libpappsomspp
Library for mass spectrometry
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interface to collect spectrums from the MsRunReader class More...
#include <spectrumcollectionhandlerinterface.h>
Public Member Functions | |
virtual void | setQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum)=0 |
virtual bool | needPeakList () const =0 |
tells if we need the peak list (if we want the binary data) for each spectrum | |
virtual bool | needMsLevelPeakList (unsigned int ms_level) const final |
tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level | |
virtual void | setNeedMsLevelPeakList (unsigned int ms_level, bool want_peak_list) final |
tells if we need the peak list given | |
virtual bool | shouldStop () |
virtual void | loadingEnded () |
virtual void | spectrumListHasSize (std::size_t size) |
virtual void | setReadAhead (bool is_read_ahead) final |
use threads to read a spectrum by batch of batch_size | |
virtual bool | isReadAhead () const |
tells if we want to read ahead spectrum | |
Private Attributes | |
bool | m_isReadAhead = false |
std::vector< bool > | m_needPeakListByMsLevel |
interface to collect spectrums from the MsRunReader class
Definition at line 55 of file spectrumcollectionhandlerinterface.h.
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virtual |
tells if we want to read ahead spectrum
Definition at line 58 of file spectrumcollectionhandlerinterface.cpp.
References m_isReadAhead.
Referenced by pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection().
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virtual |
Reimplemented in pappso::MsRunSimpleStatistics, and pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints.
Definition at line 43 of file spectrumcollectionhandlerinterface.cpp.
Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::XyMsRunReader::readSpectrumCollection(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::TimsMsRunReader::readSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel(), pappso::XyMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().
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finalvirtual |
tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level
Definition at line 64 of file spectrumcollectionhandlerinterface.cpp.
References m_needPeakListByMsLevel, and needPeakList().
Referenced by pappso::TimsDdaPrecursors::ms2ReaderGenerateMS1MS2Spectrum(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), and pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection().
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pure virtual |
tells if we need the peak list (if we want the binary data) for each spectrum
Implemented in pappso::MzxmlOutput::Translater, pappso::MsRunSimpleStatistics, pappso::MsRunReaderScanNumberMultiMap, pappso::MsRunReaderRetentionTimeLine, pappso::MsRunReaderTicChromatogram, pappso::MsRunQualifiedSpectrumLoader, and pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints.
Referenced by needMsLevelPeakList(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel().
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finalvirtual |
tells if we need the peak list given
Definition at line 82 of file spectrumcollectionhandlerinterface.cpp.
References m_needPeakListByMsLevel.
Referenced by pappso::MzxmlOutput::write(), and pappso::MzxmlOutput::write().
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pure virtual |
Implemented in pappso::MsRunReaderTicChromatogram, pappso::MsRunQualifiedSpectrumLoader, pappso::MzxmlOutput::Translater, pappso::MsRunSimpleStatistics, pappso::MsRunReaderScanNumberMultiMap, pappso::MsRunReaderRetentionTimeLine, and pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints.
Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::XyMsRunReader::readSpectrumCollection(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::XyMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().
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finalvirtual |
use threads to read a spectrum by batch of batch_size
is_read_ahead | boolean to use threads or not |
Definition at line 52 of file spectrumcollectionhandlerinterface.cpp.
References m_isReadAhead.
Referenced by pappso::MzxmlOutput::write(), and pappso::MzxmlOutput::write().
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virtual |
Definition at line 38 of file spectrumcollectionhandlerinterface.cpp.
Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().
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virtual |
Reimplemented in pappso::MsRunQualifiedSpectrumLoader.
Definition at line 47 of file spectrumcollectionhandlerinterface.cpp.
Referenced by pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().
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private |
Definition at line 90 of file spectrumcollectionhandlerinterface.h.
Referenced by isReadAhead(), and setReadAhead().
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private |
Definition at line 92 of file spectrumcollectionhandlerinterface.h.
Referenced by needMsLevelPeakList(), and setNeedMsLevelPeakList().