#include <timsmsrunreaderms2.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2:

Public Member Functions
	TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)

	TimsMsRunReaderMs2 (const TimsMsRunReaderBase &msrun_reader_base)

virtual	~TimsMsRunReaderMs2 ()

virtual MassSpectrumSPtr	massSpectrumSPtr (std::size_t spectrum_index) override
	get a MassSpectrumSPtr class given its spectrum index

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

virtual void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

virtual void	readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override

virtual pappso::XicCoordSPtr	newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
	get a xic coordinate object from a given spectrum index

virtual pappso::XicCoordSPtr	newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
	get a xic coordinate object from a given spectrum

virtual void	readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data file

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

void	setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)

void	setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)

void	setMs2BuiltinCentroid (bool centroid)
	enable or disable simple centroid filter on raw tims data for MS2

virtual std::vector< std::size_t >	getPrecursorsIDFromMzRt (int charge, double mz_val, double rt_sec, double k0)
	Get all the precursors id which match the values.

virtual bool	releaseDevice () override
	release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

virtual bool	acquireDevice () override
	acquire data back end device

virtual TimsDataSp	getTimsDataSPtr () override
	give an access to the underlying raw data pointer

virtual std::vector< double >	getRetentionTimeLine () override
	retention timeline get retention times along the MSrun in seconds

virtual Trace	getTicChromatogram () override
	get a TIC chromatogram

virtual std::size_t	spectrumStringIdentifier2SpectrumIndex (const QString &spectrum_identifier) override
	if possible, get the spectrum index given a string identifier throw a not found exception if spectrum identifier is not found

Public Member Functions inherited from pappso::TimsMsRunReaderBase
	TimsMsRunReaderBase (MsRunIdCstSPtr &msrun_id_csp)

	TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base)

virtual	~TimsMsRunReaderBase ()

virtual const OboPsiModTerm	getOboPsiModTermInstrumentModelName () const override
	get OboPsiModTerm corresponding to the instrument model name child of : [Term] id: MS:1000031 name: instrument model def: "Instrument model name not including the vendor's name." [PSI:MS] relationship: part_of MS:1000463 ! instrument

Public Member Functions inherited from pappso::MsRunReader
	MsRunReader (const 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.

void	setMonoThread (bool is_mono_thread)
	set only one is_mono_thread to true

bool	isMonoThread () const

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

Protected Attributes
TimsDdaPrecursors *	mp_timsDdaPrecursors = nullptr

Protected Attributes inherited from pappso::TimsMsRunReaderBase
TimsDataSp	msp_timsData = nullptr

Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId

MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Private Attributes
TimsDataSp	msp_timsData = nullptr

pappso::FilterInterfaceCstSPtr	msp_ms1Filter

pappso::FilterInterfaceCstSPtr	msp_ms2Filter

bool	m_builtinMs2Centroid = true
	enable builtin centroid on raw tims integers by default

Friends
class	MsFileAccessor

Detailed Description

Definition at line 38 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2() [1/2]

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( MsRunIdCstSPtr & msrun_id_csp )

Todo: write docs

Definition at line 39 of file timsmsrunreaderms2.cpp.

  : TimsMsRunReaderBase(msrun_id_csp)
{
  initialize();
}

References pappso::TimsMsRunReaderBase::TimsMsRunReaderBase(), and initialize().

Referenced by pappso::TimsMsRunReaderMs2Selected::TimsMsRunReaderMs2Selected(), and MsFileAccessor.

◆ TimsMsRunReaderMs2() [2/2]

TimsMsRunReaderMs2::TimsMsRunReaderMs2 ( const TimsMsRunReaderBase & msrun_reader_base )

Definition at line 45 of file timsmsrunreaderms2.cpp.

  : TimsMsRunReaderBase(msrun_reader_base)
{
  initialize();
}

References pappso::TimsMsRunReaderBase::TimsMsRunReaderBase(), and initialize().

◆ ~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )

virtual

Definition at line 51 of file timsmsrunreaderms2.cpp.

{
  if(msp_timsData != nullptr)
    {
      msp_timsData = nullptr;
    }
}

References msp_timsData.

Member Function Documentation

◆ accept()

bool TimsMsRunReaderMs2::accept ( const QString & file_name ) const

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

Reimplemented from pappso::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 124 of file timsmsrunreaderms2.cpp.

{
  // qDebug() << file_name;
  return true;
}

Referenced by MsFileAccessor.

◆ acquireDevice()

bool TimsMsRunReaderMs2::acquireDevice ( )

overridevirtual

acquire data back end device

Returns: bool true if done

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 266 of file timsmsrunreaderms2.cpp.

{
  if(msp_timsData == nullptr)
    {
      initialize();
      mp_timsDdaPrecursors->setMs2BuiltinCentroid(m_builtinMs2Centroid);
      mp_timsDdaPrecursors->setMs1FilterCstSPtr(msp_ms1Filter);
      mp_timsDdaPrecursors->setMs2FilterCstSPtr(msp_ms2Filter);
    }
  return true;
}

References initialize(), m_builtinMs2Centroid, mp_timsDdaPrecursors, msp_ms1Filter, msp_ms2Filter, and msp_timsData.

Referenced by getTicChromatogram(), getTimsDataSPtr(), and MsFileAccessor.

◆ getPrecursorsIDFromMzRt()

std::vector< std::size_t > pappso::TimsMsRunReaderMs2::getPrecursorsIDFromMzRt	(	int	charge,
		double	mz_val,
		double	rt_sec,
		double	k0 )

virtual

Get all the precursors id which match the values.

Returns: list of precursors Ids

Definition at line 279 of file timsmsrunreaderms2.cpp.

{
  return mp_timsDdaPrecursors->getPrecursorsByMzRtCharge(charge, mz_val, rt_sec, k0);
}

References mp_timsDdaPrecursors.

Referenced by MsFileAccessor.

◆ getRetentionTimeLine()

std::vector< double > pappso::TimsMsRunReaderMs2::getRetentionTimeLine ( )

overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns: vector of retention times (seconds)

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 322 of file timsmsrunreaderms2.cpp.

{
  return msp_timsData.get()->getRetentionTimeLineInSeconds();
}

References msp_timsData.

Referenced by MsFileAccessor.

◆ getTicChromatogram()

Trace TimsMsRunReaderMs2::getTicChromatogram ( )

overridevirtual

get a TIC chromatogram

for each retention time, computes the sum of all intensities. For IM-MS, combines the mobility spectra

Note that, formally, a TIC chromatogram is computed only for MS1 spectra.

Returns: a trace (x=rt, y=intensities)

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 328 of file timsmsrunreaderms2.cpp.

{
  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
  // chromatogram).
 
  acquireDevice();
 
  return msp_timsData->getTicChromatogram();
}

References acquireDevice(), and msp_timsData.

Referenced by MsFileAccessor.

◆ getTimsDataSPtr()

pappso::TimsDataSp pappso::TimsMsRunReaderMs2::getTimsDataSPtr ( )

overridevirtual

give an access to the underlying raw data pointer

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 288 of file timsmsrunreaderms2.cpp.

{
  acquireDevice();
  return msp_timsData;
}

References acquireDevice(), and msp_timsData.

Referenced by pappso::TimsXicExtractorInterface::TimsXicExtractorInterface(), and MsFileAccessor.

◆ hasScanNumbers()

bool TimsMsRunReaderMs2::hasScanNumbers ( ) const

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::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 252 of file timsmsrunreaderms2.cpp.

{
  return false;
}

Referenced by MsFileAccessor.

◆ initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )

overrideprotectedvirtual

Reimplemented from pappso::TimsMsRunReaderBase.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 60 of file timsmsrunreaderms2.cpp.

{
  if(msp_timsData == nullptr)
    msp_timsData = std::make_shared<TimsData>(mcsp_msRunId.get()->getFileName());
 
  if(msp_timsData == nullptr)
    {
      throw PappsoException(QObject::tr("ERROR in TimsMsRunReaderMs2::initialize "
                                        "msp_timsData is null for MsRunId %1")
                              .arg(mcsp_msRunId.get()->toString()));
    }
 
  mp_timsDdaPrecursors = msp_timsData.get()->getTimsDdaPrecursorsPtr();
}

References pappso::MsRunReader::mcsp_msRunId, mp_timsDdaPrecursors, and msp_timsData.

Referenced by TimsMsRunReaderMs2(), TimsMsRunReaderMs2(), acquireDevice(), and MsFileAccessor.

◆ massSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsMsRunReaderMs2::massSpectrumCstSPtr ( std::size_t spectrum_index )

overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 140 of file timsmsrunreaderms2.cpp.

{
  QualifiedMassSpectrum mass_spectrum = qualifiedMassSpectrum(spectrum_index, true);
  return mass_spectrum.getMassSpectrumSPtr();
}

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

Referenced by MsFileAccessor.

◆ massSpectrumSPtr()

pappso::MassSpectrumSPtr TimsMsRunReaderMs2::massSpectrumSPtr ( std::size_t spectrum_index )

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 132 of file timsmsrunreaderms2.cpp.

{
  QualifiedMassSpectrum mass_spectrum = qualifiedMassSpectrum(spectrum_index, true);
  return mass_spectrum.getMassSpectrumSPtr();
}

References pappso::QualifiedMassSpectrum::getMassSpectrumSPtr(), and qualifiedMassSpectrum().

Referenced by MsFileAccessor.

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

pappso::XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromQualifiedMassSpectrum	(	const pappso::QualifiedMassSpectrum &	mass_spectrum,
		pappso::PrecisionPtr	precision ) const

overridevirtual

get a xic coordinate object from a given spectrum

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 314 of file timsmsrunreaderms2.cpp.

{
  return newXicCoordSPtrFromSpectrumIndex(mass_spectrum.getMassSpectrumId().getSpectrumIndex(),
                                          precision);
}

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getSpectrumIndex(), and newXicCoordSPtrFromSpectrumIndex().

Referenced by MsFileAccessor.

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr TimsMsRunReaderMs2::newXicCoordSPtrFromSpectrumIndex	(	std::size_t	spectrum_index,
		pappso::PrecisionPtr	precision ) const

overridevirtual

get a xic coordinate object from a given spectrum index

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 296 of file timsmsrunreaderms2.cpp.

{
  XicCoordTimsSPtr xic_coord  = std::make_shared<XicCoordTims>();
  std::size_t precursor_index = (spectrum_index / 2) + 1;
  auto xic = this->msp_timsData.get()->getTimsDdaPrecursorsPtr()->getXicCoordTimsFromPrecursorId(
    precursor_index, precision);
 
  xic_coord.get()->mzRange      = xic.mzRange;
  xic_coord.get()->rtTarget     = xic.rtTarget;
  xic_coord.get()->scanNumBegin = xic.scanNumBegin;
  xic_coord.get()->scanNumEnd   = xic.scanNumEnd;
 
 
  return xic_coord;
}

References msp_timsData, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::XicCoordTims::scanNumBegin, and pappso::XicCoordTims::scanNumEnd.

Referenced by MsFileAccessor, and newXicCoordSPtrFromQualifiedMassSpectrum().

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsMsRunReaderMs2::qualifiedMassSpectrum	(	std::size_t	spectrum_index,
		bool	want_binary_data = true ) const

overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 148 of file timsmsrunreaderms2.cpp.

{
 
  std::size_t precursor_index = (spectrum_index / 2) + 1;
  TimsDdaPrecursors::SpectrumDescr spectrum_descr;
  try
    {
      spectrum_descr = mp_timsDdaPrecursors->getSpectrumDescrWithPrecursorId(precursor_index);
    }
  catch(ExceptionNotFound &error)
    {
      throw ExceptionNotFound(QObject::tr("spectrum_index %1 NOT FOUND in file %2 : %3")
                                .arg(spectrum_index)
                                .arg(getMsRunId().get()->getFileName())
                                .arg(error.qwhat()));
    }
 
  if(spectrum_index % 2 == 0)
    {
      // qDebug() << "MS1 spectrum precursor_index=" << precursor_index;
      // this is an MS1 spectrum
      QualifiedMassSpectrum mass_spectrum_ms1;
      mp_timsDdaPrecursors->getQualifiedMs1MassSpectrumBySpectrumDescr(
        getMsRunId(), mass_spectrum_ms1, spectrum_descr, want_binary_data);
      // qDebug(); // << mass_spectrum_ms1.toString();
 
      // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
      return mass_spectrum_ms1;
    }
  else
    {
      // qDebug() << "MS2 spectrum precursor_index=" << precursor_index;
      QualifiedMassSpectrum mass_spectrum_ms2;
      if(spectrum_descr.ms2_index != spectrum_index)
        {
          // qDebug();
          throw PappsoException(QObject::tr("ERROR in %1 %2 %3 spectrum_descr.ms2_index(%4) != "
                                            "spectrum_index(%5)")
                                  .arg(__FILE__)
                                  .arg(__FUNCTION__)
                                  .arg(__LINE__)
                                  .arg(spectrum_descr.ms2_index)
                                  .arg(spectrum_index));
        }
 
      mp_timsDdaPrecursors->getQualifiedMs2MassSpectrumBySpectrumDescr(
        getMsRunId(), mass_spectrum_ms2, spectrum_descr, want_binary_data);
      // qDebug() << mass_spectrum_ms2.toString();
 
      // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
      return mass_spectrum_ms2;
    }
}

References pappso::MsRunReader::getMsRunId(), mp_timsDdaPrecursors, pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index, and pappso::PappsoException::qwhat().

Referenced by massSpectrumCstSPtr(), massSpectrumSPtr(), and MsFileAccessor.

◆ readSpectrumCollection()

void TimsMsRunReaderMs2::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler )

overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 204 of file timsmsrunreaderms2.cpp.

{
  readSpectrumCollectionByMsLevel(handler, 0);
}

References readSpectrumCollectionByMsLevel().

Referenced by MsFileAccessor.

◆ readSpectrumCollection2()

void TimsMsRunReaderMs2::readSpectrumCollection2	(	const MsRunReadConfig &	config,
		SpectrumCollectionHandlerInterface &	handler )

overridevirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 210 of file timsmsrunreaderms2.cpp.

{
  readSpectrumCollectionByMsLevel(handler, 0);
}

References readSpectrumCollectionByMsLevel().

Referenced by MsFileAccessor.

◆ readSpectrumCollectionByMsLevel()

void TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel	(	SpectrumCollectionHandlerInterface &	handler,
		unsigned int	ms_level )

overridevirtual

function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

Implements pappso::MsRunReader.

Definition at line 218 of file timsmsrunreaderms2.cpp.

{
  // qDebug() << " ms_level=" << ms_level;
  // We'll need it to perform the looping in the spectrum list.
  std::size_t spectrum_list_size = spectrumListSize();
 
  //   qDebug() << "The spectrum list has size:" << spectrum_list_size;
 
  // Inform the handler of the spectrum list so that it can handle feedback to
  // the user.
  handler.spectrumListHasSize(spectrum_list_size);
 
  mp_timsDdaPrecursors->setMonoThread(isMonoThread());
 
  mp_timsDdaPrecursors->ms2ReaderSpectrumCollectionByMsLevel(getMsRunId(), handler, ms_level);
 
  // Now let the loading handler know that the loading of the data has ended.
  // The handler might need this "signal" to perform additional tasks or to
  // cleanup cruft.
 
  // qDebug() << "Loading ended";
  handler.loadingEnded();
}

References pappso::MsRunReader::getMsRunId(), pappso::MsRunReader::isMonoThread(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), mp_timsDdaPrecursors, pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by MsFileAccessor, readSpectrumCollection(), and readSpectrumCollection2().

◆ releaseDevice()

bool TimsMsRunReaderMs2::releaseDevice ( )

overridevirtual

release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

Returns: bool true if done

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 259 of file timsmsrunreaderms2.cpp.

{
  msp_timsData = nullptr;
  return true;
}

References msp_timsData.

Referenced by MsFileAccessor.

◆ setMs1FilterCstSPtr()

void TimsMsRunReaderMs2::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr filter )

Definition at line 108 of file timsmsrunreaderms2.cpp.

{
  msp_ms1Filter = filter;
  if(mp_timsDdaPrecursors != nullptr)
    {
      mp_timsDdaPrecursors->setMs1FilterCstSPtr(filter);
    }
  else
    {
      throw PappsoException(
        QObject::tr("ERROR in TimsMsRunReaderMs2::setMs1FilterCstSPtr "
                    "msp_timsData is null"));
    }
}

References pappso::filter, mp_timsDdaPrecursors, and msp_ms1Filter.

Referenced by MsFileAccessor.

◆ setMs2BuiltinCentroid()

void TimsMsRunReaderMs2::setMs2BuiltinCentroid ( bool centroid )

enable or disable simple centroid filter on raw tims data for MS2

Definition at line 76 of file timsmsrunreaderms2.cpp.

{
  m_builtinMs2Centroid = centroid;
  if(mp_timsDdaPrecursors != nullptr)
    {
      mp_timsDdaPrecursors->setMs2BuiltinCentroid(m_builtinMs2Centroid);
    }
  else
    {
      throw PappsoException(
        QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2BuiltinCentroid "
                    "mp_timsDdaPrecursors is null"));
    }
}

References m_builtinMs2Centroid, and mp_timsDdaPrecursors.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and MsFileAccessor.

◆ setMs2FilterCstSPtr()

void TimsMsRunReaderMs2::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr filter )

Definition at line 92 of file timsmsrunreaderms2.cpp.

{
  msp_ms2Filter = filter;
  if(mp_timsDdaPrecursors != nullptr)
    {
      mp_timsDdaPrecursors->setMs2FilterCstSPtr(msp_ms2Filter);
    }
  else
    {
      throw PappsoException(
        QObject::tr("ERROR in TimsMsRunReaderMs2::setMs2FilterCstSPtr "
                    "mp_timsDdaPrecursors is null"));
    }
}

References pappso::filter, mp_timsDdaPrecursors, and msp_ms2Filter.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and MsFileAccessor.

◆ spectrumListSize()

std::size_t TimsMsRunReaderMs2::spectrumListSize ( ) const

overridevirtual

get the totat number of spectrum conained in the MSrun data file

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 245 of file timsmsrunreaderms2.cpp.

{
  return (mp_timsDdaPrecursors->getTotalPrecursorCount() * 2);
}

References mp_timsDdaPrecursors.

Referenced by MsFileAccessor, and readSpectrumCollectionByMsLevel().

◆ spectrumStringIdentifier2SpectrumIndex()

std::size_t TimsMsRunReaderMs2::spectrumStringIdentifier2SpectrumIndex ( const QString & spectrum_identifier )

overridevirtual

if possible, get the spectrum index given a string identifier throw a not found exception if spectrum identifier is not found

Parameters

spectrum_identifier string identifier of a specific spectrum

Returns: the spectrum index

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2Selected.

Definition at line 340 of file timsmsrunreaderms2.cpp.

{
  throw pappso::ExceptionNotImplemented(
    QObject::tr("%1 %2 %3 not implemented").arg(__FILE__).arg(__FUNCTION__).arg(__LINE__));
}

Referenced by MsFileAccessor.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor

friend

Member Data Documentation

◆ m_builtinMs2Centroid

bool pappso::TimsMsRunReaderMs2::m_builtinMs2Centroid = true

private

enable builtin centroid on raw tims integers by default

Definition at line 123 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2BuiltinCentroid().

◆ mp_timsDdaPrecursors

TimsDdaPrecursors* pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors = nullptr

protected

Definition at line 114 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), getPrecursorsIDFromMzRt(), initialize(), pappso::TimsMsRunReaderMs2Selected::initialize(), qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum(), readSpectrumCollectionByMsLevel(), setMs1FilterCstSPtr(), pappso::TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr(), setMs2BuiltinCentroid(), setMs2FilterCstSPtr(), pappso::TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr(), spectrumListSize(), and pappso::TimsMsRunReaderMs2Selected::spectrumListSize().

◆ msp_ms1Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms1Filter

private

Definition at line 119 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs1FilterCstSPtr().

◆ msp_ms2Filter

pappso::FilterInterfaceCstSPtr pappso::TimsMsRunReaderMs2::msp_ms2Filter

private

Definition at line 120 of file timsmsrunreaderms2.h.

Referenced by acquireDevice(), and setMs2FilterCstSPtr().

◆ msp_timsData

TimsDataSp pappso::TimsMsRunReaderMs2::msp_timsData = nullptr

private

Definition at line 117 of file timsmsrunreaderms2.h.

Referenced by ~TimsMsRunReaderMs2(), acquireDevice(), getRetentionTimeLine(), getTicChromatogram(), getTimsDataSPtr(), initialize(), newXicCoordSPtrFromSpectrumIndex(), and releaseDevice().

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

pappsomspp/core/msrun/private/timsmsrunreaderms2.h
pappsomspp/core/msrun/private/timsmsrunreaderms2.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2() [1/2]

◆ TimsMsRunReaderMs2() [2/2]

◆ ~TimsMsRunReaderMs2()

Member Function Documentation

◆ accept()

◆ acquireDevice()

◆ getPrecursorsIDFromMzRt()

◆ getRetentionTimeLine()

◆ getTicChromatogram()

◆ getTimsDataSPtr()

◆ hasScanNumbers()

◆ initialize()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ qualifiedMassSpectrum()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ readSpectrumCollectionByMsLevel()

◆ releaseDevice()

◆ setMs1FilterCstSPtr()

◆ setMs2BuiltinCentroid()

◆ setMs2FilterCstSPtr()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Friends And Related Symbol Documentation

◆ MsFileAccessor

Member Data Documentation

◆ m_builtinMs2Centroid

◆ mp_timsDdaPrecursors

◆ msp_ms1Filter

◆ msp_ms2Filter

◆ msp_timsData