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 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 | |
virtual std::size_t | spectrumListSize () const override |
get the totat number of spectrum conained in the MSrun data file | |
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 TimsDataSp | getTimsDataSPtr () |
give an access to the underlying raw data pointer | |
virtual Trace | getTicChromatogram () override |
get a TIC chromatogram | |
virtual Trace | computeTicChromatogram () |
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MsRunReader (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. | |
virtual std::vector< double > | getRetentionTimeLine () |
retention timeline get retention times along the MSrun in seconds | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true | |
bool | isMonoThread () const |
Protected Member Functions | |
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 | |
Private Attributes | |
TimsDataSp | msp_timsData = nullptr |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 43 of file timsframesmsrunreader.h.
TimsFramesMsRunReader::TimsFramesMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 36 of file timsframesmsrunreader.cpp.
References initialize().
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virtual |
Definition at line 44 of file timsframesmsrunreader.cpp.
References msp_timsData.
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overrideprotectedvirtual |
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
Implements pappso::MsRunReader.
Definition at line 64 of file timsframesmsrunreader.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 527 of file timsframesmsrunreader.cpp.
References initialize(), and msp_timsData.
Referenced by getTicChromatogram(), and getTimsDataSPtr().
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virtual |
Definition at line 580 of file timsframesmsrunreader.cpp.
References pappso::Trace::append(), msp_timsData, and pappso::rt.
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overridevirtual |
get a TIC chromatogram
for each retention time, computes the sum of all intensities. For IM-MS, combines the mobility spectra
Note that, formally, a TIC chromatogram is computed only for MS1 spectra.
Reimplemented from pappso::MsRunReader.
Definition at line 568 of file timsframesmsrunreader.cpp.
References acquireDevice(), and msp_timsData.
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virtual |
give an access to the underlying raw data pointer
Definition at line 560 of file timsframesmsrunreader.cpp.
References acquireDevice(), and msp_timsData.
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overridevirtual |
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
Reimplemented from pappso::MsRunReader.
Definition at line 513 of file timsframesmsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 50 of file timsframesmsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, and msp_timsData.
Referenced by TimsFramesMsRunReader(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 84 of file timsframesmsrunreader.cpp.
References msp_timsData.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 72 of file timsframesmsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Definition at line 549 of file timsframesmsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Definition at line 538 of file timsframesmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 91 of file timsframesmsrunreader.cpp.
References pappso::MsRunReader::getMsRunId(), and 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 104 of file timsframesmsrunreader.cpp.
References readSpectrumCollection2().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 115 of file timsframesmsrunreader.cpp.
References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::MsRunReader::getMsRunId(), pappso::MsRunReadConfig::getParameterValue(), pappso::FrameIdDescr::m_cumulSize, 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, pappso::TimsIonMobScanIndex, and pappso::TimsIonMobScanOneOverK0.
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 497 of file timsframesmsrunreader.cpp.
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overridevirtual |
release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object
Implements pappso::MsRunReader.
Definition at line 520 of file timsframesmsrunreader.cpp.
References msp_timsData.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 506 of file timsframesmsrunreader.cpp.
References msp_timsData.
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friend |
Definition at line 45 of file timsframesmsrunreader.h.
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private |
Definition at line 103 of file timsframesmsrunreader.h.
Referenced by ~TimsFramesMsRunReader(), acquireDevice(), computeTicChromatogram(), getTicChromatogram(), getTimsDataSPtr(), initialize(), massSpectrumCstSPtr(), qualifiedMassSpectrum(), readSpectrumCollection2(), releaseDevice(), and spectrumListSize().