libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreaderdia.h>
Public Member Functions | |
TimsMsRunReaderDia (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReaderDia (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReaderDia () |
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 XicCoordSPtr | newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum index | |
virtual XicCoordSPtr | newXicCoordSPtrFromQualifiedMassSpectrum (const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const override |
get a xic coordinate object from a given spectrum | |
virtual std::size_t | spectrumListSize () const override |
get the totat number of spectrum conained in the MSrun data file | |
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 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 bool | acquireDevice () override |
acquire data back end device | |
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TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReaderBase () |
virtual TimsDataSp | getTimsDataSPtr () |
give an access to the underlying raw data pointer | |
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 Trace | getTicChromatogram () override |
get a TIC chromatogram | |
virtual std::vector< double > | getRetentionTimeLine () override |
retention timeline get retention times along the MSrun in seconds | |
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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. | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true | |
bool | isMonoThread () const |
Protected Member Functions | |
virtual void | initialize () override |
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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 | |
Private Attributes | |
TimsDiaSlices * | mp_timsDiaSlices = nullptr |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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TimsDataSp | msp_timsData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 44 of file timsmsrunreaderdia.h.
pappso::TimsMsRunReaderDia::TimsMsRunReaderDia | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Default constructor
Definition at line 38 of file timsmsrunreaderdia.cpp.
References initialize().
pappso::TimsMsRunReaderDia::TimsMsRunReaderDia | ( | const TimsMsRunReaderBase & | msrun_reader_base | ) |
Definition at line 46 of file timsmsrunreaderdia.cpp.
References initialize().
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virtual |
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overridevirtual |
acquire data back end device
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 168 of file timsmsrunreaderdia.cpp.
References pappso::TimsMsRunReaderBase::acquireDevice(), mp_timsDiaSlices, and pappso::TimsMsRunReaderBase::msp_timsData.
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overrideprotectedvirtual |
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 59 of file timsmsrunreaderdia.cpp.
Referenced by TimsMsRunReaderDia(), and TimsMsRunReaderDia().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 152 of file timsmsrunreaderdia.cpp.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 144 of file timsmsrunreaderdia.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 92 of file timsmsrunreaderdia.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 82 of file timsmsrunreaderdia.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 112 of file timsmsrunreaderdia.cpp.
References pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::MsRunReader::getMsRunId(), and mp_timsDiaSlices.
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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 124 of file timsmsrunreaderdia.cpp.
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 134 of file timsmsrunreaderdia.cpp.
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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 102 of file timsmsrunreaderdia.cpp.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 161 of file timsmsrunreaderdia.cpp.
References pappso::TimsDiaSlices::getTotalSlicesCount(), and mp_timsDiaSlices.
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friend |
Definition at line 46 of file timsmsrunreaderdia.h.
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private |
Definition at line 115 of file timsmsrunreaderdia.h.
Referenced by acquireDevice(), qualifiedMassSpectrum(), and spectrumListSize().