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 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... | |
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... | |
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 | |
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 39 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 114 of file timsmsrunreaderms2.cpp.
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 256 of file timsmsrunreaderms2.cpp.
References initialize(), m_builtinMs2Centroid, msp_ms1Filter, msp_ms2Filter, and msp_timsData.
Referenced by getTicChromatogram().
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Get all the precursors id which match the values.
Definition at line 269 of file timsmsrunreaderms2.cpp.
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overridevirtual |
retention timeline get retention times along the MSrun in seconds
Reimplemented from pappso::MsRunReader.
Definition at line 313 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::MsRunReader.
Definition at line 319 of file timsmsrunreaderms2.cpp.
References acquireDevice(), and msp_timsData.
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give an access to the underlying raw data pointer
Definition at line 278 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::MsRunReader.
Reimplemented in pappso::TimsMsRunReaderMs2Selected.
Definition at line 242 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 131 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 122 of file timsmsrunreaderms2.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
get a xic coordinate object from a given spectrum
Implements pappso::MsRunReader.
Definition at line 304 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
Implements pappso::MsRunReader.
Definition at line 286 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 140 of file timsmsrunreaderms2.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::TimsData::SpectrumDescr::ms2_index, msp_timsData, 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 200 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 207 of file timsmsrunreaderms2.cpp.
References pappso::MsRunReader::getMsRunId(), pappso::MsRunReader::isMonoThread(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), msp_timsData, 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 249 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 66 of file timsmsrunreaderms2.cpp.
References m_builtinMs2Centroid, and msp_timsData.
Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().
void TimsMsRunReaderMs2::setMs2FilterCstSPtr | ( | pappso::FilterInterfaceCstSPtr | filter | ) |
Definition at line 82 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 235 of file timsmsrunreaderms2.cpp.
References msp_timsData.
Referenced by readSpectrumCollectionByMsLevel().
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friend |
Definition at line 41 of file timsmsrunreaderms2.h.
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private |
enable builtin centroid on raw tims integers by default
Definition at line 120 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2BuiltinCentroid().
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private |
Definition at line 116 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs1FilterCstSPtr().
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private |
Definition at line 117 of file timsmsrunreaderms2.h.
Referenced by acquireDevice(), and setMs2FilterCstSPtr().
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private |
Definition at line 114 of file timsmsrunreaderms2.h.
Referenced by ~TimsMsRunReaderMs2(), acquireDevice(), getTicChromatogram(), newXicCoordSPtrFromSpectrumIndex(), qualifiedMassSpectrum(), readSpectrumCollectionByMsLevel(), releaseDevice(), setMs1FilterCstSPtr(), setMs2BuiltinCentroid(), setMs2FilterCstSPtr(), and spectrumListSize().