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 More... | |
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 More... | |
virtual void | readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More... | |
virtual std::size_t | spectrumListSize () const override |
get the totat number of spectrum conained in the MSrun data file More... | |
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 More... | |
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 More... | |
virtual bool | acquireDevice () override |
acquire data back end device More... | |
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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. More... | |
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 More... | |
Private Attributes | |
TimsData * | mpa_timsData = nullptr |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 56 of file timsmsrunreader.h.
TimsMsRunReader::TimsMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
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virtual |
Definition at line 40 of file timsmsrunreader.cpp.
References mpa_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 56 of file timsmsrunreader.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 182 of file timsmsrunreader.cpp.
References initialize(), and mpa_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 167 of file timsmsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 49 of file timsmsrunreader.cpp.
Referenced by acquireDevice(), and TimsMsRunReader().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 74 of file timsmsrunreader.cpp.
References pappso::TimsData::getMassSpectrumCstSPtrByRawIndex(), and mpa_timsData.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 65 of file timsmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 81 of file timsmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MsRunReader::getMsRunId(), pappso::TimsData::getQualifiedMassSpectrumByRawIndex(), mpa_timsData, pappso::QualifiedMassSpectrum::setMassSpectrumId(), and pappso::MassSpectrumId::setMsRunId().
Referenced by readSpectrumCollection().
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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 102 of file timsmsrunreader.cpp.
References pappso::TimsData::getMsLevelBySpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), mpa_timsData, pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().
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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 174 of file timsmsrunreader.cpp.
References mpa_timsData.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 160 of file timsmsrunreader.cpp.
References pappso::TimsData::getTotalNumberOfScans(), and mpa_timsData.
Referenced by readSpectrumCollection().
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friend |
Definition at line 76 of file timsmsrunreader.h.
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private |
Definition at line 110 of file timsmsrunreader.h.
Referenced by acquireDevice(), massSpectrumCstSPtr(), qualifiedMassSpectrum(), readSpectrumCollection(), releaseDevice(), spectrumListSize(), and ~TimsMsRunReader().