pappso::TimsFramesMsRunReader Class Reference

#include <timsframesmsrunreader.h>

Inheritance diagram for pappso::TimsFramesMsRunReader:

Public Member Functions
	TimsFramesMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
virtual	~TimsFramesMsRunReader ()
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 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 Trace	computeTicChromatogram ()
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::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
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 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

Friends
class	MsFileAccessor

Additional Inherited Members
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
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 42 of file timsframesmsrunreader.h.

Constructor & Destructor Documentation

TimsFramesMsRunReader()

TimsFramesMsRunReader::TimsFramesMsRunReader

(

MsRunIdCstSPtr &

msrun_id_csp

)

Todo

write docs

Definition at line 37 of file timsframesmsrunreader.cpp.

  : TimsMsRunReaderBase(msrun_id_csp)
{
}

References pappso::TimsMsRunReaderBase::TimsMsRunReaderBase().

Referenced by MsFileAccessor.

~TimsFramesMsRunReader()

TimsFramesMsRunReader::~TimsFramesMsRunReader ( )

virtual

Definition at line 42 of file timsframesmsrunreader.cpp.

{
  msp_timsData = nullptr;
}

References pappso::TimsMsRunReaderBase::msp_timsData.

Member Function Documentation

computeTicChromatogram()

Trace TimsFramesMsRunReader::computeTicChromatogram ( )

virtual

Definition at line 445 of file timsframesmsrunreader.cpp.

{
 
  // We want to compute the TIC chromatogram, not load the chromatogram that
  // is located in the SQL database.
  //
  // For this, we need to iterated into the frames and ask for MS1 spectra
  // only. msp_timsData has that information:
  //
  // std::vector<FrameIdDescr> m_frameIdDescrList;
  //
  // and
 
  // struct FrameIdDescr
  // {
  //   std::size_t m_frameId;   // frame id
  //   std::size_t m_size;      // frame size (number of TOF scans in frame)
  //   std::size_t m_cumulSize; // cumulative size
  // };
 
  Trace tic_chromatogram;
 
  const std::vector<FrameIdDescr> frame_descr_list = msp_timsData->getFrameIdDescrList();
 
  for(FrameIdDescr frame_id_descr : frame_descr_list)
    {
      TimsFrameCstSPtr tims_frame_csp =
        msp_timsData->getTimsFrameCstSPtrCached(frame_id_descr.m_frameId);
      std::size_t scan_begin = 0;
      std::size_t scan_end   = tims_frame_csp->getTotalNumberOfScans() - 1;
 
      // By convention, a TIC chromatogram is only performed using MS1
      // spectra.
      if(tims_frame_csp->getMsLevel() == 1)
        {
 
          // Retention times are in seconds in the Bruker world.
          double rt = tims_frame_csp->getRtInSeconds();
 
          tic_chromatogram.append(
            DataPoint(rt, tims_frame_csp->cumulateScanRangeIntensities(scan_begin, scan_end)));
        }
      else
        continue;
    }
 
  return tic_chromatogram;
}

References pappso::Trace::append(), pappso::TimsFrame::cumulateScanRangeIntensities(), pappso::TimsFrameBase::getMsLevel(), pappso::TimsFrameBase::getRtInSeconds(), pappso::TimsFrameBase::getTotalNumberOfScans(), and pappso::TimsMsRunReaderBase::msp_timsData.

Referenced by MsFileAccessor.

massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 59 of file timsframesmsrunreader.cpp.

{
  return msp_timsData->getMassSpectrumCstSPtrByGlobalScanIndex(spectrum_index);
}

References pappso::TimsMsRunReaderBase::msp_timsData.

Referenced by MsFileAccessor.

massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 49 of file timsframesmsrunreader.cpp.

{
  throw ExceptionNotImplemented(
    QObject::tr("Not yet implemented in TimsFramesMsRunReader %1.\n").arg(__LINE__));
 
  return pappso::MassSpectrumSPtr();
}

Referenced by MsFileAccessor.

qualifiedMassSpectrum()

QualifiedMassSpectrum TimsFramesMsRunReader::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 66 of file timsframesmsrunreader.cpp.

{
 
  QualifiedMassSpectrum mass_spectrum;
 
  msp_timsData->getQualifiedMassSpectrumByGlobalScanIndex(
    getMsRunId(), mass_spectrum, spectrum_index, want_binary_data);
  return mass_spectrum;
}

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

Referenced by MsFileAccessor.

readSpectrumCollection()

void TimsFramesMsRunReader::readSpectrumCollection ( SpectrumCollectionHandlerInterface & handler )

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 79 of file timsframesmsrunreader.cpp.

{
  // qDebug() << "Reading the spectrum collection with no specific
  // configuration.";
  MsRunReadConfig config;
  readSpectrumCollection2(config, handler);
}

References readSpectrumCollection2().

Referenced by MsFileAccessor.

readSpectrumCollection2()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 89 of file timsframesmsrunreader.cpp.

{
  // qDebug().noquote() << "Reading the spectrum collection with this "
  //                       "specific configuration:"
  //                    << config.toString();
 
  std::vector<std::size_t> subset_of_tims_frame_ids;
 
 
  bool asked_ion_mobility_scan_num_range = false;
 
  quint32 mobility_scan_num_range_begin = std::numeric_limits<quint32>::max();
  quint32 mobility_scan_num_range_end   = std::numeric_limits<quint32>::max();
  quint32 mobility_scan_num_range_width = std::numeric_limits<quint32>::max();
 
  double mobility_one_over_k0             = std::numeric_limits<double>::max();
  double mobility_one_over_k0_range_begin = std::numeric_limits<double>::max();
  double mobility_one_over_k0_range_end   = std::numeric_limits<double>::max();
 
  if(!config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexBegin).isNull() &&
     !config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexEnd).isNull())
    {
      mobility_scan_num_range_begin =
        config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexBegin).toUInt();
      mobility_scan_num_range_end =
        config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobScanIndexEnd).toUInt();
 
      // We need the range width below.
      mobility_scan_num_range_width =
        mobility_scan_num_range_end + 1 - mobility_scan_num_range_begin;
 
      asked_ion_mobility_scan_num_range = true;
 
      // Be sure to check in the frames loop below that the user might
      // have asked for an ion mobility range but on the basis of the 1/K0 unit.
    }
 
  const std::vector<FrameIdDescr> &frame_id_descr_list = msp_timsData->getFrameIdDescrList();
 
  // Just for the feedback to the user.
  std::size_t scan_count = 0;
 
  for(auto const &frame_record : msp_timsData->getTimsFrameRecordList())
    {
      if(handler.shouldStop())
        {
          // qDebug() << "The operation was cancelled. Breaking the loop.";
          throw ExceptionInterrupted(QObject::tr("Reading timsTOF data cancelled by the user."));
        }
 
      if(frame_record.frame_id == 0)
        continue;
 
      if(!config.acceptRetentionTimeInSeconds(frame_record.frame_time))
        continue;
 
      std::size_t ms_level = 2;
      if(frame_record.msms_type == 0)
        ms_level = 1;
 
      if(!config.acceptMsLevel(ms_level))
        continue;
 
      // FIXME: this might be the place where to actually get the list of
      // precursors' m/z and charge values.
 
      subset_of_tims_frame_ids.push_back(frame_record.frame_id);
 
      if(mobility_scan_num_range_width != std::numeric_limits<int>::max())
        {
          scan_count += mobility_scan_num_range_width;
        }
      else
        {
          scan_count += frame_id_descr_list[frame_record.frame_id].m_scanCount;
        }
    }
 
  // At this point, we have a subset of frame records.
  std::size_t frame_count = subset_of_tims_frame_ids.size();
  qDebug() << "The number of retained RT range- and MS level-matching frames : " << frame_count;
 
  // Inform the handler of the spectrum list so that it can handle feedback to
  // the user.
 
  // FIXME:
  // Either we document the number of frames (because we assume we will
  // flatten them all)...
  handler.spectrumListHasSize(frame_count);
  // Or we document the number of actual scans because we might not flatten
  // all the frames.
  // handler.spectrumListHasSize(scan_count);
 
  // Check for m/z range selection
  bool asked_mz_range   = false;
  double mz_range_begin = -1;
  double mz_range_end   = -1;
 
  if(!config.getParameterValue(MsRunReadConfigParameter::MzRangeBegin).isNull())
    {
      asked_mz_range = true;
 
      mz_range_begin = config.getParameterValue(MsRunReadConfigParameter::MzRangeBegin).toDouble();
      mz_range_end   = config.getParameterValue(MsRunReadConfigParameter::MzRangeEnd).toDouble();
 
      // qDebug() << "The m/z range asked is: " << mz_range_begin << "--"
      //          << mz_range_end;
    }
 
  // Check for m/z resolution downgrading
  // The idea is that we merge a number of mz indices into a single index,
  // which is essentially an increase of the m/z bin size, and therefore
  // of the resolution/definition of the mass spectrum.
  std::size_t mz_index_merge_window = 0;
  if(!config.getParameterValue(MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow).isNull())
    {
      mz_index_merge_window =
        config.getParameterValue(MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow).toUInt();
 
      // qDebug() << "mz_index_merge_window=" << mz_index_merge_window;
    }
 
  // The scan index is the index of the scan in the *whole* mass data file, it
  // is a sequential number of scans over all the frames.
  std::size_t scan_index = 0; // iterate in each spectrum
 
  for(std::size_t tims_frame_id : subset_of_tims_frame_ids)
    {
      if(handler.shouldStop())
        {
          // qDebug() << "The operation was cancelled. Breaking the loop.";
          throw ExceptionInterrupted(QObject::tr("Reading timsTOF data cancelled by the user."));
        }
 
      // qDebug() << "tims_frame_id=" << tims_frame_id;
 
      const FrameIdDescr &current_frame_record = frame_id_descr_list[tims_frame_id];
      // qDebug() << "tims_frame_id=" << tims_frame_id;
 
      // FIXME: from an outsider point of view, cumulated size does not
      // convey the notion of sequential scan number.
 
      scan_index = current_frame_record.m_globalScanIndex;
 
      TimsFrameCstSPtr tims_frame_csp = msp_timsData->getTimsFrameCstSPtrCached(tims_frame_id);
 
      // If the user wants to select 1/Ko values in a given range, we need to
      // compute the ion mobility scan value starting from that 1/Ko value in
      // *each* frame. Note that the computed mobility_scan_num_begin and
      // mobility_scan_num_end would override thoses possibly set with
      // TimsFramesMsRunReader_mobility_index_begin/end above.
 
      if(!config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0Begin)
            .isNull() &&
         !config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0End).isNull())
        {
          mobility_one_over_k0_range_begin =
            config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0Begin)
              .toDouble();
 
          mobility_one_over_k0_range_end =
            config.getParameterValue(MsRunReadConfigParameter::TimsFrameIonMobOneOverK0End)
              .toDouble();
 
          mobility_scan_num_range_begin =
            tims_frame_csp.get()->getScanIndexFromOneOverK0(mobility_one_over_k0_range_begin);
 
          mobility_scan_num_range_end =
            tims_frame_csp.get()->getScanIndexFromOneOverK0(mobility_one_over_k0_range_end);
 
          asked_ion_mobility_scan_num_range = true;
        }
 
      // Now that we know if the user has asked for an ion mobility range,
      // either using scan indices or 1/K0 values, we need to double check the
      // range borders.
      quint32 count_of_mobility_scans = tims_frame_csp->getTotalNumberOfScans();
 
      if(asked_ion_mobility_scan_num_range)
        {
          if(mobility_scan_num_range_end > (count_of_mobility_scans - 1))
            {
              mobility_scan_num_range_end = count_of_mobility_scans - 1;
            }
        }
      else
        {
          mobility_scan_num_range_begin = 0;
          mobility_scan_num_range_end   = count_of_mobility_scans - 1;
        }
 
      // Now that we know the mobility index range, if we did not set the
      // mobility one over K0 because that was not the unit used by
      // the caller, then we can compute these values and set them
      // later to the qualified mass spectrum parameters.
      if(mobility_one_over_k0_range_begin == std::numeric_limits<double>::max())
        mobility_one_over_k0_range_begin =
          tims_frame_csp->getOneOverK0Transformation(mobility_scan_num_range_begin);
      if(mobility_one_over_k0_range_end == std::numeric_limits<double>::max())
        mobility_one_over_k0_range_end =
          tims_frame_csp->getOneOverK0Transformation(mobility_scan_num_range_end);
 
      mobility_scan_num_range_width =
        mobility_scan_num_range_end + 1 - mobility_scan_num_range_begin;
 
      // We want to provide the inverse mobility for the scan that sits in the
      // middle of the defined range or the whole range if none is defined..
      mobility_one_over_k0 = tims_frame_csp.get()->getScanIndexFromOneOverK0(
        mobility_scan_num_range_begin + (mobility_scan_num_range_width / 2));
 
      // Now, with or without the peak list, we have to craft a qualified mass
      // spectrum that will hold all the data about the data in it.
      QualifiedMassSpectrum qualified_mass_spectrum;
 
      MassSpectrumId spectrum_id;
 
      spectrum_id.setSpectrumIndex(tims_frame_id);
      spectrum_id.setMsRunId(getMsRunId());
 
      // Can be modified to add bits that might help our case
      spectrum_id.setNativeId(QString("frame_id=%1 global_scan_index=%2 im_scan_range_begin=%3 "
                                      "im_scan_range_end=%4")
                                .arg(tims_frame_id)
                                .arg(scan_index)
                                .arg(mobility_scan_num_range_begin)
                                .arg(mobility_scan_num_range_end));
 
      qualified_mass_spectrum.setMassSpectrumId(spectrum_id);
 
      // We want to document the retention time!
 
      qualified_mass_spectrum.setRtInSeconds(tims_frame_csp.get()->getRtInSeconds());
 
      // We do want to document the ms level of the spectrum and possibly
      // the precursor's m/z and charge.
      unsigned int frame_ms_level = tims_frame_csp.get()->getMsLevel();
      qualified_mass_spectrum.setMsLevel(frame_ms_level);
 
 
      // Arrival time at half the range.
 
      qualified_mass_spectrum.setDtInMilliSeconds(tims_frame_csp.get()->getDriftTimeInMilliseconds(
        mobility_scan_num_range_begin + (mobility_scan_num_range_width / 2)));
 
      // 1/K0
      qDebug() << "mobility_one_over_k0:" << mobility_one_over_k0
               << "mobility_one_over_k0_range_begin:" << mobility_one_over_k0_range_begin
               << "mobility_one_over_k0_range_end" << mobility_one_over_k0_range_end;
 
      if(mobility_one_over_k0 == std::numeric_limits<double>::max() ||
         mobility_one_over_k0_range_begin == std::numeric_limits<double>::max() ||
         mobility_one_over_k0_range_end == std::numeric_limits<double>::max())
        throw(
          ExceptionNotPossible("Not possible that mobility_one_over_k0 and its "
                               "range are undefined."));
 
      qualified_mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IonMobOneOverK0,
                                                mobility_one_over_k0);
      qualified_mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0Begin, mobility_one_over_k0_range_begin);
      qualified_mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IonMobOneOverK0End,
                                                mobility_one_over_k0_range_end);
 
      // qDebug() << "mobility_scan_num_range_begin:"
      //          << mobility_scan_num_range_begin
      //          << "mobility_scan_num_range_end:" <<
      //          mobility_scan_num_range_end;
 
      if(mobility_scan_num_range_begin == std::numeric_limits<quint32>::max() ||
         mobility_scan_num_range_end == std::numeric_limits<quint32>::max())
        throw(
          ExceptionNotPossible("Not possible that mobility_scan_num_range values are undefined."));
 
      qualified_mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::TimsIonMobScanIndex,
                                                mobility_scan_num_range_begin +
                                                  (mobility_scan_num_range_width / 2));
      qualified_mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexBegin,
        mobility_scan_num_range_begin);
      qualified_mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexEnd, mobility_scan_num_range_end);
 
      qualified_mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::TimsFrameScansCount,
        static_cast<qlonglong>(tims_frame_csp->getTotalNumberOfScans()));
 
 
      Trace trace;
 
      if(config.needPeakList())
        {
          // Provide these two variables for the function below to fill in the
          // values. We will need them later.
          quint32 min_mz_index_out = 0;
          quint32 max_mz_index_out = 0;
 
          if(asked_mz_range)
            {
              trace = tims_frame_csp->combineScansToTraceWithDowngradedMzResolution2(
                mz_index_merge_window,
                mz_range_begin,
                mz_range_end,
                mobility_scan_num_range_begin,
                mobility_scan_num_range_end,
                min_mz_index_out,
                max_mz_index_out);
            }
          else
            {
              trace = tims_frame_csp->combineScansToTraceWithDowngradedMzResolution(
                mz_index_merge_window,
                mobility_scan_num_range_begin,
                mobility_scan_num_range_end,
                min_mz_index_out,
                max_mz_index_out);
            }
 
          // qDebug() << "Got min_mz_index_out:" << min_mz_index_out;
          // qDebug() << "Got max_mz_index_out:" << max_mz_index_out;
 
          qualified_mass_spectrum.setParameterValue(
            QualifiedMassSpectrumParameter::TimsFrameMzIndexBegin, min_mz_index_out);
          qualified_mass_spectrum.setParameterValue(
            QualifiedMassSpectrumParameter::TimsFrameMzIndexEnd, max_mz_index_out);
 
          qualified_mass_spectrum.setMassSpectrumSPtr(std::make_shared<MassSpectrum>(trace));
          qualified_mass_spectrum.setEmptyMassSpectrum(false);
        }
      else
        {
          qualified_mass_spectrum.setEmptyMassSpectrum(true);
        }
 
      handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
    }
}

References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrameBase::getDriftTimeInMilliseconds(), pappso::TimsFrameBase::getMsLevel(), pappso::MsRunReader::getMsRunId(), pappso::TimsFrameBase::getOneOverK0Transformation(), pappso::MsRunReadConfig::getParameterValue(), pappso::TimsFrameBase::getRtInSeconds(), pappso::TimsFrameBase::getScanIndexFromOneOverK0(), pappso::TimsFrameBase::getTotalNumberOfScans(), pappso::IonMobOneOverK0, pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::FrameIdDescr::m_globalScanIndex, pappso::TimsMsRunReaderBase::msp_timsData, pappso::MzRangeBegin, pappso::MzRangeEnd, pappso::MsRunReadConfig::needPeakList(), pappso::QualifiedMassSpectrum::setDtInMilliSeconds(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize(), pappso::TimsFrameIonMobOneOverK0Begin, pappso::TimsFrameIonMobOneOverK0End, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::TimsFrameMzIndexBegin, pappso::TimsFrameMzIndexEnd, pappso::TimsFrameMzIndexMergeWindow, pappso::TimsFrameScansCount, and pappso::TimsIonMobScanIndex.

Referenced by MsFileAccessor, and readSpectrumCollection().

readSpectrumCollectionByMsLevel()

void TimsFramesMsRunReader::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 429 of file timsframesmsrunreader.cpp.

{
  qDebug();
}

Referenced by MsFileAccessor.

spectrumListSize()

std::size_t TimsFramesMsRunReader::spectrumListSize ( ) const

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 438 of file timsframesmsrunreader.cpp.

{
  return msp_timsData->getTotalScanCount();
}

References pappso::TimsMsRunReaderBase::msp_timsData.

Referenced by MsFileAccessor.

spectrumStringIdentifier2SpectrumIndex()

std::size_t TimsFramesMsRunReader::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 496 of file timsframesmsrunreader.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 44 of file timsframesmsrunreader.h.

References TimsFramesMsRunReader(), computeTicChromatogram(), massSpectrumCstSPtr(), massSpectrumSPtr(), MsFileAccessor, qualifiedMassSpectrum(), readSpectrumCollection(), readSpectrumCollection2(), readSpectrumCollectionByMsLevel(), spectrumListSize(), and spectrumStringIdentifier2SpectrumIndex().

Referenced by MsFileAccessor.

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

• pappsomspp/core/msrun/private/timsframesmsrunreader.h
• pappsomspp/core/msrun/private/timsframesmsrunreader.cpp