumDescr pappso::TimsDdaPrecursors::getSpectrumDescrWithPrecursorId | ( | std::size_t | precursor_id | ) | const |
get an intermediate structure describing a spectrum
Definition at line 414 of file timsddaprecursors.cpp.
References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsData::getTimsDataDirectory(), pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsData::openDatabaseConnection(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.
Referenced by pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), and pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum().
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Definition at line 501 of file timsddaprecursors.cpp.
References pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsData::getTimsDataDirectory(), pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, pappso::TimsData::openDatabaseConnection(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.
Referenced by pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex().
std::size_t pappso::TimsDdaPrecursors::getTotalPrecursorCount | ( | ) | const |
get the number of precursors analyzed by PASEF
Definition at line 300 of file timsddaprecursors.cpp.
References m_totalPrecursorCount.
Referenced by pappso::TimsMsRunReaderMs2::spectrumListSize(), and pappso::TimsMsRunReaderMs2Selected::spectrumListSize().
XicCoordTims pappso::TimsDdaPrecursors::getXicCoordTimsFromPrecursorId | ( | std::size_t | precursor_id, |
PrecisionPtr | precision_ptr ) |
Definition at line 306 of file timsddaprecursors.cpp.
References m_mapXicCoordRecord, m_mutex, pappso::TimsData::m_timsDataDirectory, mp_timsDataOrigin, pappso::XicCoord::mzRange, pappso::TimsData::openDatabaseConnection(), pappso::XicCoord::rtTarget, pappso::XicCoordTims::scanNumBegin, pappso::XicCoordTims::scanNumEnd, pappso::PappsoException::what(), and pappso::XicCoord::xicSptr.
Referenced by pappso::TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex().
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Definition at line 1180 of file timsddaprecursors.cpp.
References getQualifiedMs1MassSpectrumBySpectrumDescr(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList().
Referenced by ms2ReaderSpectrumCollectionByMsLevel().
void pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel | ( | const MsRunIdCstSPtr & | msrun_id, |
SpectrumCollectionHandlerInterface & | handler, | ||
unsigned int | ms_level ) |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
this function will retrieve processed qualified spectrum depending on each Bruker precursors
Definition at line 941 of file timsddaprecursors.cpp.
References pappso::TimsBinDec::closeLinearRead(), pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, pappso::TimsData::getTimsBinDecPtr(), pappso::TimsData::getTimsDataDirectory(), pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, pappso::SpectrumCollectionHandlerInterface::loadingEnded(), m_isMonoThread, mp_timsDataOrigin, pappso::TimsDdaPrecursors::SpectrumDescr::ms1_index, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsData::openDatabaseConnection(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::res, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::TimsDdaPrecursors::SpectrumDescr::tims_frame_list.
Referenced by pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel().
void pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel | ( | const MsRunIdCstSPtr & | msrun_id, |
SpectrumCollectionHandlerInterface & | handler, | ||
unsigned int | ms_level ) |
function to visit an MsRunReader and get each raw Spectrum in a spectrum collection handler by Ms Levels
this function will retrieve every scans as a qualified mass spectrum
Definition at line 1213 of file timsddaprecursors.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, pappso::TimsDdaPrecursors::SpectrumDescr::collisionEnergy, fillSpectrumDescriptionWithSqlRecord(), pappso::TimsData::getFrameIdDescrList(), pappso::TimsData::getGlobalScanIndexByScanCoordinates(), pappso::MassSpectrumId::getSpectrumIndex(), pappso::TimsData::getTimsDataDirectory(), pappso::TimsData::getTimsFrameBaseCstSPtrCached(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::TimsData::getTotalScanCount(), pappso::IonMobOneOverK0, pappso::IsolationMz, pappso::TimsDdaPrecursors::SpectrumDescr::isolationMz, pappso::IsolationMzWidth, pappso::TimsDdaPrecursors::SpectrumDescr::isolationWidth, mp_timsDataOrigin, pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::TimsData::openDatabaseConnection(), pappso::TimsDdaPrecursors::SpectrumDescr::parent_frame, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_id, pappso::TimsDdaPrecursors::SpectrumDescr::precursor_ion_data, pappso::PappsoException::qwhat(), pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_end, pappso::TimsDdaPrecursors::SpectrumDescr::scan_mobility_start, pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::QualifiedMassSpectrum::size(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().
Referenced by pappso::TimsMsRunReader::readSpectrumCollectionByMsLevel().
void pappso::TimsDdaPrecursors::setMonoThread | ( | bool | is_mono_thread | ) |
set only one is_mono_thread to true
this avoid to use qtconcurrent
Definition at line 1174 of file timsddaprecursors.cpp.
References m_isMonoThread.
Referenced by pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel().
void pappso::TimsDdaPrecursors::setMs1FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr & | filter | ) |
filter interface to apply just after raw MS1 specturm extraction the filter can be a list of filters inside a FilterSuite object
Definition at line 711 of file timsddaprecursors.cpp.
References mcsp_ms1Filter.
Referenced by pappso::TimsMsRunReaderMs2::acquireDevice(), pappso::TimsMsRunReaderMs2::setMs1FilterCstSPtr(), and pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr().
void pappso::TimsDdaPrecursors::setMs2BuiltinCentroid | ( | bool | centroid | ) |
enable or disable simple centroid filter on raw tims data for MS2
Definition at line 929 of file timsddaprecursors.cpp.
References m_builtinMs2Centroid.
Referenced by pappso::TimsMsRunReaderMs2::acquireDevice(), and pappso::TimsMsRunReaderMs2::setMs2BuiltinCentroid().
void pappso::TimsDdaPrecursors::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr & | filter | ) |
filter interface to apply just after raw MS2 specturm extraction the filter can be a list of filters inside a FilterSuite object
Definition at line 706 of file timsddaprecursors.cpp.
References mcsp_ms2Filter.
Referenced by pappso::TimsMsRunReaderMs2::acquireDevice(), pappso::TimsMsRunReaderMs2::setMs2FilterCstSPtr(), and pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr().
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enable builtin centroid on raw tims integers by default
Definition at line 218 of file timsddaprecursors.h.
Referenced by getMs2BuiltinCentroid(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and setMs2BuiltinCentroid().
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Definition at line 220 of file timsddaprecursors.h.
Referenced by ms2ReaderSpectrumCollectionByMsLevel(), and setMonoThread().
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Definition at line 210 of file timsddaprecursors.h.
Referenced by getXicCoordTimsFromPrecursorId().
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Definition at line 222 of file timsddaprecursors.h.
Referenced by getXicCoordTimsFromPrecursorId().
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Definition at line 207 of file timsddaprecursors.h.
Referenced by TimsDdaPrecursors(), and getTotalPrecursorCount().
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Definition at line 214 of file timsddaprecursors.h.
Referenced by TimsDdaPrecursors(), getQualifiedMs1MassSpectrumBySpectrumDescr(), and setMs1FilterCstSPtr().
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Definition at line 213 of file timsddaprecursors.h.
Referenced by TimsDdaPrecursors(), getQualifiedMs2MassSpectrumBySpectrumDescr(), and setMs2FilterCstSPtr().
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Definition at line 205 of file timsddaprecursors.h.
Referenced by getCombinedMs2ScansByPrecursorId(), getMatchPrecursorIdByKo(), getPrecursorsByMzRtCharge(), getQualifiedMs1MassSpectrumBySpectrumDescr(), getQualifiedMs2MassSpectrumBySpectrumDescr(), getSpectrumDescrListByFrameId(), getSpectrumDescrWithPrecursorId(), getSpectrumDescrWithScanCoordinates(), getXicCoordTimsFromPrecursorId(), ms2ReaderSpectrumCollectionByMsLevel(), and rawReaderSpectrumCollectionByMsLevel().
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Definition at line 37 of file timsddaprecursors.h.