libpappsomspp
Library for mass spectrometry
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#include <xymsrunreader.h>
Public Member Functions | |
XyMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~XyMsRunReader () |
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 pappso::XicCoordSPtr | newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum index More... | |
virtual pappso::XicCoordSPtr | newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum More... | |
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 More... | |
virtual std::size_t | spectrumListSize () const override |
get the totat number of spectrum conained in the MSrun data 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... | |
virtual bool | hasScanNumbers () const |
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 std::vector< double > | getRetentionTimeLine () |
retention timeline get retention times along the MSrun in seconds More... | |
virtual Trace | getTicChromatogram () |
get a TIC chromatogram More... | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true More... | |
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 More... | |
QualifiedMassSpectrum | qualifiedMassSpectrumFromXyMSDataFile (MassSpectrumId mass_spectrum_id) const |
Protected Attributes | |
QString | m_fileName |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Friends | |
class | MsFileAccessor |
Definition at line 10 of file xymsrunreader.h.
pappso::XyMsRunReader::XyMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
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virtual |
Definition at line 47 of file xymsrunreader.cpp.
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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 53 of file xymsrunreader.cpp.
References pappso::Utils::endOfLineRegExp, and pappso::Utils::xyMassDataFormatRegExp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 308 of file xymsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 36 of file xymsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId.
Referenced by XyMsRunReader().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 112 of file xymsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 105 of file xymsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Definition at line 326 of file xymsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Definition at line 314 of file xymsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 215 of file xymsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, and qualifiedMassSpectrumFromXyMSDataFile().
Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().
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protected |
Definition at line 119 of file xymsrunreader.cpp.
References pappso::Utils::endOfLineRegExp, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::x, pappso::Utils::xyMassDataFormatRegExp, and pappso::y.
Referenced by qualifiedMassSpectrum(), readSpectrumCollection(), and readSpectrumCollectionByMsLevel().
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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 243 of file xymsrunreader.cpp.
References pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, qualifiedMassSpectrumFromXyMSDataFile(), and pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum().
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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 268 of file xymsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMsLevel(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, qualifiedMassSpectrumFromXyMSDataFile(), and pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum().
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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 302 of file xymsrunreader.cpp.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 296 of file xymsrunreader.cpp.
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friend |
Definition at line 12 of file xymsrunreader.h.
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protected |
Definition at line 50 of file xymsrunreader.h.