#include <timsmsrunreaderbase.h>

Inheritance diagram for pappso::TimsMsRunReaderBase:

Public Member Functions
	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

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

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 Trace	getTicChromatogram () override
	get a TIC chromatogram

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

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 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 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 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 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

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
TimsDataSp	msp_timsData = nullptr

Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId

MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Friends
class	MsFileAccessor

Detailed Description

Definition at line 37 of file timsmsrunreaderbase.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderBase() [1/2]

pappso::TimsMsRunReaderBase::TimsMsRunReaderBase ( MsRunIdCstSPtr & msrun_id_csp )

Default constructor

Definition at line 38 of file timsmsrunreaderbase.cpp.

                                                                     : MsRunReader(msrun_id_csp)
{
  initialize();
}

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

◆ TimsMsRunReaderBase() [2/2]

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

Definition at line 43 of file timsmsrunreaderbase.cpp.

  : MsRunReader(msrun_reader_base.getMsRunId()), msp_timsData(msrun_reader_base.msp_timsData)
{
  initialize();
}

References pappso::MsRunReader::MsRunReader(), TimsMsRunReaderBase(), pappso::MsRunReader::getMsRunId(), initialize(), and msp_timsData.

◆ ~TimsMsRunReaderBase()

pappso::TimsMsRunReaderBase::~TimsMsRunReaderBase ( )

virtual

Destructor

Definition at line 50 of file timsmsrunreaderbase.cpp.

{
 
  msp_timsData = nullptr;
}

References msp_timsData.

Member Function Documentation

◆ accept()

bool pappso::TimsMsRunReaderBase::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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 72 of file timsmsrunreaderbase.cpp.

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

Referenced by MsFileAccessor.

◆ acquireDevice()

bool pappso::TimsMsRunReaderBase::acquireDevice ( )

overridevirtual

acquire data back end device

Returns: bool true if done

Implements pappso::MsRunReader.

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

Definition at line 93 of file timsmsrunreaderbase.cpp.

{
  if(msp_timsData == nullptr)
    {
      initialize();
    }
  return true;
}

References initialize(), and msp_timsData.

Referenced by pappso::TimsMsRunReaderDia::acquireDevice(), getTicChromatogram(), getTimsDataSPtr(), and MsFileAccessor.

◆ getOboPsiModTermInstrumentModelName()

const pappso::OboPsiModTerm pappso::TimsMsRunReaderBase::getOboPsiModTermInstrumentModelName ( ) const

overridevirtual

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 from pappso::MsRunReader.

Definition at line 152 of file timsmsrunreaderbase.cpp.

{
 
  pappso::FilterOboPsiModMap psims_map;
 
  pappso::OboPsiMs psims_file(psims_map);
 
  pappso::OboPsiModTerm term;
 
  term = psims_map.getOboPsiModTermWithAccession("MS:1003123");
  /*
   * [Term]
  id: MS:1003123
  name: Bruker Daltonics timsTOF series
  def: "Bruker Daltonics timsTOF series" [PSI:MS]
  is_a: MS:1000122 ! Bruker Daltonics instrument model
  */
  /*
   *
[Term]
id: MS:1003124
name: timsTOF fleX
def: "Bruker Daltonics' timsTOF fleX" [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
[Term]
id: MS:1003229
name: timsTOF
def: "Bruker Daltonics' timsTOF." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
[Term]
id: MS:1003230
name: timsTOF Pro 2
def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
[Term]
id: MS:1003231
name: timsTOF SCP
def: "Bruker Daltonics' timsTOF SCP." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
[Term]
id: MS:1003383
name: timsTOF Ultra
def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
 
[Term]
id: MS:1003397
name: timsTOF fleX MALDI-2
def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
 
[Term]
id: MS:1003404
name: timsTOF HT
def: "Bruker Daltonics' timsTOF HT." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
 
 
[Term]
id: MS:1003412
name: timsTOF Ultra 2
def: "Bruker Daltonics timsTOF Ultra 2." [PSI:MS]
is_a: MS:1003123 ! Bruker Daltonics timsTOF series
*/
  QStringList timstof_list;
  timstof_list << "MS:1003005"
               << "MS:1003412"
               << "MS:1003404"
               << "MS:1003397"
               << "MS:1003383"
               << "MS:1003231"
               << "MS:1003230"
               << "MS:1003229"
               << "MS:1003124";
 
  QString instrument_name = msp_timsData.get()->getGlobalMetadataValue("InstrumentName").toString();
 
  for(auto &accession : timstof_list)
    {
      pappso::OboPsiModTerm test_term = psims_map.getOboPsiModTermWithAccession(accession);
      if(test_term.m_name == instrument_name)
        {
          term = test_term;
          break;
        }
    }
  return term;
}

References pappso::FilterOboPsiModMap::getOboPsiModTermWithAccession(), pappso::OboPsiModTerm::m_name, and msp_timsData.

Referenced by MsFileAccessor.

◆ getRetentionTimeLine()

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

overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns: vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 124 of file timsmsrunreaderbase.cpp.

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

References msp_timsData.

Referenced by MsFileAccessor.

◆ getTicChromatogram()

Trace pappso::TimsMsRunReaderBase::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::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 111 of file timsmsrunreaderbase.cpp.

{
  // Use the Sqlite database to fetch the total ion current chromatogram (TIC
  // chromatogram).
 
  acquireDevice();
 
  // The time unit here is seconds, not minutes!!!
  return msp_timsData->getTicChromatogram();
}

References acquireDevice(), and msp_timsData.

Referenced by MsFileAccessor.

◆ getTimsDataSPtr()

TimsDataSp pappso::TimsMsRunReaderBase::getTimsDataSPtr ( )

virtual

give an access to the underlying raw data pointer

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 103 of file timsmsrunreaderbase.cpp.

{
  acquireDevice();
  return msp_timsData;
}

References acquireDevice(), and msp_timsData.

Referenced by MsFileAccessor.

◆ hasScanNumbers()

bool pappso::TimsMsRunReaderBase::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::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 79 of file timsmsrunreaderbase.cpp.

{
  return false;
}

Referenced by MsFileAccessor.

◆ initialize()

void pappso::TimsMsRunReaderBase::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderDia, pappso::TimsMsRunReaderMs2, and pappso::TimsMsRunReaderMs2Selected.

Definition at line 57 of file timsmsrunreaderbase.cpp.

{
  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 TimsMsRunReaderBase::initialize "
                                        "msp_timsData is null for MsRunId %1")
                              .arg(mcsp_msRunId.get()->toString()));
    }
}

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

Referenced by pappso::TimsMsRunReader::TimsMsRunReader(), pappso::TimsMsRunReader::TimsMsRunReader(), TimsMsRunReaderBase(), TimsMsRunReaderBase(), acquireDevice(), and MsFileAccessor.

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

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

overridevirtual

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

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

Definition at line 140 of file timsmsrunreaderbase.cpp.

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

Referenced by MsFileAccessor.

◆ newXicCoordSPtrFromSpectrumIndex()

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

overridevirtual

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

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

Definition at line 131 of file timsmsrunreaderbase.cpp.

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

Referenced by MsFileAccessor.

◆ releaseDevice()

bool pappso::TimsMsRunReaderBase::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

Implements pappso::MsRunReader.

Reimplemented in pappso::TimsMsRunReaderMs2.

Definition at line 86 of file timsmsrunreaderbase.cpp.

{
  msp_timsData = nullptr;
  return true;
}

References msp_timsData.

Referenced by MsFileAccessor.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 39 of file timsmsrunreaderbase.h.

References TimsMsRunReaderBase(), accept(), acquireDevice(), getOboPsiModTermInstrumentModelName(), getRetentionTimeLine(), getTicChromatogram(), getTimsDataSPtr(), hasScanNumbers(), initialize(), MsFileAccessor, newXicCoordSPtrFromQualifiedMassSpectrum(), newXicCoordSPtrFromSpectrumIndex(), and releaseDevice().

Referenced by MsFileAccessor.

Member Data Documentation

◆ msp_timsData

TimsDataSp pappso::TimsMsRunReaderBase::msp_timsData = nullptr

protected

Definition at line 87 of file timsmsrunreaderbase.h.

Referenced by TimsMsRunReaderBase(), pappso::TimsFramesMsRunReader::~TimsFramesMsRunReader(), ~TimsMsRunReaderBase(), acquireDevice(), pappso::TimsMsRunReaderDia::acquireDevice(), pappso::TimsFramesMsRunReader::computeTicChromatogram(), getOboPsiModTermInstrumentModelName(), getRetentionTimeLine(), getTicChromatogram(), getTimsDataSPtr(), initialize(), pappso::TimsMsRunReaderDia::initialize(), pappso::TimsFramesMsRunReader::massSpectrumCstSPtr(), pappso::TimsMsRunReader::massSpectrumCstSPtr(), pappso::TimsFramesMsRunReader::qualifiedMassSpectrum(), pappso::TimsMsRunReader::qualifiedMassSpectrum(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollection2(), pappso::TimsMsRunReader::readSpectrumCollectionByMsLevel(), releaseDevice(), pappso::TimsFramesMsRunReader::spectrumListSize(), and pappso::TimsMsRunReader::spectrumListSize().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ TimsMsRunReaderBase() [1/2]

◆ TimsMsRunReaderBase() [2/2]

◆ ~TimsMsRunReaderBase()

Member Function Documentation

◆ accept()

◆ acquireDevice()

◆ getOboPsiModTermInstrumentModelName()

◆ getRetentionTimeLine()

◆ getTicChromatogram()

◆ getTimsDataSPtr()

◆ hasScanNumbers()

◆ initialize()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ releaseDevice()

Friends And Related Symbol Documentation

◆ MsFileAccessor

Member Data Documentation

◆ msp_timsData