libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreaderms2selected.h>
Public Member Functions | |
TimsMsRunReaderMs2Selected (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~TimsMsRunReaderMs2Selected () |
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 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... | |
void | setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter) |
void | setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter) |
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TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~TimsMsRunReaderMs2 () |
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 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... | |
void | setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter) |
void | setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter) |
void | setMs2BuiltinCentroid (bool centroid) |
enable or disable simple centroid filter on raw tims data for MS2 More... | |
virtual std::vector< std::size_t > | getPrecursorsIDFromMzRt (int charge, double mz_val, double rt_sec, double k0) |
Get all the precursors id which match the values. 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... | |
virtual std::vector< double > | getRetentionTimeLine () override |
retention timeline get retention times along the MSrun in seconds More... | |
virtual Trace | getTicChromatogram () override |
get a TIC chromatogram 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... | |
void | setMonoThread (bool is_mono_thread) |
set only one is_mono_thread to true More... | |
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 More... | |
Private Attributes | |
TimsData * | mpa_timsData = nullptr |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 41 of file timsmsrunreaderms2selected.h.
TimsMsRunReaderMs2Selected::TimsMsRunReaderMs2Selected | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 37 of file timsmsrunreaderms2selected.cpp.
References initialize().
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virtual |
Definition at line 44 of file timsmsrunreaderms2selected.cpp.
References mpa_timsData.
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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
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 91 of file timsmsrunreaderms2selected.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::TimsMsRunReaderMs2.
Definition at line 316 of file timsmsrunreaderms2selected.cpp.
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overrideprotectedvirtual |
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 53 of file timsmsrunreaderms2selected.cpp.
Referenced by TimsMsRunReaderMs2Selected().
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overridevirtual |
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 108 of file timsmsrunreaderms2selected.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 99 of file timsmsrunreaderms2selected.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 117 of file timsmsrunreaderms2selected.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), pappso::TimsData::getSpectrumDescrWithPrecursorId(), mpa_timsData, and pappso::TimsData::SpectrumDescr::ms2_index.
Referenced by massSpectrumCstSPtr(), massSpectrumSPtr(), and readSpectrumCollection().
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overridevirtual |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 163 of file timsmsrunreaderms2selected.cpp.
References pappso::SpectrumCollectionHandlerInterface::isReadAhead(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().
void TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 75 of file timsmsrunreaderms2selected.cpp.
References mpa_timsData, and pappso::TimsData::setMs1FilterCstSPtr().
void TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 59 of file timsmsrunreaderms2selected.cpp.
References mpa_timsData, and pappso::TimsData::setMs2FilterCstSPtr().
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Reimplemented from pappso::TimsMsRunReaderMs2.
Definition at line 309 of file timsmsrunreaderms2selected.cpp.
References pappso::TimsData::getTotalNumberOfPrecursors(), and mpa_timsData.
Referenced by readSpectrumCollection().
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friend |
Definition at line 43 of file timsmsrunreaderms2selected.h.
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private |
Definition at line 75 of file timsmsrunreaderms2selected.h.
Referenced by ~TimsMsRunReaderMs2Selected(), qualifiedMassSpectrum(), setMs1FilterCstSPtr(), setMs2FilterCstSPtr(), and spectrumListSize().