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 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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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 | |
TimsData * | mpa_timsData = nullptr |
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 | ) |
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virtual |
Definition at line 43 of file timsmsrunreaderms2.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
Implements pappso::MsRunReader.
Definition at line 88 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.
Definition at line 282 of file timsmsrunreaderms2.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 52 of file timsmsrunreaderms2.cpp.
Referenced by TimsMsRunReaderMs2().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 105 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.
Definition at line 96 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.
Definition at line 114 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MsRunReader::getMsRunId(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), mpa_timsData, pappso::QualifiedMassSpectrum::setMassSpectrumId(), and pappso::MassSpectrumId::setMsRunId().
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
Implements pappso::MsRunReader.
Definition at line 153 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().
void TimsMsRunReaderMs2::setMs1FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 73 of file timsmsrunreaderms2.cpp.
References mpa_timsData, and pappso::TimsData::setMs1FilterCstSPtr().
void TimsMsRunReaderMs2::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 58 of file timsmsrunreaderms2.cpp.
References mpa_timsData, and pappso::TimsData::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.
Definition at line 275 of file timsmsrunreaderms2.cpp.
References pappso::TimsData::getTotalNumberOfPrecursors(), and mpa_timsData.
Referenced by readSpectrumCollection().
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friend |
Definition at line 42 of file timsmsrunreaderms2.h.
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private |
Definition at line 74 of file timsmsrunreaderms2.h.
Referenced by ~TimsMsRunReaderMs2(), qualifiedMassSpectrum(), setMs1FilterCstSPtr(), setMs2FilterCstSPtr(), and spectrumListSize().