pappso::SpectrumCollectionHandlerInterface Class Reference

interface to collect spectrums from the MsRunReader class More...

#include <spectrumcollectionhandlerinterface.h>

Inheritance diagram for pappso::SpectrumCollectionHandlerInterface:

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

Detailed Description

interface to collect spectrums from the MsRunReader class

Definition at line 55 of file spectrumcollectionhandlerinterface.h.

Member Function Documentation

isReadAhead()

bool pappso::SpectrumCollectionHandlerInterface::isReadAhead ( ) const

virtual

tells if we want to read ahead spectrum

Reimplemented in pappso::masschroq::PrecursorParser.

Definition at line 58 of file spectrumcollectionhandlerinterface.cpp.

{
  return m_isReadAhead;
}

References m_isReadAhead.

Referenced by needPeakList(), and pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection().

loadingEnded()

void pappso::SpectrumCollectionHandlerInterface::loadingEnded ( )

virtual

Reimplemented in pappso::MsRunSimpleStatistics, and pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints.

Definition at line 43 of file spectrumcollectionhandlerinterface.cpp.

{
}

Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), needPeakList(), 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().

needMsLevelPeakList()

bool pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList ( unsigned int ms_level ) const

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.

{
  if(needPeakList() == true)
    {
      if(ms_level < m_needPeakListByMsLevel.size())
        {
          return m_needPeakListByMsLevel[ms_level];
        }
      else
        return true;
    }
  else
    {
      return false;
    }
}

References m_needPeakListByMsLevel, and needPeakList().

Referenced by pappso::TimsDdaPrecursors::ms2ReaderGenerateMS1MS2Spectrum(), needPeakList(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), and pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection().

needPeakList()

virtual bool pappso::SpectrumCollectionHandlerInterface::needPeakList ( ) const

pure virtual

tells if we need the peak list (if we want the binary data) for each spectrum

Implemented in pappso::masschroq::PrecursorParser, pappso::MsRunQualifiedSpectrumLoader, pappso::MsRunReaderRetentionTimeLine, pappso::MsRunReaderScanNumberMultiMap, pappso::MsRunReaderTicChromatogram, pappso::MsRunSimpleStatistics, pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints, and pappso::MzxmlOutput::Translater.

References isReadAhead(), loadingEnded(), needMsLevelPeakList(), setNeedMsLevelPeakList(), setReadAhead(), shouldStop(), and spectrumListHasSize().

Referenced by needMsLevelPeakList(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel().

setNeedMsLevelPeakList()

void pappso::SpectrumCollectionHandlerInterface::setNeedMsLevelPeakList ( unsigned int ms_level, bool want_peak_list )

finalvirtual

tells if we need the peak list given

Definition at line 82 of file spectrumcollectionhandlerinterface.cpp.

{
  if(ms_level < m_needPeakListByMsLevel.size())
    {
      m_needPeakListByMsLevel[ms_level] = want_peak_list;
    }
}

References m_needPeakListByMsLevel.

Referenced by needPeakList(), pappso::MzxmlOutput::write(), and pappso::MzxmlOutput::write().

setQualifiedMassSpectrum()

virtual void pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum ( const QualifiedMassSpectrum & spectrum )

pure virtual

Implemented in pappso::masschroq::PrecursorParser, pappso::MsRunQualifiedSpectrumLoader, pappso::MsRunReaderRetentionTimeLine, pappso::MsRunReaderScanNumberMultiMap, pappso::MsRunReaderTicChromatogram, pappso::MsRunSimpleStatistics, pappso::MsRunXicExtractor::MsRunXicExtractorReadPoints, and pappso::MzxmlOutput::Translater.

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().

setReadAhead()

void pappso::SpectrumCollectionHandlerInterface::setReadAhead ( bool is_read_ahead )

finalvirtual

use threads to read a spectrum by batch of batch_size

Parameters

is_read_ahead

boolean to use threads or not

Definition at line 52 of file spectrumcollectionhandlerinterface.cpp.

{
  m_isReadAhead = is_read_ahead;
}

References m_isReadAhead.

Referenced by needPeakList(), pappso::MzxmlOutput::write(), and pappso::MzxmlOutput::write().

shouldStop()

bool pappso::SpectrumCollectionHandlerInterface::shouldStop ( )

virtual

Definition at line 38 of file spectrumcollectionhandlerinterface.cpp.

{
  return false;
}

Referenced by pappso::TimsDdaPrecursors::ms2ReaderSpectrumCollectionByMsLevel(), needPeakList(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

spectrumListHasSize()

void pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize ( std::size_t size )

virtual

Reimplemented in pappso::MsRunQualifiedSpectrumLoader.

Definition at line 47 of file spectrumcollectionhandlerinterface.cpp.

{
}

Referenced by needPeakList(), pappso::TimsDdaPrecursors::rawReaderSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2Selected::readSpectrumCollection(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel(), and pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

Member Data Documentation

m_isReadAhead

bool pappso::SpectrumCollectionHandlerInterface::m_isReadAhead = false

private

Definition at line 90 of file spectrumcollectionhandlerinterface.h.

Referenced by isReadAhead(), and setReadAhead().

m_needPeakListByMsLevel

std::vector<bool> pappso::SpectrumCollectionHandlerInterface::m_needPeakListByMsLevel

private

Initial value:

= {true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true}

Definition at line 92 of file spectrumcollectionhandlerinterface.h.

                                            {true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true,
                                               true};

Referenced by needMsLevelPeakList(), and setNeedMsLevelPeakList().

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The documentation for this class was generated from the following files:

• pappsomspp/core/msrun/spectrumcollectionhandlerinterface.h
• pappsomspp/core/msrun/spectrumcollectionhandlerinterface.cpp