libpappsomspp
Library for mass spectrometry
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#include <timsmsrunreaderms2.h>
Public Member Functions | |
TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~TimsMsRunReaderMs2 () |
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 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) |
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... | |
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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... | |
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 |
pappso::FilterInterfaceCstSPtr | msp_ms1Filter |
pappso::FilterInterfaceCstSPtr | msp_ms2Filter |
bool | m_builtinMs2Centroid = true |
enable builtin centroid on raw tims integers by default More... | |
Friends | |
class | MsFileAccessor |
Additional Inherited Members | |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Definition at line 40 of file timsmsrunreaderms2.h.
TimsMsRunReaderMs2::TimsMsRunReaderMs2 | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 37 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
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 113 of file timsmsrunreaderms2.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 329 of file timsmsrunreaderms2.cpp.
References initialize(), m_builtinMs2Centroid, msp_ms1Filter, msp_ms2Filter, and msp_timsData.
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Get all the precursors id which match the values.
Definition at line 342 of file timsmsrunreaderms2.cpp.
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give an access to the underlying raw data pointer
Definition at line 351 of file timsmsrunreaderms2.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.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 315 of file timsmsrunreaderms2.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 52 of file timsmsrunreaderms2.cpp.
Referenced by TimsMsRunReaderMs2(), and acquireDevice().
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overridevirtual |
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 130 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 121 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 139 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MsRunReader::getMsRunId(), msp_timsData, pappso::QualifiedMassSpectrum::setMassSpectrumId(), and pappso::MassSpectrumId::setMsRunId().
Referenced by massSpectrumCstSPtr(), massSpectrumSPtr(), and readSpectrumCollectionByMsLevel().
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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 178 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 185 of file timsmsrunreaderms2.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().
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 322 of file timsmsrunreaderms2.cpp.
References msp_timsData.
void TimsMsRunReaderMs2::setMs1FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
void TimsMsRunReaderMs2::setMs2BuiltinCentroid | ( | bool | centroid | ) |
enable or disable simple centroid filter on raw tims data for MS2
Definition at line 65 of file timsmsrunreaderms2.cpp.
References m_builtinMs2Centroid, and msp_timsData.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void TimsMsRunReaderMs2::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 81 of file timsmsrunreaderms2.cpp.
References msp_ms2Filter, and msp_timsData.
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 308 of file timsmsrunreaderms2.cpp.
References msp_timsData.
Referenced by readSpectrumCollectionByMsLevel().
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friend |
Definition at line 42 of file timsmsrunreaderms2.h.
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private |
enable builtin centroid on raw tims integers by default
Definition at line 104 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2BuiltinCentroid().
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private |
Definition at line 100 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs1FilterCstSPtr().
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private |
Definition at line 101 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2FilterCstSPtr().
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private |
Definition at line 98 of file timsmsrunreaderms2.h.
Referenced by ~TimsMsRunReaderMs2(), acquireDevice(), qualifiedMassSpectrum(), releaseDevice(), setMs1FilterCstSPtr(), setMs2BuiltinCentroid(), setMs2FilterCstSPtr(), and spectrumListSize().