base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory More...

#include <msrunreader.h>

Inheritance diagram for pappso::MsRunReader:

Public Member Functions
	MsRunReader (const 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

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

virtual XicCoordSPtr	newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, PrecisionPtr precision) const =0
	get a xic coordinate object from a given spectrum index

virtual XicCoordSPtr	newXicCoordSPtrFromQualifiedMassSpectrum (const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const =0
	get a xic coordinate object from a given spectrum

virtual std::size_t	spectrumListSize () const =0
	get the totat number of spectrum conained in the MSrun data file

virtual void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

virtual void	readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0

virtual void	readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

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.

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

virtual std::size_t	spectrumStringIdentifier2SpectrumIndex (const QString &spectrum_identifier)=0
	if possible, get the spectrum index given a string identifier throw a not found exception if spectrum identifier is not found

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

virtual bool	acquireDevice ()=0
	acquire data back end device

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

virtual Trace	getTicChromatogram ()
	get a TIC chromatogram

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

bool	isMonoThread () const

virtual const OboPsiModTerm	getOboPsiModTermInstrumentModelName () const
	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

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

Protected Attributes
MsRunIdCstSPtr	mcsp_msRunId

MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Private Attributes
bool	m_isMonoThread = false

Friends
class	MsFileAccessor

Detailed Description

base class to read MSrun the only way to build a MsRunReader object is to use the MsRunReaderFactory

Definition at line 63 of file msrunreader.h.

Constructor & Destructor Documentation

◆ MsRunReader() [1/2]

pappso::MsRunReader::MsRunReader ( const MsRunIdCstSPtr & ms_run_id )

Definition at line 44 of file msrunreader.cpp.

                                                        : mcsp_msRunId(ms_run_id)
{
}

References mcsp_msRunId.

Referenced by pappso::BafAsciiMsRunReader::BafAsciiMsRunReader(), MsRunReader(), pappso::PwizMsRunReader::PwizMsRunReader(), pappso::TimsMsRunReaderBase::TimsMsRunReaderBase(), pappso::TimsMsRunReaderBase::TimsMsRunReaderBase(), pappso::XyMsRunReader::XyMsRunReader(), and MsFileAccessor.

◆ MsRunReader() [2/2]

pappso::MsRunReader::MsRunReader ( const MsRunReader & other )

Definition at line 48 of file msrunreader.cpp.

                                                 : mcsp_msRunId(other.mcsp_msRunId)
{
  mpa_multiMapScanNumber = nullptr;
  m_isMonoThread         = other.m_isMonoThread;
}

References MsRunReader(), m_isMonoThread, mcsp_msRunId, and mpa_multiMapScanNumber.

◆ ~MsRunReader()

pappso::MsRunReader::~MsRunReader ( )

virtual

Definition at line 62 of file msrunreader.cpp.

{
  if(mpa_multiMapScanNumber == nullptr)
    delete mpa_multiMapScanNumber;
}

References mpa_multiMapScanNumber.

Member Function Documentation

◆ accept()

virtual bool pappso::MsRunReader::accept ( const QString & file_name ) const

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::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

◆ acquireDevice()

virtual bool pappso::MsRunReader::acquireDevice ( )

pure virtual

acquire data back end device

Returns: bool true if done

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::XyMsRunReader.

References getOboPsiModTermInstrumentModelName(), getRetentionTimeLine(), getTicChromatogram(), isMonoThread(), and setMonoThread().

◆ getMsRunId()

const MsRunIdCstSPtr & pappso::MsRunReader::getMsRunId ( ) const

Definition at line 56 of file msrunreader.cpp.

{
  return mcsp_msRunId;
}

References mcsp_msRunId.

Referenced by pappso::TimsMsRunReaderBase::TimsMsRunReaderBase(), MsFileAccessor, pappso::TimsFramesMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReaderDia::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2::qualifiedMassSpectrum(), pappso::TimsMsRunReaderMs2Selected::qualifiedMassSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollectionByMsLevel(), pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel(), and pappso::MzxmlOutput::writeHeader().

◆ getOboPsiModTermInstrumentModelName()

const pappso::OboPsiModTerm pappso::MsRunReader::getOboPsiModTermInstrumentModelName ( ) const

virtual

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

Reimplemented in pappso::PwizMsRunReader, and pappso::TimsMsRunReaderBase.

Definition at line 181 of file msrunreader.cpp.

{
  throw ExceptionNotFound(
    QObject::tr("instrument model name not found in %1").arg(mcsp_msRunId.get()->getFileName()));
}

References mcsp_msRunId.

Referenced by acquireDevice().

◆ getRetentionTimeLine()

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

virtual

retention timeline get retention times along the MSrun in seconds

Returns: vector of retention times (seconds)

Reimplemented in pappso::TimsMsRunReaderBase, and pappso::TimsMsRunReaderMs2.

Definition at line 118 of file msrunreader.cpp.

{
  qDebug();
 
  try
    {
 
      MsRunReaderRetentionTimeLine reader_timeline;
      MsRunReadConfig config;
      config.setMsLevels({1});
      config.setNeedPeakList(false);
      // readSpectrumCollectionByMsLevel(reader_timeline, 1);
      readSpectrumCollection2(config, reader_timeline);
 
      return reader_timeline.getRetentionTimeLine();
    }
 
  catch(ExceptionNotFound &error)
    {
      throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
                                .arg(mcsp_msRunId.get()->getFileName())
                                .arg(error.qwhat()));
    }
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("error reading file %1 : %2")
                              .arg(mcsp_msRunId.get()->getFileName())
                              .arg(error.qwhat()));
    }
}

References pappso::MsRunReaderRetentionTimeLine::getRetentionTimeLine(), mcsp_msRunId, pappso::PappsoException::qwhat(), readSpectrumCollection2(), pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::setNeedPeakList().

Referenced by acquireDevice().

◆ getTicChromatogram()

Trace pappso::MsRunReader::getTicChromatogram ( )

virtual

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 in pappso::TimsMsRunReaderBase, and pappso::TimsMsRunReaderMs2.

Definition at line 151 of file msrunreader.cpp.

{
  qDebug();
 
  try
    {
      MsRunReaderTicChromatogram ms_run_reader;
 
      readSpectrumCollection(ms_run_reader);
 
      return ms_run_reader.getTicChromatogram();
    }
 
  catch(ExceptionNotFound &error)
    {
      throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
                                .arg(mcsp_msRunId.get()->getFileName())
                                .arg(error.qwhat()));
    }
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("error reading file %1 : %2")
                              .arg(mcsp_msRunId.get()->getFileName())
                              .arg(error.qwhat()));
    }
}

References pappso::MsRunReaderTicChromatogram::getTicChromatogram(), mcsp_msRunId, pappso::PappsoException::qwhat(), and readSpectrumCollection().

Referenced by acquireDevice().

◆ hasScanNumbers()

bool pappso::MsRunReader::hasScanNumbers ( ) const

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::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 112 of file msrunreader.cpp.

{
  return false;
}

Referenced by readSpectrumCollectionByMsLevel().

◆ initialize()

virtual void pappso::MsRunReader::initialize ( )

protectedpure virtual

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

◆ isMonoThread()

bool pappso::MsRunReader::isMonoThread ( ) const

Definition at line 75 of file msrunreader.cpp.

{
  return m_isMonoThread;
}

References m_isMonoThread.

Referenced by acquireDevice(), and pappso::TimsMsRunReaderMs2::readSpectrumCollectionByMsLevel().

◆ massSpectrumCstSPtr()

virtual MassSpectrumCstSPtr pappso::MsRunReader::massSpectrumCstSPtr ( std::size_t spectrum_index )

pure virtual

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

◆ massSpectrumSPtr()

virtual MassSpectrumSPtr pappso::MsRunReader::massSpectrumSPtr ( std::size_t spectrum_index )

pure virtual

get a MassSpectrumSPtr class given its spectrum index

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

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

pure virtual

get a xic coordinate object from a given spectrum

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::XyMsRunReader.

◆ newXicCoordSPtrFromSpectrumIndex()

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

pure virtual

get a xic coordinate object from a given spectrum index

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::XyMsRunReader.

◆ qualifiedMassSpectrum()

virtual QualifiedMassSpectrum pappso::MsRunReader::qualifiedMassSpectrum	(	std::size_t	spectrum_index,
		bool	want_binary_data = true ) const

pure virtual

get a QualifiedMassSpectrum class given its scan number

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

◆ readSpectrumCollection()

virtual void pappso::MsRunReader::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler )

pure virtual

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

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

Referenced by getTicChromatogram(), scanNumber2SpectrumIndex(), and pappso::MzxmlOutput::write().

◆ readSpectrumCollection2()

virtual void pappso::MsRunReader::readSpectrumCollection2	(	const MsRunReadConfig &	config,
		SpectrumCollectionHandlerInterface &	handler )

pure virtual

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

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

◆ readSpectrumCollectionByMsLevel()

virtual void pappso::MsRunReader::readSpectrumCollectionByMsLevel	(	SpectrumCollectionHandlerInterface &	handler,
		unsigned int	ms_level )

pure virtual

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

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::XyMsRunReader.

References hasScanNumbers(), and scanNumber2SpectrumIndex().

◆ releaseDevice()

virtual bool pappso::MsRunReader::releaseDevice ( )

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

Returns: bool true if done

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsMsRunReaderBase, pappso::TimsMsRunReaderMs2, and pappso::XyMsRunReader.

◆ scanNumber2SpectrumIndex()

std::size_t pappso::MsRunReader::scanNumber2SpectrumIndex ( std::size_t scan_number )

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 82 of file msrunreader.cpp.

{
  qDebug() << " " << mpa_multiMapScanNumber;
 
  if(mpa_multiMapScanNumber == nullptr)
    {
      mpa_multiMapScanNumber = new MsRunReaderScanNumberMultiMap();
      readSpectrumCollection(*mpa_multiMapScanNumber);
    }
  try
    {
      return mpa_multiMapScanNumber->getSpectrumIndexFromScanNumber(scan_number);
    }
 
  catch(ExceptionNotFound &error)
    {
      throw ExceptionNotFound(QObject::tr("error reading file %1 : %2")
                                .arg(mcsp_msRunId.get()->getFileName())
                                .arg(error.qwhat()));
    }
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("error reading file %1 : %2")
                              .arg(mcsp_msRunId.get()->getFileName())
                              .arg(error.qwhat()));
    }
}

References mcsp_msRunId, mpa_multiMapScanNumber, pappso::PappsoException::qwhat(), and readSpectrumCollection().

Referenced by readSpectrumCollectionByMsLevel().

◆ setMonoThread()

void pappso::MsRunReader::setMonoThread ( bool is_mono_thread )

set only one is_mono_thread to true

this avoid to use qtconcurrent

Definition at line 69 of file msrunreader.cpp.

{
  m_isMonoThread = is_mono_thread;
}

References m_isMonoThread.

Referenced by acquireDevice().

◆ spectrumListSize()

virtual std::size_t pappso::MsRunReader::spectrumListSize ( ) const

pure virtual

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

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

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

◆ spectrumStringIdentifier2SpectrumIndex()

virtual std::size_t pappso::MsRunReader::spectrumStringIdentifier2SpectrumIndex ( const QString & spectrum_identifier )

pure virtual

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

Implemented in pappso::BafAsciiMsRunReader, pappso::PwizMsRunReader, pappso::TimsFramesMsRunReader, pappso::TimsMsRunReader, pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, pappso::TimsMsRunReaderMs2Selected, and pappso::XyMsRunReader.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 66 of file msrunreader.h.

References MsRunReader(), getMsRunId(), and MsFileAccessor.

Referenced by MsFileAccessor.

Member Data Documentation

◆ m_isMonoThread

bool pappso::MsRunReader::m_isMonoThread = false

private

Definition at line 201 of file msrunreader.h.

Referenced by MsRunReader(), isMonoThread(), and setMonoThread().

◆ mcsp_msRunId

MsRunIdCstSPtr pappso::MsRunReader::mcsp_msRunId

protected

Definition at line 189 of file msrunreader.h.

Referenced by MsRunReader(), MsRunReader(), getMsRunId(), getOboPsiModTermInstrumentModelName(), pappso::PwizMsRunReader::getOboPsiModTermInstrumentModelName(), getRetentionTimeLine(), getTicChromatogram(), pappso::BafAsciiMsRunReader::initialize(), pappso::PwizMsRunReader::initialize(), pappso::TimsMsRunReaderBase::initialize(), pappso::TimsMsRunReaderDia::initialize(), pappso::TimsMsRunReaderMs2::initialize(), pappso::TimsMsRunReaderMs2Selected::initialize(), pappso::XyMsRunReader::initialize(), pappso::PwizMsRunReader::processRetentionTime(), pappso::PwizMsRunReader::qualifiedMassSpectrum(), pappso::XyMsRunReader::qualifiedMassSpectrum(), pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData(), pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile(), pappso::XyMsRunReader::readSpectrumCollection(), pappso::BafAsciiMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionByMsLevel(), pappso::XyMsRunReader::readSpectrumCollectionByMsLevel(), pappso::PwizMsRunReader::readSpectrumCollectionWithMsrunReadConfig(), and scanNumber2SpectrumIndex().

◆ mpa_multiMapScanNumber

MsRunReaderScanNumberMultiMap* pappso::MsRunReader::mpa_multiMapScanNumber = nullptr

protected

Definition at line 190 of file msrunreader.h.

Referenced by MsRunReader(), ~MsRunReader(), and scanNumber2SpectrumIndex().

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

pappsomspp/core/msrun/msrunreader.h
pappsomspp/core/msrun/msrunreader.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ MsRunReader() [1/2]

◆ MsRunReader() [2/2]

◆ ~MsRunReader()

Member Function Documentation

◆ accept()

◆ acquireDevice()

◆ getMsRunId()

◆ getOboPsiModTermInstrumentModelName()

◆ getRetentionTimeLine()

◆ getTicChromatogram()

◆ hasScanNumbers()

◆ initialize()

◆ isMonoThread()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ qualifiedMassSpectrum()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ readSpectrumCollectionByMsLevel()

◆ releaseDevice()

◆ scanNumber2SpectrumIndex()

◆ setMonoThread()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Friends And Related Symbol Documentation

◆ MsFileAccessor

Member Data Documentation

◆ m_isMonoThread

◆ mcsp_msRunId

◆ mpa_multiMapScanNumber