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... | |
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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... | |
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 185 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 720 of file pwizmsrunreader.cpp.
References pappso::QualifiedMassSpectrum::getMassSpectrumCstSPtr(), and qualifiedMassSpectrum().
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protected |
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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 908 of file pwizmsrunreader.cpp.
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overrideprotectedvirtual |
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overridevirtual |
Implements pappso::MsRunReader.
Definition at line 742 of file pwizmsrunreader.cpp.
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overridevirtual |
get a MassSpectrumSPtr class given its spectrum index
Implements pappso::MsRunReader.
Definition at line 735 of file pwizmsrunreader.cpp.
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overridevirtual |
get a QualifiedMassSpectrum class given its scan number
Implements pappso::MsRunReader.
Definition at line 749 of file pwizmsrunreader.cpp.
Referenced by accept().
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protected |
Definition at line 666 of file pwizmsrunreader.cpp.
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protected |
Definition at line 236 of file pwizmsrunreader.cpp.
References pappso::MsRunReader::mcsp_msRunId, pappso::MGF, and msp_msData.
Referenced by 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 775 of file pwizmsrunreader.cpp.
References getPwizSpectrumPtr(), pappso::MsRunReader::mcsp_msRunId, qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), and pappso::SpectrumCollectionHandlerInterface::shouldStop().
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overridevirtual |
get the totat number of spectrum conained in the MSrun data file
Implements pappso::MsRunReader.
Definition at line 902 of file pwizmsrunreader.cpp.
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friend |
Definition at line 89 of file pwizmsrunreader.h.
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private |
Definition at line 132 of file pwizmsrunreader.h.
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protected |
Definition at line 112 of file pwizmsrunreader.h.
Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().