libpappsomspp
Library for mass spectrometry
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#include <timsframesmsrunreader.h>
Public Member Functions | |
TimsFramesMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~TimsFramesMsRunReader () |
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 | |
virtual Trace | computeTicChromatogram () |
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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 42 of file timsframesmsrunreader.h.
TimsFramesMsRunReader::TimsFramesMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 37 of file timsframesmsrunreader.cpp.
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virtual |
Definition at line 42 of file timsframesmsrunreader.cpp.
References pappso::TimsMsRunReaderBase::msp_timsData.
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virtual |
Definition at line 504 of file timsframesmsrunreader.cpp.
References pappso::Trace::append(), pappso::TimsFrame::cumulateScanRangeIntensities(), pappso::TimsData::getFrameIdDescrList(), pappso::TimsFrameBase::getMsLevel(), pappso::TimsFrameBase::getRtInSeconds(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::TimsFrameBase::getTotalNumberOfScans(), pappso::TimsMsRunReaderBase::msp_timsData, and pappso::rt.
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 61 of file timsframesmsrunreader.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 49 of file timsframesmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 68 of file timsframesmsrunreader.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 81 of file timsframesmsrunreader.cpp.
References readSpectrumCollection2().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 92 of file timsframesmsrunreader.cpp.
References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrameBase::getDriftTimeInMilliseconds(), pappso::TimsData::getFrameIdDescrList(), pappso::TimsFrameBase::getMsLevel(), pappso::MsRunReader::getMsRunId(), pappso::TimsFrameBase::getOneOverK0Transformation(), pappso::MsRunReadConfig::getParameterValue(), pappso::TimsFrameBase::getRtInSeconds(), pappso::TimsFrameBase::getScanIndexFromOneOverK0(), pappso::TimsData::getTimsFrameCstSPtrCached(), pappso::TimsData::getTimsFrameRecordList(), pappso::TimsFrameBase::getTotalNumberOfScans(), pappso::IonMobOneOverK0, pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::FrameIdDescr::m_globalScanIndex, 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::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, pappso::TimsFrameScansCount, and pappso::TimsIonMobScanIndex.
Referenced by readSpectrumCollection().
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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 487 of file timsframesmsrunreader.cpp.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 496 of file timsframesmsrunreader.cpp.
References pappso::TimsData::getTotalScanCount(), and pappso::TimsMsRunReaderBase::msp_timsData.
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friend |
Definition at line 44 of file timsframesmsrunreader.h.