libpappsomspp
Library for mass spectrometry
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#include <pwizmsrunreader.h>
Public Member Functions | |
PwizMsRunReader (MsRunIdCstSPtr &msrun_id_csp) | |
virtual | ~PwizMsRunReader () |
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... | |
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... | |
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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... | |
bool | processRetentionTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const |
bool | processDriftTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const |
QualifiedMassSpectrum | qualifiedMassSpectrumFromPwizMSData (std::size_t spectrum_index, bool want_binary_data, bool &ok) const |
QualifiedMassSpectrum | qualifiedMassSpectrumFromPwizSpectrumPtr (const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const |
pwiz::msdata::SpectrumPtr | getPwizSpectrumPtr (pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const |
Protected Attributes | |
pwiz::msdata::MSDataPtr | msp_msData = nullptr |
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MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Private Attributes | |
bool | m_hasScanNumbers = false |
Friends | |
class | MsFileAccessor |
Definition at line 66 of file pwizmsrunreader.h.
pappso::PwizMsRunReader::PwizMsRunReader | ( | MsRunIdCstSPtr & | msrun_id_csp | ) |
Definition at line 74 of file pwizmsrunreader.cpp.
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virtual |
Definition at line 192 of file pwizmsrunreader.cpp.
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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 753 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), and qualifiedMassSpectrum().
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overridevirtual |
acquire data back end device
Implements pappso::MsRunReader.
Definition at line 956 of file pwizmsrunreader.cpp.
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protected |
Definition at line 198 of file pwizmsrunreader.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 943 of file pwizmsrunreader.cpp.
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overrideprotectedvirtual |
Implements pappso::MsRunReader.
Definition at line 86 of file pwizmsrunreader.cpp.
Referenced by spectrumListSize().
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 775 of file pwizmsrunreader.cpp.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 768 of file pwizmsrunreader.cpp.
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protected |
Definition at line 311 of file pwizmsrunreader.cpp.
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protected |
Definition at line 243 of file pwizmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 782 of file pwizmsrunreader.cpp.
Referenced by accept().
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protected |
Definition at line 699 of file pwizmsrunreader.cpp.
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protected |
Definition at line 379 of file pwizmsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, pappso::MGF, and msp_msData.
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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 808 of file pwizmsrunreader.cpp.
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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 949 of file pwizmsrunreader.cpp.
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 937 of file pwizmsrunreader.cpp.
References initialize().
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friend |
Definition at line 89 of file pwizmsrunreader.h.
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private |
Definition at line 142 of file pwizmsrunreader.h.
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protected |
Definition at line 116 of file pwizmsrunreader.h.
Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().