libpappsomspp
Library for mass spectrometry
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#include <pwizmsrunreader.h>
Public Member Functions | |
PwizMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~PwizMsRunReader () |
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 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 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 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 | |
const OboPsiModTerm | getOboPsiModTermNativeIDFormat () const |
get OboPsiModTerm corresponding to the nativeID format format of mz data | |
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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 | |
virtual Trace | getTicChromatogram () |
get a TIC chromatogram | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true | |
bool | isMonoThread () const |
Protected Member Functions | |
virtual void | readSpectrumCollectionWithMsrunReadConfig (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) |
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 | |
bool | processRetentionTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const |
bool | processDriftTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const |
QualifiedMassSpectrum | qualifiedMassSpectrumFromPwizMSData (std::size_t spectrum_index, bool want_binary_data, bool &ok) const |
QualifiedMassSpectrum | qualifiedMassSpectrumFromPwizSpectrumPtr (const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const |
pwiz::msdata::SpectrumPtr | getPwizSpectrumPtr (pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const |
Protected Attributes | |
pwiz::msdata::MSDataPtr | msp_msData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Private Attributes | |
bool | m_hasScanNumbers = false |
Friends | |
class | MsFileAccessor |
Definition at line 45 of file pwizmsrunreader.h.
pappso::PwizMsRunReader::PwizMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 53 of file pwizmsrunreader.cpp.
References initialize().
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virtual |
Definition at line 169 of file pwizmsrunreader.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 777 of file pwizmsrunreader.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 1142 of file pwizmsrunreader.cpp.
References initialize(), and msp_msData.
Referenced by readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().
const OboPsiModTerm pappso::PwizMsRunReader::getOboPsiModTermNativeIDFormat | ( | ) | const |
get OboPsiModTerm corresponding to the nativeID format format of mz data
Definition at line 175 of file pwizmsrunreader.cpp.
References pappso::OboPsiModTerm::m_accession, pappso::OboPsiModTerm::m_definition, pappso::OboPsiModTerm::m_name, and msp_msData.
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protected |
Definition at line 206 of file pwizmsrunreader.cpp.
Referenced by qualifiedMassSpectrumFromPwizMSData(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().
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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 1129 of file pwizmsrunreader.cpp.
References m_hasScanNumbers.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 65 of file pwizmsrunreader.cpp.
References m_hasScanNumbers, pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::mzXML, and pappso::Utils::toUtf8StandardString().
Referenced by PwizMsRunReader(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 799 of file pwizmsrunreader.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 792 of file pwizmsrunreader.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 1164 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getPrecursorMz(), and pappso::QualifiedMassSpectrum::getRtInSeconds().
Referenced by newXicCoordSPtrFromSpectrumIndex().
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Definition at line 1153 of file pwizmsrunreader.cpp.
References newXicCoordSPtrFromQualifiedMassSpectrum(), and qualifiedMassSpectrum().
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protected |
Definition at line 319 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::setDtInMilliSeconds().
Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().
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protected |
Definition at line 251 of file pwizmsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, pappso::MGF, and pappso::QualifiedMassSpectrum::setRtInSeconds().
Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 806 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MsRunReader::mcsp_msRunId, pappso::MGF, and qualifiedMassSpectrumFromPwizMSData().
Referenced by massSpectrumCstSPtr(), massSpectrumSPtr(), and newXicCoordSPtrFromSpectrumIndex().
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protected |
Definition at line 723 of file pwizmsrunreader.cpp.
References getPwizSpectrumPtr(), pappso::MsRunReader::mcsp_msRunId, msp_msData, qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::MassSpectrumId::setNativeId(), and pappso::MassSpectrumId::setSpectrumIndex().
Referenced by qualifiedMassSpectrum().
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protected |
Definition at line 387 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::QualifiedMassSpectrum::getPrecursorIonData(), pappso::QualifiedMassSpectrum::getPrecursorNativeId(), pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::MGF, msp_msData, processDriftTime(), processRetentionTime(), pappso::PappsoException::qwhat(), pappso::ScanNumber, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), and pappso::MassSpectrum::sortMz().
Referenced by qualifiedMassSpectrumFromPwizMSData(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().
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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 832 of file pwizmsrunreader.cpp.
References readSpectrumCollectionByMsLevel().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 839 of file pwizmsrunreader.cpp.
References readSpectrumCollectionWithMsrunReadConfig().
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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 848 of file pwizmsrunreader.cpp.
References acquireDevice(), pappso::QualifiedMassSpectrum::getMsLevel(), getPwizSpectrumPtr(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().
Referenced by readSpectrumCollection().
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protectedvirtual |
Definition at line 986 of file pwizmsrunreader.cpp.
References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), acquireDevice(), pappso::QualifiedMassSpectrum::getMsLevel(), getPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::MsRunReadConfig::needPeakList(), qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().
Referenced by readSpectrumCollection2().
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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 1135 of file pwizmsrunreader.cpp.
References msp_msData.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 1123 of file pwizmsrunreader.cpp.
References msp_msData.
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friend |
Definition at line 47 of file pwizmsrunreader.h.
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private |
Definition at line 128 of file pwizmsrunreader.h.
Referenced by hasScanNumbers(), and initialize().
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protected |
Definition at line 124 of file pwizmsrunreader.h.
Referenced by acquireDevice(), getOboPsiModTermNativeIDFormat(), initialize(), qualifiedMassSpectrumFromPwizMSData(), qualifiedMassSpectrumFromPwizSpectrumPtr(), readSpectrumCollectionByMsLevel(), readSpectrumCollectionWithMsrunReadConfig(), releaseDevice(), and spectrumListSize().