libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreaderbase.h>
Public Member Functions | |
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 bool | acquireDevice () override |
acquire data back end device | |
virtual Trace | getTicChromatogram () override |
get a TIC chromatogram | |
virtual std::vector< double > | getRetentionTimeLine () override |
retention timeline get retention times along the MSrun in seconds | |
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 | |
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MsRunReader (const MsRunIdCstSPtr &ms_run_id) | |
MsRunReader (const MsRunReader &other) | |
virtual | ~MsRunReader () |
const MsRunIdCstSPtr & | getMsRunId () const |
virtual MassSpectrumSPtr | massSpectrumSPtr (std::size_t spectrum_index)=0 |
get a MassSpectrumSPtr class given its spectrum index | |
virtual MassSpectrumCstSPtr | massSpectrumCstSPtr (std::size_t spectrum_index)=0 |
virtual QualifiedMassSpectrum | qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const =0 |
get a QualifiedMassSpectrum class given its scan number | |
virtual std::size_t | spectrumListSize () const =0 |
get the totat number of spectrum conained in the MSrun data file | |
virtual void | readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0 |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler | |
virtual void | readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0 |
virtual void | readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0 |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels | |
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 |
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 | |
Protected Attributes | |
TimsDataSp | msp_timsData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Friends | |
class | MsFileAccessor |
Definition at line 37 of file timsmsrunreaderbase.h.
pappso::TimsMsRunReaderBase::TimsMsRunReaderBase | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Default constructor
Definition at line 36 of file timsmsrunreaderbase.cpp.
References initialize().
pappso::TimsMsRunReaderBase::TimsMsRunReaderBase | ( | const TimsMsRunReaderBase & | msrun_reader_base | ) |
Definition at line 42 of file timsmsrunreaderbase.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.
Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.
Definition at line 75 of file timsmsrunreaderbase.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderDia, and pappso::TimsMsRunReaderMs2.
Definition at line 96 of file timsmsrunreaderbase.cpp.
References initialize(), and msp_timsData.
Referenced by pappso::TimsMsRunReaderDia::acquireDevice(), getTicChromatogram(), and getTimsDataSPtr().
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overridevirtual |
retention timeline get retention times along the MSrun in seconds
Reimplemented from pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2.
Definition at line 127 of file timsmsrunreaderbase.cpp.
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overridevirtual |
get a TIC chromatogram
for each retention time, computes the sum of all intensities. For IM-MS, combines the mobility spectra
Note that, formally, a TIC chromatogram is computed only for MS1 spectra.
Reimplemented from pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2.
Definition at line 114 of file timsmsrunreaderbase.cpp.
References acquireDevice(), and msp_timsData.
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virtual |
give an access to the underlying raw data pointer
Reimplemented in pappso::TimsMsRunReaderMs2.
Definition at line 106 of file timsmsrunreaderbase.cpp.
References acquireDevice(), and msp_timsData.
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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.
Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.
Definition at line 82 of file timsmsrunreaderbase.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.
Definition at line 58 of file timsmsrunreaderbase.cpp.
References pappso::MsRunReader::mcsp_msRunId, and msp_timsData.
Referenced by pappso::TimsMsRunReader::TimsMsRunReader(), pappso::TimsMsRunReader::TimsMsRunReader(), TimsMsRunReaderBase(), TimsMsRunReaderBase(), and acquireDevice().
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderDia.
Definition at line 145 of file timsmsrunreaderbase.cpp.
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overridevirtual |
get a xic coordinate object from a given spectrum index
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderDia.
Definition at line 134 of file timsmsrunreaderbase.cpp.
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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.
Reimplemented in pappso::TimsMsRunReaderMs2.
Definition at line 89 of file timsmsrunreaderbase.cpp.
References msp_timsData.
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friend |
Definition at line 39 of file timsmsrunreaderbase.h.
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protected |
Definition at line 84 of file timsmsrunreaderbase.h.
Referenced by pappso::TimsFramesMsRunReader::~TimsFramesMsRunReader(), ~TimsMsRunReaderBase(), acquireDevice(), pappso::TimsMsRunReaderDia::acquireDevice(), pappso::TimsFramesMsRunReader::computeTicChromatogram(), getTicChromatogram(), getTimsDataSPtr(), initialize(), pappso::TimsFramesMsRunReader::massSpectrumCstSPtr(), pappso::TimsMsRunReader::massSpectrumCstSPtr(), pappso::TimsFramesMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollectionByMsLevel(), releaseDevice(), pappso::TimsFramesMsRunReader::spectrumListSize(), and pappso::TimsMsRunReader::spectrumListSize().