#include <timsmsrunreaderdia.h>

Inheritance diagram for pappso::TimsMsRunReaderDia:

Public Member Functions
	TimsMsRunReaderDia (MsRunIdCstSPtr &msrun_id_csp)

	TimsMsRunReaderDia (const TimsMsRunReaderBase &msrun_reader_base)

virtual	~TimsMsRunReaderDia ()

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

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 More...

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

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

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

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

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

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 More...

virtual bool	acquireDevice () override
	acquire data back end device More...

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 More...

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

	TimsMsRunReaderBase (const TimsMsRunReaderBase &msrun_reader_base)

virtual	~TimsMsRunReaderBase ()

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

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 More...

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 More...

virtual bool	acquireDevice () override
	acquire data back end device More...

virtual Trace	getTicChromatogram () override
	get a TIC chromatogram More...

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

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

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

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 More...

Public Member Functions inherited from pappso::MsRunReader
	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 More...

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 More...

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

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

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

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

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 More...

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. More...

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 More...

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 More...

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 More...

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

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

virtual Trace	getTicChromatogram ()
	get a TIC chromatogram More...

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

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 More...

Protected Member Functions
virtual void	initialize () override

Protected Member Functions inherited from pappso::TimsMsRunReaderBase
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 More...

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 More...

Private Attributes
TimsDiaSlices *	mp_timsDiaSlices = nullptr

Friends
class	MsFileAccessor

Additional Inherited Members
Protected Attributes inherited from pappso::TimsMsRunReaderBase
TimsDataSp	msp_timsData = nullptr

Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId

MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Detailed Description

Definition at line 44 of file timsmsrunreaderdia.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderDia() [1/2]

pappso::TimsMsRunReaderDia::TimsMsRunReaderDia ( MsRunIdCstSPtr & msrun_id_csp )

Default constructor

Definition at line 38 of file timsmsrunreaderdia.cpp.

  : TimsMsRunReaderBase(msrun_id_csp)
{
  // qInfo() << msp_timsData.get();
  initialize();
}

References initialize().

◆ TimsMsRunReaderDia() [2/2]

pappso::TimsMsRunReaderDia::TimsMsRunReaderDia ( const TimsMsRunReaderBase & msrun_reader_base )

Definition at line 46 of file timsmsrunreaderdia.cpp.

  : TimsMsRunReaderBase(msrun_reader_base)
{
  initialize();
}

References initialize().

◆ ~TimsMsRunReaderDia()

pappso::TimsMsRunReaderDia::~TimsMsRunReaderDia ( )

virtual

Destructor

Definition at line 52 of file timsmsrunreaderdia.cpp.

53{

54}

Member Function Documentation

◆ acquireDevice()

bool pappso::TimsMsRunReaderDia::acquireDevice ( )

overridevirtual

acquire data back end device

Returns: bool true if done

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 153 of file timsmsrunreaderdia.cpp.

{
  if(TimsMsRunReaderBase::acquireDevice())
    {
      qDebug() << msp_timsData.get();
      mp_timsDiaSlices = msp_timsData.get()->getTimsDiaSlicesPtr();
      return true;
    }
  return false;
  qDebug();
}

References pappso::TimsMsRunReaderBase::acquireDevice(), mp_timsDiaSlices, and pappso::TimsMsRunReaderBase::msp_timsData.

◆ initialize()

void pappso::TimsMsRunReaderDia::initialize ( )

overrideprotectedvirtual

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 58 of file timsmsrunreaderdia.cpp.

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

Referenced by TimsMsRunReaderDia().

◆ massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 139 of file timsmsrunreaderdia.cpp.

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

◆ massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 133 of file timsmsrunreaderdia.cpp.

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

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

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

overridevirtual

get a xic coordinate object from a given spectrum

Reimplemented from pappso::TimsMsRunReaderBase.

Definition at line 88 of file timsmsrunreaderdia.cpp.

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

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr pappso::TimsMsRunReaderDia::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 79 of file timsmsrunreaderdia.cpp.

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

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::TimsMsRunReaderDia::qualifiedMassSpectrum	(	std::size_t	spectrum_index,
		bool	want_binary_data = `true`
	)		const

overridevirtual

get a QualifiedMassSpectrum class given its scan number

Implements pappso::MsRunReader.

Definition at line 105 of file timsmsrunreaderdia.cpp.

{
 
  // spectrum index is a global slice index
  QualifiedMassSpectrum q_dia_spectrum;
  mp_timsDiaSlices->getMs2QualifiedSpectrumByGlobalSliceIndex(
    getMsRunId(), q_dia_spectrum, spectrum_index, want_binary_data);
  return q_dia_spectrum;
}

References pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::MsRunReader::getMsRunId(), and mp_timsDiaSlices.

◆ readSpectrumCollection()

void pappso::TimsMsRunReaderDia::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler )

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 116 of file timsmsrunreaderdia.cpp.

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

◆ readSpectrumCollection2()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 124 of file timsmsrunreaderdia.cpp.

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

◆ readSpectrumCollectionByMsLevel()

void pappso::TimsMsRunReaderDia::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 96 of file timsmsrunreaderdia.cpp.

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

◆ spectrumListSize()

std::size_t pappso::TimsMsRunReaderDia::spectrumListSize ( ) const

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 146 of file timsmsrunreaderdia.cpp.

{
 
  return mp_timsDiaSlices->getTotalSlicesCount();
}

References pappso::TimsDiaSlices::getTotalSlicesCount(), and mp_timsDiaSlices.

◆ spectrumStringIdentifier2SpectrumIndex()

std::size_t pappso::TimsMsRunReaderDia::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.

Definition at line 166 of file timsmsrunreaderdia.cpp.

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

Friends And Related Function Documentation

◆ MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 46 of file timsmsrunreaderdia.h.

Member Data Documentation

◆ mp_timsDiaSlices

TimsDiaSlices* pappso::TimsMsRunReaderDia::mp_timsDiaSlices = nullptr

private

Definition at line 119 of file timsmsrunreaderdia.h.

Referenced by acquireDevice(), qualifiedMassSpectrum(), and spectrumListSize().

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

pappsomspp/msrun/private/timsmsrunreaderdia.h
pappsomspp/msrun/private/timsmsrunreaderdia.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TimsMsRunReaderDia() [1/2]

◆ TimsMsRunReaderDia() [2/2]

◆ ~TimsMsRunReaderDia()

Member Function Documentation

◆ acquireDevice()

◆ initialize()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ qualifiedMassSpectrum()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ readSpectrumCollectionByMsLevel()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Friends And Related Function Documentation

◆ MsFileAccessor

Member Data Documentation

◆ mp_timsDiaSlices