libpappsomspp
Library for mass spectrometry
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#include <bafasciimsrunreader.h>
Public Member Functions | |
BafAsciiMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~BafAsciiMsRunReader () |
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 | 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 | |
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MsRunReader (const 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 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 | |
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 | |
QString | craftLineParserRegExpPattern () const |
QRegularExpression | craftLineParserRegExp (QString &pattern) const |
bool | parseMassSpectrumLine (QString &line, MassSpectrumLineData &ms_line_data, QRegularExpression &line_regexp) const |
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 | |
QualifiedMassSpectrum | qualifiedMassSpectrumFromBafAsciiMSDataFile (std::size_t spectrum_index, bool want_binary_data) const |
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Protected Attributes | |
QString | m_fileName |
std::size_t | m_spectrumCount = 0 |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Friends | |
class | MsFileAccessor |
Definition at line 23 of file bafasciimsrunreader.h.
pappso::BafAsciiMsRunReader::BafAsciiMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 27 of file bafasciimsrunreader.cpp.
References initialize().
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virtual |
Definition at line 53 of file bafasciimsrunreader.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 229 of file bafasciimsrunreader.cpp.
References craftLineParserRegExp(), craftLineParserRegExpPattern(), line, m_spectrumCount, and parseMassSpectrumLine().
Referenced by initialize().
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 686 of file bafasciimsrunreader.cpp.
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protected |
Definition at line 101 of file bafasciimsrunreader.cpp.
Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().
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protected |
Definition at line 58 of file bafasciimsrunreader.cpp.
References pappso::Utils::unsignedDoubleNumberNoExponentialRegExp.
Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 37 of file bafasciimsrunreader.cpp.
References accept(), and pappso::MsRunReader::mcsp_msRunId.
Referenced by BafAsciiMsRunReader().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 299 of file bafasciimsrunreader.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 292 of file bafasciimsrunreader.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 703 of file bafasciimsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Definition at line 692 of file bafasciimsrunreader.cpp.
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protected |
Definition at line 116 of file bafasciimsrunreader.cpp.
References pappso::MassSpectrumLineData::dash, pappso::MassSpectrumLineData::ionizationMode, pappso::MassSpectrumLineData::ionSourceType, line, pappso::MassSpectrumLineData::msLevel, pappso::MassSpectrumLineData::mz_range, pappso::MassSpectrumLineData::peakCount, pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::peakShapeType, and pappso::MassSpectrumLineData::retentionTime.
Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 459 of file bafasciimsrunreader.cpp.
References qualifiedMassSpectrumFromBafAsciiMSDataFile().
Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().
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protected |
Definition at line 306 of file bafasciimsrunreader.cpp.
References craftLineParserRegExp(), craftLineParserRegExpPattern(), line, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::MassSpectrumLineData::msLevel, pappso::mz, parseMassSpectrumLine(), pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::retentionTime, pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), and pappso::QualifiedMassSpectrum::setRtInSeconds().
Referenced by qualifiedMassSpectrum().
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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 476 of file bafasciimsrunreader.cpp.
References readSpectrumCollectionByMsLevel().
Referenced by readSpectrumCollection2().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 666 of file bafasciimsrunreader.cpp.
References 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 484 of file bafasciimsrunreader.cpp.
References craftLineParserRegExp(), craftLineParserRegExpPattern(), pappso::QualifiedMassSpectrum::getMsLevel(), line, pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::MassSpectrumLineData::msLevel, pappso::mz, pappso::SpectrumCollectionHandlerInterface::needPeakList(), parseMassSpectrumLine(), pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::retentionTime, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), and pappso::SpectrumCollectionHandlerInterface::shouldStop().
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 680 of file bafasciimsrunreader.cpp.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 674 of file bafasciimsrunreader.cpp.
References m_spectrumCount.
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friend |
Definition at line 25 of file bafasciimsrunreader.h.
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protected |
Definition at line 67 of file bafasciimsrunreader.h.
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mutableprotected |
Definition at line 70 of file bafasciimsrunreader.h.
Referenced by accept(), and spectrumListSize().