pappso::masschroq::PrecursorParser Class Reference

#include <precursorparser.h>

Inheritance diagram for pappso::masschroq::PrecursorParser:

Public Member Functions
	PrecursorParser (pappso::MsRunReaderCstSPtr msrun_reader)
virtual	~PrecursorParser ()
virtual void	setQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &qspectrum) override
virtual bool	needPeakList () const override
	tells if we need the peak list (if we want the binary data) for each spectrum
virtual bool	isReadAhead () const override
	tells if we want to read ahead spectrum
const PrecursorSp &	getPrecursorSPtrBySpectrumIndex (std::size_t spectrum_index) const
const PrecursorSp &	getPrecursorSPtrByScanNumber (std::size_t spectrum_index) const
Public Member Functions inherited from pappso::SpectrumCollectionHandlerInterface
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

Private Member Functions
void	mapScanNumberPrecursor (std::size_t scan_num, PrecursorSp precursor)
	map precursor to its scan number as parsed in the xml file of this msrun
void	mapSpectrumIndexToPrecursor (std::size_t spectrum_index, PrecursorSp precursor)
	map spectrum index to precursor new modern method to replace obsolete scan number

Private Attributes
pappso::MsRunReaderCstSPtr	msp_msrunReader
std::map< std::size_t, PrecursorSp >	m_scanNumber2PrecursorMap
std::map< std::size_t, PrecursorSp >	m_spectrumIndex2PrecursorMap

Detailed Description

Todo

write docs

Definition at line 40 of file precursorparser.h.

Constructor & Destructor Documentation

PrecursorParser()

pappso::masschroq::PrecursorParser::PrecursorParser

(

pappso::MsRunReaderCstSPtr

msrun_reader

)

Definition at line 35 of file precursorparser.cpp.

{
  msp_msrunReader = msrun_reader;
}

References msp_msrunReader.

~PrecursorParser()

pappso::masschroq::PrecursorParser::~PrecursorParser ( )

virtual

Definition at line 41 of file precursorparser.cpp.

{
}

Member Function Documentation

getPrecursorSPtrByScanNumber()

const pappso::masschroq::PrecursorSp & pappso::masschroq::PrecursorParser::getPrecursorSPtrByScanNumber

(

std::size_t

spectrum_index

)

const

Definition at line 160 of file precursorparser.cpp.

{
  auto it = m_scanNumber2PrecursorMap.find(spectrum_index);
  if(it != m_scanNumber2PrecursorMap.end())
    {
    }
  else
    {
      throw pappso::PappsoException(QObject::tr("scan number %1 not found in %2")
                                      .arg(spectrum_index)
                                      .arg(msp_msrunReader.get()->getMsRunId()->getXmlId()));
    }
  return it->second;
}

References m_scanNumber2PrecursorMap, and msp_msrunReader.

getPrecursorSPtrBySpectrumIndex()

const pappso::masschroq::PrecursorSp & pappso::masschroq::PrecursorParser::getPrecursorSPtrBySpectrumIndex

(

std::size_t

spectrum_index

)

const

Definition at line 143 of file precursorparser.cpp.

{
  auto it = m_spectrumIndex2PrecursorMap.find(spectrum_index);
  if(it != m_spectrumIndex2PrecursorMap.end())
    {
    }
  else
    {
      throw pappso::PappsoException(QObject::tr("spectrum index %1 not found in %2")
                                      .arg(spectrum_index)
                                      .arg(msp_msrunReader.get()->getMsRunId()->getXmlId()));
    }
  return it->second;
}

References m_spectrumIndex2PrecursorMap, and msp_msrunReader.

isReadAhead()

bool pappso::masschroq::PrecursorParser::isReadAhead ( ) const

overridevirtual

tells if we want to read ahead spectrum

Reimplemented from pappso::SpectrumCollectionHandlerInterface.

Definition at line 105 of file precursorparser.cpp.

{
  return true;
}

mapScanNumberPrecursor()

void pappso::masschroq::PrecursorParser::mapScanNumberPrecursor ( std::size_t scan_num, PrecursorSp precursor )

private

map precursor to its scan number as parsed in the xml file of this msrun

Definition at line 111 of file precursorparser.cpp.

{
 
  if(precursor.get()->getXicCoordSPtr().get() == nullptr)
    {
      throw pappso::PappsoException(
        QObject::tr("precursor.get()->getXicCoordSPtr().get() == nullptr scan_num=%1\n")
          .arg(scan_num));
    }
  m_scanNumber2PrecursorMap[scan_num] = precursor;
}

References pappso::masschroq::Precursor::getXicCoordSPtr(), and m_scanNumber2PrecursorMap.

Referenced by setQualifiedMassSpectrum().

mapSpectrumIndexToPrecursor()

void pappso::masschroq::PrecursorParser::mapSpectrumIndexToPrecursor ( std::size_t spectrum_index, PrecursorSp precursor )

private

map spectrum index to precursor new modern method to replace obsolete scan number

Definition at line 125 of file precursorparser.cpp.

{
 
  qDebug() << " spectrum_index=" << spectrum_index;
 
  if(precursor.get()->getXicCoordSPtr().get() == nullptr)
    {
      throw pappso::PappsoException(
        QObject::tr("precursor.get()->getXicCoordSPtr().get() == nullptr \n")
          .arg(msp_msrunReader.get()->getMsRunId()->getXmlId())
          .arg(spectrum_index));
    }
  m_spectrumIndex2PrecursorMap[spectrum_index] = precursor;
  qDebug() << " spectrum_index=" << spectrum_index;
}

References pappso::masschroq::Precursor::getXicCoordSPtr(), m_spectrumIndex2PrecursorMap, and msp_msrunReader.

Referenced by setQualifiedMassSpectrum().

needPeakList()

bool pappso::masschroq::PrecursorParser::needPeakList ( ) const

overridevirtual

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

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 46 of file precursorparser.cpp.

{
  return false;
}

setQualifiedMassSpectrum()

void pappso::masschroq::PrecursorParser::setQualifiedMassSpectrum ( const pappso::QualifiedMassSpectrum & qspectrum )

overridevirtual

adding this new precursor to the msrun's hash map of scan_num -> precursor

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 51 of file precursorparser.cpp.

{
 
  if(qspectrum.getMsLevel() > 1)
    {
 
      pappso::masschroq::PrecursorSp precursor = std::make_shared<pappso::masschroq::Precursor>(
        qspectrum.getPrecursorSpectrumIndex(),
        qspectrum.getPrecursorMz(),
        qspectrum.getPrecursorIntensity(),
        msp_msrunReader.get()->newXicCoordSPtrFromQualifiedMassSpectrum(
          qspectrum, pappso::PrecisionFactory::getPpmInstance(10)));
 
 
      qDebug() << " native_id=" << qspectrum.getMassSpectrumId().getNativeId()
               << " scan idx=" << qspectrum.getMassSpectrumId().getSpectrumIndex()
               << " precursor_idx=" << qspectrum.getPrecursorSpectrumIndex()
               << " precursor.get()->getXicCoordSPtr().get()->toString="
               << precursor.get()->getXicCoordSPtr().get()->toString();
      if(precursor.get()->getXicCoordSPtr().get() == nullptr)
        {
          throw pappso::PappsoException(QObject::tr("precursor.get()->getXicCoordSPtr().get() == "
                                                    "nullptr\nindex=%1 %2 %3 %4")
                                          .arg(qspectrum.getMassSpectrumId().getNativeId())
                                          .arg(__FILE__)
                                          .arg(__FUNCTION__)
                                          .arg(__LINE__));
        }
      /// adding this new precursor to the msrun's hash map of scan_num ->
      /// precursor
      qDebug();
      if(qspectrum.getMassSpectrumId().getNativeId().contains("scan="))
        {
          qDebug();
          mapScanNumberPrecursor(pappso::Utils::extractScanNumberFromMzmlNativeId(
                                   qspectrum.getMassSpectrumId().getNativeId()),
                                 precursor);
          mapSpectrumIndexToPrecursor(qspectrum.getMassSpectrumId().getSpectrumIndex(), precursor);
          qDebug();
        }
      else
        {
          qDebug();
          mapScanNumberPrecursor(qspectrum.getMassSpectrumId().getSpectrumIndex(), precursor);
 
          mapSpectrumIndexToPrecursor(qspectrum.getMassSpectrumId().getSpectrumIndex(), precursor);
          qDebug();
        }
      qDebug();
    }
}

References pappso::Utils::extractScanNumberFromMzmlNativeId(), pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::QualifiedMassSpectrum::getMsLevel(), pappso::MassSpectrumId::getNativeId(), pappso::PrecisionFactory::getPpmInstance(), pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getPrecursorMz(), pappso::QualifiedMassSpectrum::getPrecursorSpectrumIndex(), pappso::MassSpectrumId::getSpectrumIndex(), pappso::masschroq::Precursor::getXicCoordSPtr(), mapScanNumberPrecursor(), mapSpectrumIndexToPrecursor(), and msp_msrunReader.

Member Data Documentation

m_scanNumber2PrecursorMap

std::map<std::size_t, PrecursorSp> pappso::masschroq::PrecursorParser::m_scanNumber2PrecursorMap

private

Definition at line 73 of file precursorparser.h.

Referenced by getPrecursorSPtrByScanNumber(), and mapScanNumberPrecursor().

m_spectrumIndex2PrecursorMap

std::map<std::size_t, PrecursorSp> pappso::masschroq::PrecursorParser::m_spectrumIndex2PrecursorMap

private

Definition at line 74 of file precursorparser.h.

Referenced by getPrecursorSPtrBySpectrumIndex(), and mapSpectrumIndexToPrecursor().

msp_msrunReader

pappso::MsRunReaderCstSPtr pappso::masschroq::PrecursorParser::msp_msrunReader

private

Definition at line 71 of file precursorparser.h.

Referenced by PrecursorParser(), getPrecursorSPtrByScanNumber(), getPrecursorSPtrBySpectrumIndex(), mapSpectrumIndexToPrecursor(), and setQualifiedMassSpectrum().

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

• pappsomspp/core/masschroq/input/precursorparser.h
• pappsomspp/core/masschroq/input/precursorparser.cpp