libpappsomspp
Library for mass spectrometry
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base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...
#include <msrunreader.h>
Public Member Functions | |
MsRunReader (MsRunIdCstSPtr &ms_run_id) | |
MsRunReader (const MsRunReader &other) | |
virtual | ~MsRunReader () |
const MsRunIdCstSPtr & | getMsRunId () const |
virtual MassSpectrumSPtr | massSpectrumSPtr (std::size_t spectrum_index)=0 |
get a MassSpectrumSPtr class given its spectrum index More... | |
virtual MassSpectrumCstSPtr | massSpectrumCstSPtr (std::size_t spectrum_index)=0 |
virtual QualifiedMassSpectrum | qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const =0 |
get a QualifiedMassSpectrum class given its scan number More... | |
virtual std::size_t | spectrumListSize () const =0 |
get the totat number of spectrum conained in the MSrun data file More... | |
virtual void | readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0 |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More... | |
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... | |
virtual bool | hasScanNumbers () const |
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 ()=0 |
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 ()=0 |
acquire data back end device More... | |
Protected Member Functions | |
virtual void | initialize ()=0 |
virtual bool | accept (const QString &file_name) const =0 |
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... | |
Protected Attributes | |
MsRunIdCstSPtr | mcsp_msRunId |
MsRunReaderScanNumberMultiMap * | mpa_multiMapScanNumber = nullptr |
Friends | |
class | MsFileAccessor |
base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory
Definition at line 178 of file msrunreader.h.
pappso::MsRunReader::MsRunReader | ( | MsRunIdCstSPtr & | ms_run_id | ) |
Definition at line 220 of file msrunreader.cpp.
pappso::MsRunReader::MsRunReader | ( | const MsRunReader & | other | ) |
Definition at line 224 of file msrunreader.cpp.
References mpa_multiMapScanNumber.
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virtual |
Definition at line 238 of file msrunreader.cpp.
References mpa_multiMapScanNumber.
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protectedpure virtual |
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
Implemented in pappso::TimsMsRunReaderMs2, pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
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pure virtual |
acquire data back end device
Implemented in pappso::TimsMsRunReaderMs2, pappso::PwizMsRunReader, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
const MsRunIdCstSPtr & pappso::MsRunReader::getMsRunId | ( | ) | const |
Definition at line 232 of file msrunreader.cpp.
References mcsp_msRunId.
Referenced by pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum(), and pappso::MzxmlOutput::writeHeader().
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virtual |
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 in pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReader.
Definition at line 277 of file msrunreader.cpp.
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protectedpure virtual |
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pure virtual |
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pure virtual |
get a MassSpectrumSPtr class given its spectrum index
Implemented in pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
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pure virtual |
get a QualifiedMassSpectrum class given its scan number
Implemented in pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
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pure virtual |
function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
Implemented in pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
Referenced by scanNumber2SpectrumIndex(), and pappso::MzxmlOutput::write().
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pure virtual |
release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object
Implemented in pappso::TimsMsRunReaderMs2, pappso::PwizMsRunReader, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
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virtual |
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.
Definition at line 246 of file msrunreader.cpp.
References pappso::MsRunReaderScanNumberMultiMap::getSpectrumIndexFromScanNumber(), mcsp_msRunId, mpa_multiMapScanNumber, pappso::PappsoException::qwhat(), and readSpectrumCollection().
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pure virtual |
get the totat number of spectrum conained in the MSrun data file
Implemented in pappso::PwizMsRunReader, pappso::TimsMsRunReaderMs2Selected, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReader, and pappso::XyMsRunReader.
Referenced by pappso::MzxmlOutput::writeHeader().
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friend |
Definition at line 181 of file msrunreader.h.
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protected |
Definition at line 241 of file msrunreader.h.
Referenced by getMsRunId(), pappso::XyMsRunReader::initialize(), pappso::XyMsRunReader::qualifiedMassSpectrum(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::XyMsRunReader::readSpectrumCollection(), and scanNumber2SpectrumIndex().
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protected |
Definition at line 242 of file msrunreader.h.
Referenced by MsRunReader(), scanNumber2SpectrumIndex(), and ~MsRunReader().