libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreaderms2.h>
Public Member Functions | |
TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReaderMs2 (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReaderMs2 () |
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 | 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 | |
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 | |
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. | |
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 TimsDataSp | getTimsDataSPtr () |
give an access to the underlying raw data pointer | |
virtual std::vector< double > | getRetentionTimeLine () override |
retention timeline get retention times along the MSrun in seconds | |
virtual Trace | getTicChromatogram () override |
get a TIC chromatogram | |
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TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp) | |
TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base) | |
virtual | ~TimsMsRunReaderBase () |
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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 |
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 | |
TimsDdaPrecursors * | mp_timsDdaPrecursors = nullptr |
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TimsDataSp | msp_timsData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Private Attributes | |
TimsDataSp | msp_timsData = nullptr |
pappso::FilterInterfaceCstSPtr | msp_ms1Filter |
pappso::FilterInterfaceCstSPtr | msp_ms2Filter |
bool | m_builtinMs2Centroid = true |
enable builtin centroid on raw tims integers by default | |
Friends | |
class | MsFileAccessor |
Definition at line 38 of file timsmsrunreaderms2.h.
TimsMsRunReaderMs2::TimsMsRunReaderMs2 | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 38 of file timsmsrunreaderms2.cpp.
References initialize().
TimsMsRunReaderMs2::TimsMsRunReaderMs2 | ( | const TimsMsRunReaderBase & | msrun_reader_base | ) |
Definition at line 44 of file timsmsrunreaderms2.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
Reimplemented from pappso::TimsMsRunReaderBase.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 125 of file timsmsrunreaderms2.cpp.
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overridevirtual |
acquire data back end device
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 275 of file timsmsrunreaderms2.cpp.
References initialize(), m_builtinMs2Centroid, mp_timsDdaPrecursors, msp_ms1Filter, msp_ms2Filter, msp_timsData, pappso::TimsDdaPrecursors::setMs1FilterCstSPtr(), pappso::TimsDdaPrecursors::setMs2BuiltinCentroid(), and pappso::TimsDdaPrecursors::setMs2FilterCstSPtr().
Referenced by getTicChromatogram().
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Get all the precursors id which match the values.
Definition at line 288 of file timsmsrunreaderms2.cpp.
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overridevirtual |
retention timeline get retention times along the MSrun in seconds
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 334 of file timsmsrunreaderms2.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::TimsMsRunReaderBase.
Definition at line 340 of file timsmsrunreaderms2.cpp.
References acquireDevice(), and msp_timsData.
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give an access to the underlying raw data pointer
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 298 of file timsmsrunreaderms2.cpp.
Referenced by pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().
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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::TimsMsRunReaderBase.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 261 of file timsmsrunreaderms2.cpp.
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overrideprotectedvirtual |
Reimplemented from pappso::TimsMsRunReaderBase.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 59 of file timsmsrunreaderms2.cpp.
Referenced by TimsMsRunReaderMs2(), TimsMsRunReaderMs2(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 142 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 133 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a xic coordinate object from a given spectrum
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 325 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getSpectrumIndex(), and newXicCoordSPtrFromSpectrumIndex().
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overridevirtual |
get a xic coordinate object from a given spectrum index
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 306 of file timsmsrunreaderms2.cpp.
References msp_timsData.
Referenced by newXicCoordSPtrFromQualifiedMassSpectrum().
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 151 of file timsmsrunreaderms2.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::TimsDdaPrecursors::getQualifiedMs1MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), pappso::TimsDdaPrecursors::getSpectrumDescrWithPrecursorId(), mp_timsDdaPrecursors, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, and pappso::PappsoException::qwhat().
Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().
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overridevirtual |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 211 of file timsmsrunreaderms2.cpp.
References readSpectrumCollectionByMsLevel().
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overridevirtual |
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 218 of file timsmsrunreaderms2.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 226 of file timsmsrunreaderms2.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::MsRunReader::isMonoThread(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), mp_timsDdaPrecursors, pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), pappso::TimsDdaPrecursors::setMonoThread(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().
Referenced by readSpectrumCollection(), and readSpectrumCollection2().
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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
Reimplemented from pappso::TimsMsRunReaderBase.
Definition at line 268 of file timsmsrunreaderms2.cpp.
References msp_timsData.
void TimsMsRunReaderMs2::setMs1FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 109 of file timsmsrunreaderms2.cpp.
References mp_timsDdaPrecursors, msp_ms1Filter, and pappso::TimsDdaPrecursors::setMs1FilterCstSPtr().
void TimsMsRunReaderMs2::setMs2BuiltinCentroid | ( | bool | centroid | ) |
enable or disable simple centroid filter on raw tims data for MS2
Definition at line 77 of file timsmsrunreaderms2.cpp.
References m_builtinMs2Centroid, mp_timsDdaPrecursors, and pappso::TimsDdaPrecursors::setMs2BuiltinCentroid().
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void TimsMsRunReaderMs2::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 93 of file timsmsrunreaderms2.cpp.
References mp_timsDdaPrecursors, msp_ms2Filter, and pappso::TimsDdaPrecursors::setMs2FilterCstSPtr().
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 254 of file timsmsrunreaderms2.cpp.
References pappso::TimsDdaPrecursors::getTotalPrecursorCount(), and mp_timsDdaPrecursors.
Referenced by readSpectrumCollectionByMsLevel().
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Definition at line 40 of file timsmsrunreaderms2.h.
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private |
enable builtin centroid on raw tims integers by default
Definition at line 124 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2BuiltinCentroid().
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protected |
Definition at line 115 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum(), readSpectrumCollectionByMsLevel(), setMs1FilterCstSPtr(), pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr(), setMs2BuiltinCentroid(), setMs2FilterCstSPtr(), pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr(), spectrumListSize(), and pappso::TimsMsRunReaderMs2Selected::spectrumListSize().
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Definition at line 120 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs1FilterCstSPtr().
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Definition at line 121 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2FilterCstSPtr().
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private |
Definition at line 118 of file timsmsrunreaderms2.h.
Referenced by ~TimsMsRunReaderMs2(), acquireDevice(), getTicChromatogram(), newXicCoordSPtrFromSpectrumIndex(), and releaseDevice().