#include <timsmsrunreaderms2selected.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2Selected:

Public Member Functions
	TimsMsRunReaderMs2Selected (MsRunIdCstSPtr &msrun_id_csp)

virtual	~TimsMsRunReaderMs2Selected ()

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 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)

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::TimsMsRunReaderMs2
	TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)

	TimsMsRunReaderMs2 (const TimsMsRunReaderBase &msrun_reader_base)

virtual	~TimsMsRunReaderMs2 ()

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

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

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

Private Attributes
TimsData *	mpa_timsData = nullptr

Friends
class	MsFileAccessor

Additional Inherited Members
Protected Attributes inherited from pappso::TimsMsRunReaderMs2
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

Detailed Description

Definition at line 41 of file timsmsrunreaderms2selected.h.

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2Selected()

TimsMsRunReaderMs2Selected::TimsMsRunReaderMs2Selected ( MsRunIdCstSPtr & msrun_id_csp )

Todo: write docs

Definition at line 38 of file timsmsrunreaderms2selected.cpp.

  : TimsMsRunReaderMs2(msrun_id_csp)
{
  initialize();
}

References pappso::TimsMsRunReaderMs2::TimsMsRunReaderMs2(), and initialize().

Referenced by MsFileAccessor.

◆ ~TimsMsRunReaderMs2Selected()

TimsMsRunReaderMs2Selected::~TimsMsRunReaderMs2Selected ( )

virtual

Definition at line 44 of file timsmsrunreaderms2selected.cpp.

{
  if(mpa_timsData != nullptr)
    {
      delete mpa_timsData;
    }
}

References mpa_timsData.

Member Function Documentation

◆ accept()

bool TimsMsRunReaderMs2Selected::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::TimsMsRunReaderMs2.

Definition at line 91 of file timsmsrunreaderms2selected.cpp.

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

Referenced by MsFileAccessor.

◆ hasScanNumbers()

bool TimsMsRunReaderMs2Selected::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::TimsMsRunReaderMs2.

Definition at line 313 of file timsmsrunreaderms2selected.cpp.

{
  return false;
}

Referenced by MsFileAccessor.

◆ initialize()

void pappso::TimsMsRunReaderMs2Selected::initialize ( )

overrideprotectedvirtual

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 53 of file timsmsrunreaderms2selected.cpp.

{
  mpa_timsData = new TimsData(mcsp_msRunId.get()->getFileName());
 
  mp_timsDdaPrecursors = mpa_timsData->getTimsDdaPrecursorsPtr();
}

References pappso::MsRunReader::mcsp_msRunId, pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors, and mpa_timsData.

Referenced by TimsMsRunReaderMs2Selected(), and MsFileAccessor.

◆ massSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr TimsMsRunReaderMs2Selected::massSpectrumCstSPtr ( std::size_t spectrum_index )

overridevirtual

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 107 of file timsmsrunreaderms2selected.cpp.

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

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

Referenced by MsFileAccessor.

◆ massSpectrumSPtr()

pappso::MassSpectrumSPtr TimsMsRunReaderMs2Selected::massSpectrumSPtr ( std::size_t spectrum_index )

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 99 of file timsmsrunreaderms2selected.cpp.

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

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

Referenced by MsFileAccessor.

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum TimsMsRunReaderMs2Selected::qualifiedMassSpectrum	(	std::size_t	spectrum_index,
		bool	want_binary_data = true ) const

overridevirtual

get a QualifiedMassSpectrum class given its scan number

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 115 of file timsmsrunreaderms2selected.cpp.

{
 
  std::size_t precursor_index = (spectrum_index / 2) + 1;
 
  TimsDdaPrecursors::SpectrumDescr spectrum_descr =
    mp_timsDdaPrecursors->getSpectrumDescrWithPrecursorId(precursor_index);
 
  if(spectrum_index % 2 == 0)
    {
      qDebug();
      // 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();
      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 != spectrum_index")
              .arg(__FILE__)
              .arg(__FUNCTION__)
              .arg(__LINE__));
        }
      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(), pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors, and pappso::TimsDdaPrecursors::SpectrumDescr::ms2_index.

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

◆ readSpectrumCollection()

void TimsMsRunReaderMs2Selected::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler )

overridevirtual

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

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 160 of file timsmsrunreaderms2selected.cpp.

{
  const bool want_binary_data = handler.needPeakList();
  // const bool want_binary_data = false;
 
  // 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);
 
  std::vector<size_t> selected_precursor{63905,
                                         73549,
                                         105675,
                                         130439,
                                         177297,
                                         177369,
                                         177483,
                                         190453,
                                         196967,
                                         246691,
                                         271215,
                                         289423,
                                         310669};
  // QFile temp_output("/data/temp.txt");
  // temp_output.open(QIODevice::WriteOnly | QIODevice::Text);
  // QTextStream out(&temp_output);
 
  // Iterate in the full list of spectra.
  bool readAhead = handler.isReadAhead();
 
  if(readAhead)
    {
 
      std::size_t process_list_size = 300;
 
      struct tmp_item
      {
        QualifiedMassSpectrum qualified_mass_spectrum;
        std::size_t iter;
        bool want_binary_data;
      };
 
      for(std::size_t i = 0; i < spectrum_list_size; i += process_list_size)
        {
          // QTextStream out(&temp_output);
          qDebug();
          // If the user of this reader instance wants to stop reading the
          // spectra, then break this loop.
          if(handler.shouldStop())
            {
              qDebug() << "The operation was cancelled. Breaking the loop.";
              break;
            }
          std::vector<tmp_item> item_list;
          for(std::size_t iter = 0; (iter < process_list_size) && ((iter + i) < spectrum_list_size);
              iter++)
            {
              if(std::find(selected_precursor.begin(), selected_precursor.end(), iter + i) !=
                 selected_precursor.end())
                {
                  bool get_data = want_binary_data;
                  if((iter + i) % 2 == 0)
                    { // MS1
                      get_data = handler.needMsLevelPeakList(1);
                    }
                  else
                    {
                      get_data = handler.needMsLevelPeakList(2);
                    }
 
                  item_list.push_back({QualifiedMassSpectrum(), iter + i, get_data});
                }
            }
          qDebug() << item_list.size();
          // Use QtConcurrentBlocking::mapped to apply the scale function to all
          // the images in the list.
          QtConcurrent::blockingMap(item_list.begin(), item_list.end(), [this](tmp_item &one_item) {
            qDebug() << one_item.iter;
            one_item.qualified_mass_spectrum =
              qualifiedMassSpectrum(one_item.iter, one_item.want_binary_data);
 
            // qDebug() << one_item.qualified_mass_spectrum.size() << " " <<
            // one_item.qualified_mass_spectrum.getMassSpectrumSPtr().get()->toString();
          });
 
          qDebug() << item_list.size();
          for(auto &item : item_list)
            {
              // qDebug() <<
              // item.qualified_mass_spectrum.getMassSpectrumSPtr()
              //              .get()
              //              ->toString();
              handler.setQualifiedMassSpectrum(item.qualified_mass_spectrum);
              qDebug();
            }
        }
    }
  else
    {
      for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
        {
          qDebug();
          // If the user of this reader instance wants to stop reading the
          // spectra, then break this loop.
          if(handler.shouldStop())
            {
              qDebug() << "The operation was cancelled. Breaking the loop.";
              break;
            }
          bool get_data = want_binary_data;
          if(iter % 2 == 0)
            { // MS1
              if(!handler.needMsLevelPeakList(1))
                {
                  get_data = false;
                }
            }
          QualifiedMassSpectrum qualified_mass_spectrum = qualifiedMassSpectrum(iter, get_data);
          handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
          qDebug();
        }
    }
  // End of
  // for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
 
  // 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";
  // temp_output.close();
  handler.loadingEnded();
}

References pappso::SpectrumCollectionHandlerInterface::isReadAhead(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), and spectrumListSize().

Referenced by MsFileAccessor, and readSpectrumCollection2().

◆ readSpectrumCollection2()

void TimsMsRunReaderMs2Selected::readSpectrumCollection2	(	const MsRunReadConfig &	config,
		SpectrumCollectionHandlerInterface &	handler )

overridevirtual

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 299 of file timsmsrunreaderms2selected.cpp.

{
  return readSpectrumCollection(handler);
}

References readSpectrumCollection().

Referenced by MsFileAccessor.

◆ setMs1FilterCstSPtr()

void TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr ( pappso::FilterInterfaceCstSPtr filter )

Definition at line 76 of file timsmsrunreaderms2selected.cpp.

{
  if(mp_timsDdaPrecursors != nullptr)
    {
      mp_timsDdaPrecursors->setMs1FilterCstSPtr(filter);
    }
  else
    {
      throw PappsoException(
        QObject::tr("ERROR in TimsMsRunReaderMs2Selected::setMs1FilterCstSPtr "
                    "mp_timsDdaPrecursors is null"));
    }
}

References pappso::filter, and pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors.

Referenced by MsFileAccessor.

◆ setMs2FilterCstSPtr()

void TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr ( pappso::FilterInterfaceCstSPtr filter )

Definition at line 61 of file timsmsrunreaderms2selected.cpp.

{
  if(mp_timsDdaPrecursors != nullptr)
    {
      mp_timsDdaPrecursors->setMs2FilterCstSPtr(filter);
    }
  else
    {
      throw PappsoException(
        QObject::tr("ERROR in TimsMsRunReaderMs2Selected::setMs2FilterCstSPtr "
                    "mp_timsDdaPrecursors is null"));
    }
}

References pappso::filter, and pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors.

Referenced by MsFileAccessor.

◆ spectrumListSize()

std::size_t TimsMsRunReaderMs2Selected::spectrumListSize ( ) const

overridevirtual

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

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 306 of file timsmsrunreaderms2selected.cpp.

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

References pappso::TimsMsRunReaderMs2::mp_timsDdaPrecursors.

Referenced by MsFileAccessor, and readSpectrumCollection().

◆ spectrumStringIdentifier2SpectrumIndex()

std::size_t TimsMsRunReaderMs2Selected::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

Reimplemented from pappso::TimsMsRunReaderMs2.

Definition at line 320 of file timsmsrunreaderms2selected.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

Definition at line 43 of file timsmsrunreaderms2selected.h.

References TimsMsRunReaderMs2Selected(), accept(), pappso::filter, hasScanNumbers(), initialize(), massSpectrumCstSPtr(), massSpectrumSPtr(), MsFileAccessor, qualifiedMassSpectrum(), readSpectrumCollection(), readSpectrumCollection2(), setMs1FilterCstSPtr(), setMs2FilterCstSPtr(), spectrumListSize(), and spectrumStringIdentifier2SpectrumIndex().

Referenced by MsFileAccessor.

Member Data Documentation

◆ mpa_timsData

TimsData* pappso::TimsMsRunReaderMs2Selected::mpa_timsData = nullptr

private

Definition at line 77 of file timsmsrunreaderms2selected.h.

Referenced by ~TimsMsRunReaderMs2Selected(), and initialize().

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

pappsomspp/core/msrun/private/timsmsrunreaderms2selected.h
pappsomspp/core/msrun/private/timsmsrunreaderms2selected.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TimsMsRunReaderMs2Selected()

◆ ~TimsMsRunReaderMs2Selected()

Member Function Documentation

◆ accept()

◆ hasScanNumbers()

◆ initialize()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ qualifiedMassSpectrum()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ setMs1FilterCstSPtr()

◆ setMs2FilterCstSPtr()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Friends And Related Symbol Documentation

◆ MsFileAccessor

Member Data Documentation

◆ mpa_timsData