libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreader.h>
Public Member Functions | |
TimsMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReader (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReader () |
virtual MassSpectrumSPtr | massSpectrumSPtr (std::size_t spectrum_index) override |
get a MassSpectrumSPtr class given its spectrum index | |
virtual MassSpectrumCstSPtr | massSpectrumCstSPtr (std::size_t spectrum_index) override |
virtual QualifiedMassSpectrum | qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override |
get a QualifiedMassSpectrum class given its scan number | |
virtual void | readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler | |
virtual void | readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override |
virtual void | readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels | |
virtual std::size_t | spectrumListSize () const override |
get the totat number of spectrum conained in the MSrun data file | |
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TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReaderBase () |
virtual TimsDataSp | getTimsDataSPtr () |
give an access to the underlying raw data pointer | |
virtual bool | hasScanNumbers () const override |
tells if spectra can be accessed using scan numbers by default, it returns false. Only overrided functions can check if scan numbers are available in the current file | |
virtual bool | releaseDevice () override |
release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object | |
virtual bool | acquireDevice () override |
acquire data back end device | |
virtual Trace | getTicChromatogram () override |
get a TIC chromatogram | |
virtual std::vector< double > | getRetentionTimeLine () override |
retention timeline get retention times along the MSrun in seconds | |
virtual pappso::XicCoordSPtr | newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum index | |
virtual pappso::XicCoordSPtr | newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum | |
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MsRunReader (const MsRunIdCstSPtr &ms_run_id) | |
MsRunReader (const MsRunReader &other) | |
virtual | ~MsRunReader () |
const MsRunIdCstSPtr & | getMsRunId () const |
virtual std::size_t | scanNumber2SpectrumIndex (std::size_t scan_number) |
if possible, converts a scan number into a spectrum index This is a convenient function to help transition from the old scan number (not implemented by all vendors) to more secure spectrum index (not vendor dependant). It is better to not rely on this function. | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true | |
bool | isMonoThread () const |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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virtual void | initialize () override |
virtual bool | accept (const QString &file_name) const override |
tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format | |
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TimsDataSp | msp_timsData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 36 of file timsmsrunreader.h.
TimsMsRunReader::TimsMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 37 of file timsmsrunreader.cpp.
References pappso::TimsMsRunReaderBase::initialize().
TimsMsRunReader::TimsMsRunReader | ( | const TimsMsRunReaderBase & | msrun_reader_base | ) |
Definition at line 42 of file timsmsrunreader.cpp.
References pappso::TimsMsRunReaderBase::initialize().
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virtual |
Definition at line 49 of file timsmsrunreader.cpp.
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 64 of file timsmsrunreader.cpp.
References pappso::TimsData::getMassSpectrumCstSPtrByGlobalScanIndex(), and pappso::TimsMsRunReaderBase::msp_timsData.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 55 of file timsmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 71 of file timsmsrunreader.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::TimsData::getQualifiedMassSpectrumByGlobalScanIndex(), and pappso::TimsMsRunReaderBase::msp_timsData.
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overridevirtual |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Implements pappso::MsRunReader.
Definition at line 84 of file timsmsrunreader.cpp.
References readSpectrumCollectionByMsLevel().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 91 of file timsmsrunreader.cpp.
References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::BrukerPrecursorIndex, pappso::CollisionEnergy, pappso::TimsFrameBase::getDriftTimeInMilliseconds(), pappso::TimsData::getFrameIdDescrList(), pappso::TimsDiaSlices::getGlobalSliceIndexBeginByFrameId(), pappso::TimsDiaSlices::getLastMs1FrameIdByMs2FrameId(), pappso::TimsDiaSlices::getMapFrame2WindowGroupPtr(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::TimsFrame::getMobilityScan(), pappso::TimsFrameBase::getMsLevel(), pappso::MsRunReader::getMsRunId(), pappso::TimsFrameBase::getOneOverK0Transformation(), pappso::MsRunReadConfig::getParameterValue(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::TimsFrameBase::getRtInSeconds(), pappso::TimsFrameBase::getScanIndexFromOneOverK0(), pappso::TimsDdaPrecursors::getSpectrumDescrListByFrameId(), pappso::TimsData::getTimsDdaPrecursorsPtr(), pappso::TimsData::getTimsDiaSlicesPtr(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::TimsData::getTimsFrameRecordList(), pappso::TimsFrameBase::getTotalNumberOfScans(), pappso::IonMobOneOverK0, pappso::TimsData::isDdaRun(), pappso::TimsData::isDiaRun(), pappso::IsolationMz, pappso::IsolationMzWidth, pappso::FrameIdDescr::m_globalScanIndex, pappso::FrameIdDescr::m_scanCount, pappso::TimsMsRunReaderBase::msp_timsData, pappso::MzRangeBegin, pappso::MzRangeEnd, pappso::MsRunReadConfig::needPeakList(), 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::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), pappso::TimsFrameIonMobOneOverK0Begin, pappso::TimsFrameIonMobOneOverK0End, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::TimsFrameMzIndexBegin, pappso::TimsFrameMzIndexEnd, pappso::TimsFrameMzIndexMergeWindow, and pappso::MsRunReadConfig::toString().
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overridevirtual |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels
Implements pappso::MsRunReader.
Definition at line 539 of file timsmsrunreader.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::TimsData::getTimsDdaPrecursorsPtr(), pappso::TimsData::isDdaRun(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::TimsMsRunReaderBase::msp_timsData, and pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel().
Referenced by readSpectrumCollection().
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 572 of file timsmsrunreader.cpp.
References pappso::TimsData::getTotalScanCount(), and pappso::TimsMsRunReaderBase::msp_timsData.
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friend |
Definition at line 38 of file timsmsrunreader.h.