pappso::TimsMsRunReaderMs2 Class Reference

#include <timsmsrunreaderms2.h>

Inheritance diagram for pappso::TimsMsRunReaderMs2:

Public Member Functions
	TimsMsRunReaderMs2 (MsRunIdCstSPtr &msrun_id_csp)
virtual	~TimsMsRunReaderMs2 ()
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 void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data file 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...
void	setMs2FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
void	setMs1FilterCstSPtr (pappso::FilterInterfaceCstSPtr filter)
Public Member Functions inherited from pappso::MsRunReader
	MsRunReader (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. More...

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 More...

Private Attributes
TimsData *	mpa_timsData = nullptr

Friends
class	MsFileAccessor

Additional Inherited Members
Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId
MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Detailed Description

Definition at line 56 of file timsmsrunreaderms2.h.

Constructor & Destructor Documentation

TimsMsRunReaderMs2()

TimsMsRunReaderMs2::TimsMsRunReaderMs2

(

MsRunIdCstSPtr &

msrun_id_csp

)

Todo:

write docs

Definition at line 36 of file timsmsrunreaderms2.cpp.

  : MsRunReader(msrun_id_csp)
{
  initialize();

References initialize().

~TimsMsRunReaderMs2()

TimsMsRunReaderMs2::~TimsMsRunReaderMs2 ( )

virtual

Definition at line 42 of file timsmsrunreaderms2.cpp.

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

References mpa_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

Implements pappso::MsRunReader.

Definition at line 87 of file timsmsrunreaderms2.cpp.

{
  qDebug() << file_name;
  return true;

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::MsRunReader.

Definition at line 281 of file timsmsrunreaderms2.cpp.

{
  return false;

initialize()

void pappso::TimsMsRunReaderMs2::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 51 of file timsmsrunreaderms2.cpp.

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

Referenced by TimsMsRunReaderMs2().

massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 104 of file timsmsrunreaderms2.cpp.

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

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

massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 95 of file timsmsrunreaderms2.cpp.

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

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

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.

Definition at line 113 of file timsmsrunreaderms2.cpp.

{
 
  std::size_t precursor_index = (spectrum_index / 2) + 1;
 
  if(spectrum_index % 2 == 0)
    {
      qDebug();
      // this is an MS1 spectrum
      QualifiedMassSpectrum mass_spectrum_ms1 =
        mpa_timsData->getQualifiedMs1MassSpectrumByPrecursorId(
          spectrum_index, precursor_index, want_binary_data);
      MassSpectrumId spectrum_id(mass_spectrum_ms1.getMassSpectrumId());
      spectrum_id.setMsRunId(getMsRunId());
      mass_spectrum_ms1.setMassSpectrumId(spectrum_id);
      qDebug(); // << mass_spectrum_ms1.toString();
 
      // qDebug() << mass_spectrum_ms1.getMassSpectrumSPtr().get()->toString();
      return mass_spectrum_ms1;
    }
  else
    {
      qDebug();
      QualifiedMassSpectrum mass_spectrum_ms2;
      mpa_timsData->getQualifiedMs2MassSpectrumByPrecursorId(
        mass_spectrum_ms2, spectrum_index, precursor_index, want_binary_data);
      MassSpectrumId spectrum_id(mass_spectrum_ms2.getMassSpectrumId());
      spectrum_id.setMsRunId(getMsRunId());
      mass_spectrum_ms2.setMassSpectrumId(spectrum_id);
      qDebug(); // << mass_spectrum_ms2.toString();
 
      // qDebug() << mass_spectrum_ms2.getMassSpectrumSPtr().get()->toString();
      return mass_spectrum_ms2;
    }

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MsRunReader::getMsRunId(), pappso::TimsData::getQualifiedMs1MassSpectrumByPrecursorId(), pappso::TimsData::getQualifiedMs2MassSpectrumByPrecursorId(), mpa_timsData, pappso::QualifiedMassSpectrum::setMassSpectrumId(), and pappso::MassSpectrumId::setMsRunId().

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

readSpectrumCollection()

void TimsMsRunReaderMs2::readSpectrumCollection ( SpectrumCollectionHandlerInterface &  handler )

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 152 of file timsmsrunreaderms2.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);
 
  // 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)
        {
          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++)
            {
 
              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";
  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().

setMs1FilterCstSPtr()

void TimsMsRunReaderMs2::setMs1FilterCstSPtr

(

pappso::FilterInterfaceCstSPtr

filter

)

Definition at line 72 of file timsmsrunreaderms2.cpp.

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

References mpa_timsData, and pappso::TimsData::setMs1FilterCstSPtr().

setMs2FilterCstSPtr()

void TimsMsRunReaderMs2::setMs2FilterCstSPtr

(

pappso::FilterInterfaceCstSPtr

filter

)

Definition at line 57 of file timsmsrunreaderms2.cpp.

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

References mpa_timsData, and pappso::TimsData::setMs2FilterCstSPtr().

spectrumListSize()

std::size_t TimsMsRunReaderMs2::spectrumListSize ( ) const

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 274 of file timsmsrunreaderms2.cpp.

{
  return (mpa_timsData->getTotalNumberOfPrecursors() * 2);

References pappso::TimsData::getTotalNumberOfPrecursors(), and mpa_timsData.

Referenced by readSpectrumCollection().

Friends And Related Function Documentation

MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 75 of file timsmsrunreaderms2.h.

Member Data Documentation

mpa_timsData

TimsData* pappso::TimsMsRunReaderMs2::mpa_timsData = nullptr

private

Definition at line 107 of file timsmsrunreaderms2.h.

Referenced by qualifiedMassSpectrum(), setMs1FilterCstSPtr(), setMs2FilterCstSPtr(), spectrumListSize(), and ~TimsMsRunReaderMs2().

---

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

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