#include <mzcbormsrunreader.h>

Inheritance diagram for pappso::MzcborMsRunReader:

Public Member Functions
	MzcborMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
virtual	~MzcborMsRunReader ()
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
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler
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
virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data 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 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
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 if there are some Thermo native ids, this should be set to true
virtual std::size_t	scanNumber2SpectrumIndex (std::size_t scan_number) override
	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.
const std::vector< qint64 > &	getSpectrumIndexPositionInFile () const
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
virtual Trace	getTicChromatogram () override
	get a TIC chromatogram
virtual std::vector< double >	getRetentionTimeLine () override
	retention timeline get retention times along the MSrun in seconds
std::shared_ptr< pappso::cbor::mzcbor::Spectrum >	getMzcborSpectrumSp (std::size_t spectrum_index, bool want_binary_data) const
	get spectrum mzML element
Public Member Functions inherited from pappso::MsRunReader
	MsRunReader (const MsRunIdCstSPtr &ms_run_id)
	MsRunReader (const MsRunReader &other)
virtual	~MsRunReader ()
const MsRunIdCstSPtr &	getMsRunId () const
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
virtual void	fillMzcborSpectrum (std::size_t spectrum_index, pappso::cbor::mzcbor::Spectrum &spectrum, bool want_binary_data) const

Protected Attributes
QFileInfo	m_cborFileInfo
std::vector< qint64 >	m_spectrumIndexPositionInFile
std::vector< qint64 >	m_spectrumTotalIonCountList
std::vector< std::uint8_t >	m_spectrumMsLevelList
std::vector< double >	m_spectrumRtList
std::map< QString, std::size_t >	m_nativeId2SpectrumIndexMap
std::map< std::size_t, std::size_t >	m_scan2SpectrumIndexMap
QFile *	mpa_mzcborFileDevice = nullptr
Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId
MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Private Member Functions
void	readSpectrumCollectionWithMsrunReadConfig (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)

Detailed Description

Todo: write docs

Definition at line 41 of file mzcbormsrunreader.h.

Constructor & Destructor Documentation

◆ MzcborMsRunReader()

pappso::MzcborMsRunReader::MzcborMsRunReader ( MsRunIdCstSPtr & msrun_id_csp )

Default constructor

Definition at line 41 of file mzcbormsrunreader.cpp.

  : pappso::MsRunReader(msrun_id_csp)
{
  initialize();
  qDebug();
}

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

◆ ~MzcborMsRunReader()

pappso::MzcborMsRunReader::~MzcborMsRunReader ( )

virtual

Destructor

Definition at line 48 of file mzcbormsrunreader.cpp.

{
  releaseDevice();
}

References releaseDevice().

Member Function Documentation

◆ accept()

bool pappso::MzcborMsRunReader::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 195 of file mzcbormsrunreader.cpp.

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

◆ acquireDevice()

bool pappso::MzcborMsRunReader::acquireDevice ( )

overridevirtual

acquire data back end device

Returns: bool true if done

Implements pappso::MsRunReader.

Definition at line 211 of file mzcbormsrunreader.cpp.

{
  if(mpa_mzcborFileDevice == nullptr)
    {
      mpa_mzcborFileDevice = new QFile(m_cborFileInfo.absoluteFilePath());
      mpa_mzcborFileDevice->open(QIODevice::ReadOnly);
    }
  return true;
}

References m_cborFileInfo, and mpa_mzcborFileDevice.

Referenced by initialize(), massSpectrumSPtr(), and readSpectrumCollectionWithMsrunReadConfig().

◆ fillMzcborSpectrum()

void pappso::MzcborMsRunReader::fillMzcborSpectrum	(	std::size_t	spectrum_index,
		pappso::cbor::mzcbor::Spectrum &	spectrum,
		bool	want_binary_data ) const

protectedvirtual

Definition at line 582 of file mzcbormsrunreader.cpp.

{
 
  if(spectrum_index >= m_spectrumIndexPositionInFile.size())
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("spectrum index %1 not found").arg(spectrum_index));
    }
  if(mpa_mzcborFileDevice == nullptr)
    {
 
      throw pappso::PappsoException(
        QObject::tr("mzCBOR file device is not ready, use acquireDevice() before access"));
    }
  qDebug() << spectrum_index << " " << m_spectrumIndexPositionInFile[spectrum_index];
 
 
  // qDebug() << spectrum_index << " " << m_spectrumIndexPositionInFile[spectrum_index-1];
 
 
  if(mpa_mzcborFileDevice->seek(m_spectrumIndexPositionInFile[spectrum_index]))
    {
      pappso::cbor::CborStreamReader cbor_stream_reader(mpa_mzcborFileDevice);
      cbor_stream_reader.setDevice(mpa_mzcborFileDevice);
 
 
      try
        {
          spectrum.fromCbor(cbor_stream_reader, want_binary_data);
        }
      catch(const pappso::PappsoException &error)
        {
 
          throw pappso::PappsoException(QObject::tr("ERROR reading spectrum %1 cbor:\n%2")
                                          .arg(spectrum_index)
                                          .arg(error.qwhat()));
        }
      // cbor_stream_reader.leaveContainer();
 
      if(spectrum.id.isEmpty())
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR reading spectrum %1 cbor:\nspectrum not found").arg(spectrum_index));
        }
    }
  else
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR reading spectrum %1 cbor:\nseek failed").arg(spectrum_index));
    }
  // mzcbor_file.close();
}

References pappso::cbor::mzcbor::Spectrum::fromCbor(), pappso::cbor::mzcbor::Spectrum::id, m_spectrumIndexPositionInFile, mpa_mzcborFileDevice, and pappso::PappsoException::qwhat().

Referenced by getMzcborSpectrumSp(), massSpectrumSPtr(), newXicCoordSPtrFromSpectrumIndex(), and qualifiedMassSpectrum().

◆ getMzcborSpectrumSp()

std::shared_ptr< pappso::cbor::mzcbor::Spectrum > pappso::MzcborMsRunReader::getMzcborSpectrumSp	(	std::size_t	spectrum_index,
		bool	want_binary_data ) const

get spectrum mzML element

Parameters

spectrum_index	spectrum to retrieve
want_binary_data	true to get peak list

Returns: shared pointer on spectrum structure

Definition at line 684 of file mzcbormsrunreader.cpp.

{
  std::shared_ptr<pappso::cbor::mzcbor::Spectrum> cbor_spectrum_sp =
    std::make_shared<pappso::cbor::mzcbor::Spectrum>();
 
  fillMzcborSpectrum(spectrum_index, *cbor_spectrum_sp, want_binary_data);
 
  return cbor_spectrum_sp;
}

References fillMzcborSpectrum().

◆ getOboPsiModTermInstrumentModelName()

const OboPsiModTerm pappso::MzcborMsRunReader::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 204 of file mzcbormsrunreader.cpp.

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

◆ getRetentionTimeLine()

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

overridevirtual

retention timeline get retention times along the MSrun in seconds

Returns: vector of retention times (seconds)

Reimplemented from pappso::MsRunReader.

Definition at line 662 of file mzcbormsrunreader.cpp.

{
  qDebug();
  std::vector<double> time_line;
  if((m_spectrumRtList.size() > 0) && (m_spectrumMsLevelList.size() == m_spectrumRtList.size()))
    {
      for(std::size_t i = 0; i < m_spectrumRtList.size(); i++)
        {
          if(m_spectrumMsLevelList.at(i) == 1)
            {
              time_line.push_back(m_spectrumRtList.at(i));
            }
        }
    }
  else
    {
      return MsRunReader::getRetentionTimeLine();
    }
  return time_line;
}

References pappso::MsRunReader::getRetentionTimeLine(), m_spectrumMsLevelList, and m_spectrumRtList.

◆ getSpectrumIndexPositionInFile()

const std::vector< qint64 > & pappso::MzcborMsRunReader::getSpectrumIndexPositionInFile ( ) const

Definition at line 55 of file mzcbormsrunreader.cpp.

{
 
  return m_spectrumIndexPositionInFile;
}

References m_spectrumIndexPositionInFile.

◆ getTicChromatogram()

Trace pappso::MzcborMsRunReader::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.

Definition at line 639 of file mzcbormsrunreader.cpp.

{
  qDebug() << m_spectrumMsLevelList.size() << " " << m_spectrumTotalIonCountList.size();
  Trace chromatogram;
  if((m_spectrumTotalIonCountList.size() > 0) &&
     (m_spectrumMsLevelList.size() == m_spectrumTotalIonCountList.size()))
    {
      for(std::size_t i = 0; i < m_spectrumTotalIonCountList.size(); i++)
        {
          if(m_spectrumMsLevelList.at(i) == 1)
            {
              chromatogram.push_back(
                {m_spectrumRtList.at(i), (double)m_spectrumTotalIonCountList.at(i)});
            }
        }
    }
  else
    {
      return MsRunReader::getTicChromatogram();
    }
  return chromatogram;
}

References pappso::MsRunReader::getTicChromatogram(), m_spectrumMsLevelList, m_spectrumRtList, and m_spectrumTotalIonCountList.

◆ hasScanNumbers()

bool pappso::MzcborMsRunReader::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 if there are some Thermo native ids, this should be set to true

Reimplemented from pappso::MsRunReader.

Definition at line 153 of file mzcbormsrunreader.cpp.

{
  if(m_nativeId2SpectrumIndexMap.size() > 0)
    {
      if(m_nativeId2SpectrumIndexMap.begin()->first.contains("scan="))
        return true;
    }
  return false;
}

References m_nativeId2SpectrumIndexMap.

◆ initialize()

void pappso::MzcborMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 62 of file mzcbormsrunreader.cpp.

{
  qDebug();
  m_cborFileInfo.setFile(mcsp_msRunId->getFileName());
 
  if(!m_cborFileInfo.exists())
    throw ExceptionNotFound(m_cborFileInfo.absoluteFilePath());
 
 
  // build the index
  acquireDevice();
 
  QString str_index_file = m_cborFileInfo.absoluteFilePath();
  QFileInfo mzcbor_index_fileinfo(str_index_file.append(".idx"));
  if(mzcbor_index_fileinfo.exists())
    {
      qDebug() << "mzcbor_index_fileinfo.exists()";
      QFile mzcbor_index_file(mzcbor_index_fileinfo.absoluteFilePath());
      mzcbor_index_file.open(QIODevice::ReadOnly);
 
      pappso::cbor::mzcbor::MzcborIndexReader index_reader;
      index_reader.readCbor(&mzcbor_index_file);
      index_reader.close();
      mzcbor_index_file.close();
 
      qDebug();
      std::vector<QString> run_id_list = index_reader.getRunIdList();
      if(run_id_list.size() > 0)
        {
          std::size_t run_position = 0;
          if(run_id_list.size() > 1)
            {
              std::size_t i_run = 0;
              for(const QString &run_id : run_id_list)
                {
                  if(run_id == getMsRunId().get()->getRunId())
                    {
                      run_position = i_run;
                    }
                  i_run++;
                }
            }
 
          m_spectrumIndexPositionInFile =
            index_reader.getRunAndSpectrumOffsetList().at(run_position);
 
 
          if(index_reader.getRunAndSpectrumTotalIonCountList().size() > run_position)
            {
              m_spectrumTotalIonCountList =
                index_reader.getRunAndSpectrumTotalIonCountList().at(run_position);
            }
          if(index_reader.getRunAndSpectrumMsLevelList().size() > run_position)
            {
              m_spectrumMsLevelList = index_reader.getRunAndSpectrumMsLevelList().at(run_position);
            }
 
          if(index_reader.getRunAndSpectrumRtList().size() > run_position)
            {
              m_spectrumRtList = index_reader.getRunAndSpectrumRtList().at(run_position);
            }
          // qFatal() << m_spectrumTotalIonCountList.size();
 
          std::size_t i = 0;
          for(const QString &native_id : index_reader.getRunAndSpectrumIdList().at(run_position))
            {
              m_nativeId2SpectrumIndexMap.insert({native_id, i});
              i++;
            }
        }
    }
 
  if(m_spectrumIndexPositionInFile.size() == 0)
    {
 
      pappso::UiMonitorVoid monitor;
      pappso::cbor::mzcbor::MzcborBuildIndexReader mzcbor_build_index_reader(getMsRunId());
      mzcbor_build_index_reader.readCbor(mpa_mzcborFileDevice, monitor);
 
 
      qDebug();
      mzcbor_build_index_reader.close();
      // releaseDevice();
      qDebug();
 
      m_spectrumIndexPositionInFile = mzcbor_build_index_reader.getSpectrumIndexPositionInFile();
      m_nativeId2SpectrumIndexMap   = mzcbor_build_index_reader.getNativeId2SpectrumIndexMap();
    }
}

Referenced by MzcborMsRunReader().

◆ massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 288 of file mzcbormsrunreader.cpp.

{
  return massSpectrumSPtr(spectrum_index);
}

References massSpectrumSPtr().

◆ massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 294 of file mzcbormsrunreader.cpp.

{
  MassSpectrumSPtr mass_spectrum_sp;
  try
    {
      acquireDevice();
      pappso::cbor::mzcbor::Spectrum cbor_spectrum;
 
      fillMzcborSpectrum(spectrum_index, cbor_spectrum, true);
      if(cbor_spectrum.binaryDataArrayList.size() == 2)
        {
          mass_spectrum_sp = std::make_shared<MassSpectrum>();
          cbor_spectrum.decodeTrace(*(mass_spectrum_sp.get()));
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("cbor_spectrum.binaryDataArrayList.size() != 2"));
        }
    }
  catch(const pappso::PappsoException &pappso_error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(QObject::tr("Error reading data (massSpectrumSPtr) using the "
                                                "mzcbor reader: %1")
                                      .arg(pappso_error.what()));
    }
  return mass_spectrum_sp;
}

References acquireDevice(), pappso::cbor::mzcbor::Spectrum::binaryDataArrayList, pappso::cbor::mzcbor::Spectrum::decodeTrace(), fillMzcborSpectrum(), and pappso::PappsoException::what().

Referenced by massSpectrumCstSPtr().

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

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

overridevirtual

get a xic coordinate object from a given spectrum

Implements pappso::MsRunReader.

Definition at line 236 of file mzcbormsrunreader.cpp.

{
 
  XicCoordSPtr xic_coord = std::make_shared<XicCoord>();
 
  xic_coord.get()->rtTarget = mass_spectrum.getRtInSeconds();
  xic_coord.get()->mzRange  = MzRange(mass_spectrum.getPrecursorMz(), precision);
  return xic_coord;
}

References pappso::QualifiedMassSpectrum::getPrecursorMz(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::XicCoord::mzRange, and pappso::XicCoord::rtTarget.

◆ newXicCoordSPtrFromSpectrumIndex()

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

overridevirtual

get a xic coordinate object from a given spectrum index

Implements pappso::MsRunReader.

Definition at line 248 of file mzcbormsrunreader.cpp.

{
 
  pappso::cbor::mzcbor::Spectrum cbor_spectrum;
 
  fillMzcborSpectrum(spectrum_index, cbor_spectrum, false);
 
  XicCoordSPtr xic_coord = std::make_shared<XicCoord>();
 
  xic_coord.get()->rtTarget = cbor_spectrum.getRtInSeconds();
 
  bool get_mz = false;
  if(cbor_spectrum.precursorList.size() > 0)
    {
 
      for(auto &precursor : cbor_spectrum.precursorList)
        {
          for(auto &ion : precursor.selectedIonList)
            {
              xic_coord.get()->mzRange = MzRange(ion.getMz(), precision);
              get_mz                   = true;
            }
        }
      if(!get_mz)
        {
          throw pappso::ExceptionNotFound(
            QObject::tr("precursor m/z not found for this spectrum index %1").arg(spectrum_index));
        }
    }
  else
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("no precursor found for this spectrum index %1").arg(spectrum_index));
    }
 
  return xic_coord;
}

References fillMzcborSpectrum(), pappso::cbor::mzcbor::Spectrum::getRtInSeconds(), pappso::XicCoord::mzRange, pappso::cbor::mzcbor::Spectrum::precursorList, and pappso::XicCoord::rtTarget.

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::MzcborMsRunReader::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 326 of file mzcbormsrunreader.cpp.

{
  qDebug();
  try
    {
      pappso::cbor::mzcbor::Spectrum cbor_spectrum;
 
      fillMzcborSpectrum(spectrum_index, cbor_spectrum, want_binary_data);
      qDebug() << cbor_spectrum.index;
      QualifiedMassSpectrum qualified_mass_spectrum;
 
      MassSpectrumId spectrum_id(mcsp_msRunId, spectrum_index);
      spectrum_id.setNativeId(cbor_spectrum.id);
 
      spectrum_id.setSpectrumIndex(cbor_spectrum.index);
 
      qualified_mass_spectrum.setMassSpectrumId(spectrum_id);
      qualified_mass_spectrum.setRtInSeconds(cbor_spectrum.getRtInSeconds());
      if(cbor_spectrum.precursorList.size() > 0)
        {
          qualified_mass_spectrum.setPrecursorNativeId(
            cbor_spectrum.precursorList.at(0).spectrumRef);
          qualified_mass_spectrum.setPrecursorSpectrumIndex(
            m_nativeId2SpectrumIndexMap.at(cbor_spectrum.precursorList.at(0).spectrumRef));
          // qWarning() << "pappso::MzcborMsRunReader::qualifiedMassSpectrum";
 
          for(auto &precursor : cbor_spectrum.precursorList)
            {
 
              // *****************************************************
              // get isolation window (very simplified)
              // *****************************************************
 
              try
                {
                  // qWarning() << "pappso::MzcborMsRunReader::qualifiedMassSpectrum";
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowTargetMz,
                    precursor.isolationWindow.getTargetMz());
 
 
                  auto it = precursor.isolationWindow.cvParamMap.find("MS:1000828");
 
                  if(it == precursor.isolationWindow.cvParamMap.end())
                    {
                      throw pappso::ExceptionNotFound(QObject::tr(
                        "isolation window lower offset MS:1000828 not found in cvParam map"));
                    }
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowLowerOffset,
                    it->second.valueDouble);
 
 
                  it = precursor.isolationWindow.cvParamMap.find("MS:1000829");
 
                  if(it == precursor.isolationWindow.cvParamMap.end())
                    {
                      throw pappso::ExceptionNotFound(QObject::tr(
                        "isolation window upper offset MS:1000829 not found in cvParam map"));
                    }
 
                  qualified_mass_spectrum.setParameterValue(
                    QualifiedMassSpectrumParameter::IsolationWindowUpperOffset,
                    it->second.valueDouble);
                }
              catch(const pappso::ExceptionNotFound &not_found)
                {
                  // isolation window not available
                  // throw not_found;
                }
              // *****************************************************
              // end get isolation window (very simplified)
              // *****************************************************
 
              for(auto &ion : precursor.selectedIonList)
                {
                  PrecursorIonData precursor_ion_data;
                  precursor_ion_data.charge = ion.getChargeState();
                  bool is_ok;
                  precursor_ion_data.intensity = ion.getIntensity(&is_ok);
                  precursor_ion_data.mz        = ion.getMz();
                  qualified_mass_spectrum.appendPrecursorIonData(precursor_ion_data);
                }
            }
        }
 
 
      qDebug();
      qualified_mass_spectrum.setMsLevel(cbor_spectrum.getMsLevel());
 
      qDebug();
      qualified_mass_spectrum.setEmptyMassSpectrum(!cbor_spectrum.defaultArrayLength);
      if(cbor_spectrum.binaryDataArrayList.size() == 2)
        {
          MassSpectrumSPtr mass_spectrum_sp = std::make_shared<MassSpectrum>();
          cbor_spectrum.decodeTrace(*(mass_spectrum_sp.get()));
          qualified_mass_spectrum.setMassSpectrumSPtr(mass_spectrum_sp);
        }
 
      qDebug() << "spectrum id=" << cbor_spectrum.id;
 
      return qualified_mass_spectrum;
    }
 
  catch(const pappso::PappsoException &pappso_error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (qualifiedMassSpectrum) using the "
                    "mzcbor reader: %1")
          .arg(pappso_error.what()));
    }
}

◆ readSpectrumCollection()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 443 of file mzcbormsrunreader.cpp.

{
 
  throw pappso::ExceptionNotImplemented(
    QObject::tr("%1 %2 %3 not implemented").arg(__FILE__).arg(__FUNCTION__).arg(__LINE__));
  MsRunReadConfig config;
  std::vector<size_t> ms_levels;
  for(std::size_t i = 1; i < 9; i++)
    {
      if(handler.needMsLevelPeakList(i))
        {
          ms_levels.push_back(i);
        }
    }
  config.setMsLevels(ms_levels);
  config.setNeedPeakList(handler.needPeakList());
  // readSpectrumCollectionByMsLevel(reader_timeline, 1);
 
  try
    {
      readSpectrumCollectionWithMsrunReadConfig(config, handler);
    }
  catch(const pappso::PappsoException &pappso_error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (spectrum collection2) using the "
                    "mzcbor reader: %1")
          .arg(pappso_error.what()));
    }
  catch(std::exception &error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (spectrum collection) using the "
                    "mzcbor reader: %1")
          .arg(error.what()));
    }
}

References pappso::SpectrumCollectionHandlerInterface::needMsLevelPeakList(), pappso::SpectrumCollectionHandlerInterface::needPeakList(), readSpectrumCollectionWithMsrunReadConfig(), pappso::MsRunReadConfig::setMsLevels(), pappso::MsRunReadConfig::setNeedPeakList(), and pappso::PappsoException::what().

◆ readSpectrumCollection2()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 486 of file mzcbormsrunreader.cpp.

{
  qDebug();
  try
    {
      readSpectrumCollectionWithMsrunReadConfig(config, handler);
    }
  catch(const pappso::PappsoException &pappso_error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (spectrum collection2) using the "
                    "mzcbor reader: %1")
          .arg(pappso_error.what()));
    }
  catch(std::exception &error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (spectrum collection2) using the "
                    "mzcbor reader: %1")
          .arg(error.what()));
    }
}

References readSpectrumCollectionWithMsrunReadConfig(), and pappso::PappsoException::what().

Referenced by readSpectrumCollectionByMsLevel().

◆ readSpectrumCollectionByMsLevel()

void pappso::MzcborMsRunReader::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 515 of file mzcbormsrunreader.cpp.

{
  MsRunReadConfig config;
  config.setMsLevels({ms_level});
  config.setNeedPeakList(handler.needPeakList());
  // readSpectrumCollectionByMsLevel(reader_timeline, 1);
  readSpectrumCollection2(config, handler);
}

References pappso::SpectrumCollectionHandlerInterface::needPeakList(), readSpectrumCollection2(), pappso::MsRunReadConfig::setMsLevels(), and pappso::MsRunReadConfig::setNeedPeakList().

◆ readSpectrumCollectionWithMsrunReadConfig()

void pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig	(	const MsRunReadConfig &	config,
		SpectrumCollectionHandlerInterface &	handler )

private

Definition at line 546 of file mzcbormsrunreader.cpp.

{
  // acquireDevice();
  try
    {
      acquireDevice();
      pappso::UiMonitorVoid monitor;
      pappso::cbor::mzcbor::MzcborSpectrumCollectionReader mzcbor_spectrum_collection_reader(
        config, handler);
      mzcbor_spectrum_collection_reader.setMsRunId(getMsRunId());
      mzcbor_spectrum_collection_reader.setNativeId2SpectrumIndexMapPtr(
        &m_nativeId2SpectrumIndexMap);
      mzcbor_spectrum_collection_reader.readCbor(mpa_mzcborFileDevice, monitor);
 
 
      qDebug();
      mzcbor_spectrum_collection_reader.close();
      qDebug();
    }
  catch(const pappso::PappsoException &pappso_err)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig:\n%1")
          .arg(pappso_err.qwhat()));
    }
  // 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.
}

References acquireDevice(), pappso::cbor::mzcbor::MzcborReaderBase::close(), pappso::MsRunReader::getMsRunId(), m_nativeId2SpectrumIndexMap, mpa_mzcborFileDevice, pappso::PappsoException::qwhat(), pappso::cbor::mzcbor::MzcborReaderBase::readCbor(), pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setMsRunId(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::setNativeId2SpectrumIndexMapPtr().

Referenced by readSpectrumCollection(), and readSpectrumCollection2().

◆ releaseDevice()

bool pappso::MzcborMsRunReader::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.

Definition at line 223 of file mzcbormsrunreader.cpp.

{
  if(mpa_mzcborFileDevice != nullptr)
    {
      mpa_mzcborFileDevice->close();
      delete mpa_mzcborFileDevice;
      mpa_mzcborFileDevice = nullptr;
    }
  return true;
}

References mpa_mzcborFileDevice.

Referenced by ~MzcborMsRunReader().

◆ scanNumber2SpectrumIndex()

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

overridevirtual

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.

Reimplemented from pappso::MsRunReader.

Definition at line 164 of file mzcbormsrunreader.cpp.

{
  if(m_scan2SpectrumIndexMap.size() == 0)
    {
      for(auto &index_pair : m_nativeId2SpectrumIndexMap)
        {
          QStringList native_id_list = index_pair.first.split("=");
          if(native_id_list.size() < 2)
            {
            }
          else
            {
              std::size_t scan_number = native_id_list.back().toULong();
              m_scan2SpectrumIndexMap.insert(
                std::pair<std::size_t, std::size_t>(scan_number, index_pair.second));
            }
        }
    }
 
  auto it = m_scan2SpectrumIndexMap.find(scan_number);
 
  if(it == m_scan2SpectrumIndexMap.end())
    {
      throw ExceptionNotFound(QObject::tr("error reading file %1 : scan %2 not found")
                                .arg(mcsp_msRunId.get()->getFileName())
                                .arg(scan_number));
    }
  return it->second;
}

References m_nativeId2SpectrumIndexMap, m_scan2SpectrumIndexMap, and pappso::MsRunReader::mcsp_msRunId.

◆ spectrumListSize()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 526 of file mzcbormsrunreader.cpp.

{
  return m_spectrumIndexPositionInFile.size();
}

References m_spectrumIndexPositionInFile.

◆ spectrumStringIdentifier2SpectrumIndex()

std::size_t pappso::MzcborMsRunReader::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 532 of file mzcbormsrunreader.cpp.

{
  auto it = m_nativeId2SpectrumIndexMap.find(spectrum_identifier);
  if(it == m_nativeId2SpectrumIndexMap.end())
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("spectrum identifier %1 not found").arg(spectrum_identifier));
    }
  return it->second;
}

References m_nativeId2SpectrumIndexMap.

Member Data Documentation

◆ m_cborFileInfo

QFileInfo pappso::MzcborMsRunReader::m_cborFileInfo

protected

Definition at line 133 of file mzcbormsrunreader.h.

Referenced by acquireDevice(), and initialize().

◆ m_nativeId2SpectrumIndexMap

std::map<QString, std::size_t> pappso::MzcborMsRunReader::m_nativeId2SpectrumIndexMap

protected

Definition at line 138 of file mzcbormsrunreader.h.

Referenced by hasScanNumbers(), initialize(), qualifiedMassSpectrum(), readSpectrumCollectionWithMsrunReadConfig(), scanNumber2SpectrumIndex(), and spectrumStringIdentifier2SpectrumIndex().

◆ m_scan2SpectrumIndexMap

std::map<std::size_t, std::size_t> pappso::MzcborMsRunReader::m_scan2SpectrumIndexMap

protected

Definition at line 139 of file mzcbormsrunreader.h.

Referenced by scanNumber2SpectrumIndex().

◆ m_spectrumIndexPositionInFile

std::vector<qint64> pappso::MzcborMsRunReader::m_spectrumIndexPositionInFile

protected

Definition at line 134 of file mzcbormsrunreader.h.

Referenced by fillMzcborSpectrum(), getSpectrumIndexPositionInFile(), initialize(), and spectrumListSize().

◆ m_spectrumMsLevelList

std::vector<std::uint8_t> pappso::MzcborMsRunReader::m_spectrumMsLevelList

protected

Definition at line 136 of file mzcbormsrunreader.h.

Referenced by getRetentionTimeLine(), getTicChromatogram(), and initialize().

◆ m_spectrumRtList

std::vector<double> pappso::MzcborMsRunReader::m_spectrumRtList

protected

Definition at line 137 of file mzcbormsrunreader.h.

Referenced by getRetentionTimeLine(), getTicChromatogram(), and initialize().

◆ m_spectrumTotalIonCountList

std::vector<qint64> pappso::MzcborMsRunReader::m_spectrumTotalIonCountList

protected

Definition at line 135 of file mzcbormsrunreader.h.

Referenced by getTicChromatogram(), and initialize().

◆ mpa_mzcborFileDevice

QFile* pappso::MzcborMsRunReader::mpa_mzcborFileDevice = nullptr

protected

Definition at line 141 of file mzcbormsrunreader.h.

Referenced by acquireDevice(), fillMzcborSpectrum(), initialize(), readSpectrumCollectionWithMsrunReadConfig(), and releaseDevice().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ MzcborMsRunReader()

◆ ~MzcborMsRunReader()

Member Function Documentation

◆ accept()

◆ acquireDevice()

◆ fillMzcborSpectrum()

◆ getMzcborSpectrumSp()

◆ getOboPsiModTermInstrumentModelName()

◆ getRetentionTimeLine()

◆ getSpectrumIndexPositionInFile()

◆ getTicChromatogram()

◆ hasScanNumbers()

◆ initialize()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ qualifiedMassSpectrum()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ readSpectrumCollectionByMsLevel()

◆ readSpectrumCollectionWithMsrunReadConfig()

◆ releaseDevice()

◆ scanNumber2SpectrumIndex()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Member Data Documentation

◆ m_cborFileInfo

◆ m_nativeId2SpectrumIndexMap

◆ m_scan2SpectrumIndexMap

◆ m_spectrumIndexPositionInFile

◆ m_spectrumMsLevelList

◆ m_spectrumRtList

◆ m_spectrumTotalIonCountList

◆ mpa_mzcborFileDevice