libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreader.h>
Public Member Functions | |
TimsMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
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 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 | |
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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 37 of file timsmsrunreader.h.
TimsMsRunReader::TimsMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 35 of file timsmsrunreader.cpp.
References initialize().
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virtual |
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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 61 of file timsmsrunreader.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 471 of file timsmsrunreader.cpp.
References initialize(), and msp_timsData.
Referenced by getTicChromatogram(), and getTimsDataSPtr().
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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 513 of file timsmsrunreader.cpp.
References acquireDevice(), and msp_timsData.
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virtual |
give an access to the underlying raw data pointer
Definition at line 505 of file timsmsrunreader.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 457 of file timsmsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 47 of file timsmsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, and msp_timsData.
Referenced by TimsMsRunReader(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 78 of file timsmsrunreader.cpp.
References msp_timsData.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 69 of file timsmsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Definition at line 494 of file timsmsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Definition at line 482 of file timsmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 85 of file timsmsrunreader.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 98 of file timsmsrunreader.cpp.
References readSpectrumCollectionByMsLevel().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 105 of file timsmsrunreader.cpp.
References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MsRunReader::getMsRunId(), pappso::MsRunReadConfig::getParameterValue(), pappso::FrameIdDescr::m_cumulSize, pappso::FrameIdDescr::m_size, 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::TimsIonMobScanOneOverK0, 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 422 of file timsmsrunreader.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), and msp_timsData.
Referenced by readSpectrumCollection().
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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 464 of file timsmsrunreader.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 450 of file timsmsrunreader.cpp.
References msp_timsData.
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friend |
Definition at line 39 of file timsmsrunreader.h.
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private |
Definition at line 97 of file timsmsrunreader.h.
Referenced by ~TimsMsRunReader(), acquireDevice(), getTicChromatogram(), getTimsDataSPtr(), initialize(), massSpectrumCstSPtr(), qualifiedMassSpectrum(), readSpectrumCollection2(), readSpectrumCollectionByMsLevel(), releaseDevice(), and spectrumListSize().