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 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 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 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... | |
virtual TimsDataSp | getTimsDataSPtr () |
give an access to the underlying raw data pointer 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 std::vector< double > | getRetentionTimeLine () |
retention timeline get retention times along the MSrun in seconds 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 | |
TimsDataSp | msp_timsData = nullptr |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 38 of file timsmsrunreader.h.
TimsMsRunReader::TimsMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 34 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 59 of file timsmsrunreader.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 150 of file timsmsrunreader.cpp.
References initialize(), and msp_timsData.
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virtual |
give an access to the underlying raw data pointer
Definition at line 184 of file timsmsrunreader.cpp.
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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 136 of file timsmsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 46 of file timsmsrunreader.cpp.
Referenced by TimsMsRunReader(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 76 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 67 of file timsmsrunreader.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Definition at line 173 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 161 of file timsmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 83 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 96 of file timsmsrunreader.cpp.
References readSpectrumCollectionByMsLevel().
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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 104 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 143 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 129 of file timsmsrunreader.cpp.
References msp_timsData.
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friend |
Definition at line 40 of file timsmsrunreader.h.
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private |
Definition at line 93 of file timsmsrunreader.h.
Referenced by ~TimsMsRunReader(), acquireDevice(), massSpectrumCstSPtr(), qualifiedMassSpectrum(), readSpectrumCollectionByMsLevel(), releaseDevice(), and spectrumListSize().