pappso::PwizMsRunReader Class Reference

#include <pwizmsrunreader.h>

Inheritance diagram for pappso::PwizMsRunReader:

Public Member Functions
	PwizMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
virtual	~PwizMsRunReader ()
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...
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...
bool	processRetentionTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
bool	processDriftTime (pwiz::msdata::Spectrum *spectrum_p, QualifiedMassSpectrum &qualified_mass_spectrum) const
QualifiedMassSpectrum	qualifiedMassSpectrumFromPwizMSData (std::size_t spectrum_index, bool want_binary_data, bool &ok) const
QualifiedMassSpectrum	qualifiedMassSpectrumFromPwizSpectrumPtr (const MassSpectrumId &massSpectrumId, pwiz::msdata::Spectrum *spectrum_p, bool want_binary_data, bool &ok) const
pwiz::msdata::SpectrumPtr	getPwizSpectrumPtr (pwiz::msdata::SpectrumList *p_spectrum_list, std::size_t spectrum_index, bool want_binary_data) const

Protected Attributes
pwiz::msdata::MSDataPtr	msp_msData = nullptr
Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId
MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Private Attributes
bool	m_hasScanNumbers = false

Friends
class	MsFileAccessor

Detailed Description

Definition at line 45 of file pwizmsrunreader.h.

Constructor & Destructor Documentation

PwizMsRunReader()

pappso::PwizMsRunReader::PwizMsRunReader

(

MsRunIdCstSPtr &

msrun_id_csp

)

Definition at line 53 of file pwizmsrunreader.cpp.

  : MsRunReader(msrun_id_csp)
{
  // The initialization needs to be done immediately so that we get the pwiz
  // MsDataPtr corresponding to the right ms_run_id in the parameter. That
  // pointer will be set to msp_msData.
 
  initialize();
}

References initialize().

~PwizMsRunReader()

pappso::PwizMsRunReader::~PwizMsRunReader ( )

virtual

Definition at line 164 of file pwizmsrunreader.cpp.

{
}

Member Function Documentation

accept()

bool pappso::PwizMsRunReader::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 726 of file pwizmsrunreader.cpp.

{
  // We want to know if we can handle the file_name.
  pwiz::msdata::ReaderList reader_list;
 
  std::string reader_type = reader_list.identify(file_name.toStdString());
 
  if(!reader_type.empty())
    return true;
 
  return false;
}

getPwizSpectrumPtr()

pwiz::msdata::SpectrumPtr pappso::PwizMsRunReader::getPwizSpectrumPtr ( pwiz::msdata::SpectrumList *  p_spectrum_list, std::size_t  spectrum_index, bool  want_binary_data  ) const

protected

Definition at line 170 of file pwizmsrunreader.cpp.

{
  pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp;
 
  try
    {
      native_pwiz_spectrum_sp =
        p_spectrum_list->spectrum(spectrum_index, want_binary_data);
    }
  catch(std::runtime_error &error)
    {
      qDebug() << "getPwizSpectrumPtr error " << error.what() << " "
               << typeid(error).name();
 
      throw ExceptionNotFound(QObject::tr("Pwiz spectrum index %1 not found in "
                                          "MS file std::runtime_error :\n%2")
                                .arg(spectrum_index)
                                .arg(error.what()));
    }
  catch(std::exception &error)
    {
      qDebug() << "getPwizSpectrumPtr error " << error.what()
               << typeid(error).name();
 
      throw ExceptionNotFound(
        QObject::tr("Pwiz spectrum index %1 not found in MS file :\n%2")
          .arg(spectrum_index)
          .arg(error.what()));
    }
 
  if(native_pwiz_spectrum_sp.get() == nullptr)
    {
      throw ExceptionNotFound(
        QObject::tr(
          "Pwiz spectrum index %1 not found in MS file : null pointer")
          .arg(spectrum_index));
    }
 
  return native_pwiz_spectrum_sp;
}

Referenced by qualifiedMassSpectrumFromPwizMSData(), and readSpectrumCollection().

hasScanNumbers()

bool pappso::PwizMsRunReader::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 915 of file pwizmsrunreader.cpp.

{
  return m_hasScanNumbers;
}

References m_hasScanNumbers.

initialize()

void pappso::PwizMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 65 of file pwizmsrunreader.cpp.

{
  std::string file_name_std =
    Utils::toUtf8StandardString(mcsp_msRunId->getFileName());
 
  // Make a backup of the current locale
  std::string env_backup = setlocale(LC_ALL, "");
  // struct lconv *lc       = localeconv();
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
  //<< "env_backup=" << env_backup.c_str() << "lc->decimal_point"
  //<< lc->decimal_point;
 
  // Now actually search the useful MSDataPtr to the member variable.
 
  pwiz::msdata::DefaultReaderList defaultReaderList;
 
  std::vector<pwiz::msdata::MSDataPtr> msDataPtrVector;
 
  try
    {
      defaultReaderList.read(file_name_std, msDataPtrVector);
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failed to read the data from file %1")
                    .arg(QString::fromStdString(file_name_std));
    }
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
  //<< "The number of runs is:" << msDataPtrVector.size()
  //<< "The number of spectra in first run is:"
  //<< msDataPtrVector.at(0)->run.spectrumListPtr->size();
 
  // Single-run file handling here.
 
  // Specific case of the MGF data format: we do not have a run id for that kind
  // of data. In this case there must be a single run!
 
  if(mcsp_msRunId->getRunId().isEmpty())
    {
      if(msDataPtrVector.size() != 1)
        throw(
          ExceptionNotPossible("For the kind of file at hand there can only be "
                               "one run in the file."));
 
      // At this point we know the single msDataPtr is the one we are looking
      // for.
 
      msp_msData = msDataPtrVector.front();
    }
 
  else
    {
      // Multi-run file handling here.
      for(auto &msDataPtr : msDataPtrVector)
        {
          if(msDataPtr->run.id == mcsp_msRunId->getRunId().toStdString())
            {
              msp_msData = msDataPtr;
 
              // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
              //<< "Found the right MSDataPtr for run id.";
 
              break;
            }
        }
    }
 
  if(msp_msData == nullptr)
    {
      throw(ExceptionNotPossible(
        "Could not find a MSDataPtr matching the requested run id."));
    }
 
 
  // check if this MS run can be used with scan numbers
  // MS:1000490 Agilent instrument model
  pwiz::cv::CVID native_id_format =
    pwiz::msdata::id::getDefaultNativeIDFormat(*msp_msData.get());
 
  // msp_msData.get()->getDefaultNativeIDFormat();
 
  if(native_id_format == pwiz::cv::CVID::MS_Thermo_nativeID_format)
    {
      m_hasScanNumbers = true;
    }
  else
    {
      m_hasScanNumbers = false;
    }
 
  if(mcsp_msRunId.get()->getMzFormat() == MzFormat::mzXML)
    {
      m_hasScanNumbers = true;
    }
}

References m_hasScanNumbers, pappso::MsRunReader::mcsp_msRunId, msp_msData, and pappso::Utils::toUtf8StandardString().

Referenced by PwizMsRunReader().

massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 748 of file pwizmsrunreader.cpp.

{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  return qualifiedMassSpectrum(spectrum_index, true).getMassSpectrumCstSPtr();
}

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

massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 741 of file pwizmsrunreader.cpp.

{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  return qualifiedMassSpectrum(spectrum_index, true).getMassSpectrumSPtr();
}

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

processDriftTime()

bool pappso::PwizMsRunReader::processDriftTime ( pwiz::msdata::Spectrum *  spectrum_p, QualifiedMassSpectrum &  qualified_mass_spectrum  ) const

protected

Definition at line 283 of file pwizmsrunreader.cpp.

{
  // Not all the acquisitions have ion mobility data. We need to test
  // that:
 
  if(spectrum_p->scanList.scans[0].hasCVParam(
       pwiz::msdata::MS_ion_mobility_drift_time))
    {
 
      // qDebug() << "as strings:"
      //<< QString::fromStdString(
      // spectrum_p->scanList.scans[0]
      //.cvParam(pwiz::msdata::MS_ion_mobility_drift_time)
      //.valueAs<std::string>());
 
      pappso_double driftTime =
        spectrum_p->scanList.scans[0]
          .cvParam(pwiz::msdata::MS_ion_mobility_drift_time)
          .valueAs<double>();
 
      // qDebug() << "driftTime:" << driftTime;
 
      // Old version requiring use of QString.
      // pappso_double driftTime =
      // QString(spectrum_p->scanList.scans[0]
      //.cvParam(pwiz::msdata::MS_ion_mobility_drift_time)
      //.value.c_str())
      //.toDouble();
 
      // Now make positively sure that the obtained value is correct.
      // Note that I suffered a lot with Waters Synapt data that
      // contained apparently correct drift time XML element that in
      // fact contained either NaN or inf. When such mass spectra were
      // encountered, the mz,i data were bogus and crashed the data
      // loading functions. We just want to skip this kind of bogus mass
      // spectrum by letting the caller  know that the drift time was
      // bogus ("I" is Filippo Rusconi).
 
      if(std::isnan(driftTime) || std::isinf(driftTime))
        {
          // qDebug() << "detected as nan or inf.";
 
          return false;
        }
      else
        {
          // The mzML standard stipulates that drift times are in
          // milliseconds.
          qualified_mass_spectrum.setDtInMilliSeconds(driftTime);
        }
    }
  // End of
  // if(spectrum_p->scanList.scans[0].hasCVParam(
  // pwiz::msdata::MS_ion_mobility_drift_time))
  else
    {
      // Not a bogus mass spectrum but also not a drift spectrum, set -1
      // as the drift time value.
      qualified_mass_spectrum.setDtInMilliSeconds(-1);
    }
 
  return true;
}

References pappso::QualifiedMassSpectrum::setDtInMilliSeconds().

Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().

processRetentionTime()

bool pappso::PwizMsRunReader::processRetentionTime ( pwiz::msdata::Spectrum *  spectrum_p, QualifiedMassSpectrum &  qualified_mass_spectrum  ) const

protected

Definition at line 215 of file pwizmsrunreader.cpp.

{
 
  //  We now have to set the retention time at which this mass spectrum
  //  was acquired. This is the scan start time.
 
  if(!spectrum_p->scanList.scans[0].hasCVParam(
       pwiz::msdata::MS_scan_start_time))
    {
      if(mcsp_msRunId.get()->getMzFormat() == MzFormat::MGF)
        { // MGF could not have scan start time
          qualified_mass_spectrum.setRtInSeconds(-1);
        }
      else
        {
          throw(ExceptionNotPossible(
            "The spectrum has no scan start time value set."));
        }
    }
  else
    {
      pwiz::data::CVParam retention_time_cv_param =
        spectrum_p->scanList.scans[0].cvParam(pwiz::msdata::MS_scan_start_time);
 
      // Try to get the units of the retention time value.
 
      std::string unit_name = retention_time_cv_param.unitsName();
      // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
      //<< "Unit name for the retention time:"
      //<< QString::fromStdString(unit_name);
 
      if(unit_name == "second")
        {
          qualified_mass_spectrum.setRtInSeconds(
            retention_time_cv_param.valueAs<double>());
        }
      else if(unit_name == "minute")
        {
          qualified_mass_spectrum.setRtInSeconds(
            retention_time_cv_param.valueAs<double>() * 60);
        }
      else
        throw(
          ExceptionNotPossible("Could not determine the unit for the "
                               "scan start time value."));
    }
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
  //<< "Retention time for spectrum is:"
  //<< qualified_mass_spectrum.getRtInSeconds();
 
  // Old version not checking unit (by default unit is minutes for RT,
  // not seconds)
  //
  // pappso_double retentionTime =
  // QString(spectrum_p->scanList.scans[0]
  //.cvParam(pwiz::msdata::MS_scan_start_time)
  //.value.c_str())
  //.toDouble();
  // qualified_mass_spectrum.setRtInSeconds(retentionTime);
 
  return true;
}

References pappso::MsRunReader::mcsp_msRunId, and pappso::QualifiedMassSpectrum::setRtInSeconds().

Referenced by qualifiedMassSpectrumFromPwizSpectrumPtr().

qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::PwizMsRunReader::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 755 of file pwizmsrunreader.cpp.

{
 
  QualifiedMassSpectrum spectrum;
  bool ok = false;
 
  spectrum =
    qualifiedMassSpectrumFromPwizMSData(spectrum_index, want_binary_data, ok);
 
  if(mcsp_msRunId->getMzFormat() == pappso::MzFormat::MGF)
    {
      if(spectrum.getRtInSeconds() == 0)
        {
          // spectrum = qualifiedMassSpectrumFromPwizMSData(scan_num - 1);
        }
    }
 
  // if(!ok)
  // qDebug() << "Encountered a mass spectrum for which the status is bad.";
 
  return spectrum;
}

References pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MsRunReader::mcsp_msRunId, and qualifiedMassSpectrumFromPwizMSData().

Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().

qualifiedMassSpectrumFromPwizMSData()

QualifiedMassSpectrum pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizMSData ( std::size_t  spectrum_index, bool  want_binary_data, bool &  ok  ) const

protected

Definition at line 672 of file pwizmsrunreader.cpp.

{
 
  std::string env;
  env = setlocale(LC_ALL, "");
  // struct lconv *lc = localeconv();
 
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
  //<< "env=" << env.c_str()
  //<< "lc->decimal_point:" << lc->decimal_point;
 
  setlocale(LC_ALL, "C");
 
  MassSpectrumId massSpectrumId(mcsp_msRunId);
 
  if(msp_msData == nullptr)
    {
      setlocale(LC_ALL, env.c_str());
      return (QualifiedMassSpectrum(massSpectrumId));
    }
 
  // const bool want_binary_data = true;
 
  pwiz::msdata::SpectrumListPtr spectrum_list_p =
    msp_msData->run.spectrumListPtr;
 
  if(spectrum_index == spectrum_list_p.get()->size())
    {
      setlocale(LC_ALL, env.c_str());
      throw ExceptionNotFound(
        QObject::tr("The spectrum index cannot be equal to the size of the "
                    "spectrum list."));
    }
 
  // At this point we know the spectrum index might be sane, so store it in
  // the mass spec id object.
  massSpectrumId.setSpectrumIndex(spectrum_index);
 
  pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
    getPwizSpectrumPtr(spectrum_list_p.get(), spectrum_index, want_binary_data);
 
  setlocale(LC_ALL, env.c_str());
 
  massSpectrumId.setNativeId(
    QString::fromStdString(native_pwiz_spectrum_sp->id));
 
  return qualifiedMassSpectrumFromPwizSpectrumPtr(
    massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
}

References getPwizSpectrumPtr(), pappso::MsRunReader::mcsp_msRunId, msp_msData, qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::MassSpectrumId::setNativeId(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by qualifiedMassSpectrum().

qualifiedMassSpectrumFromPwizSpectrumPtr()

QualifiedMassSpectrum pappso::PwizMsRunReader::qualifiedMassSpectrumFromPwizSpectrumPtr ( const MassSpectrumId &  massSpectrumId, pwiz::msdata::Spectrum *  spectrum_p, bool  want_binary_data, bool &  ok  ) const

protected

Definition at line 351 of file pwizmsrunreader.cpp.

{
  // qDebug();
 
  std::string env;
  env = setlocale(LC_ALL, "");
  setlocale(LC_ALL, "C");
 
  QualifiedMassSpectrum qualified_mass_spectrum(massSpectrumId);
 
  try
    {
 
      // We want to store the ms level for this spectrum
 
      int msLevel =
        (spectrum_p->cvParam(pwiz::msdata::MS_ms_level).valueAs<int>());
 
      qualified_mass_spectrum.setMsLevel(msLevel);
 
      // We want to know if this spectrum is a fragmentation spectrum obtained
      // from a selected precursor ion.
 
      std::size_t precursor_list_size = spectrum_p->precursors.size();
 
      //qDebug() << "For spectrum at index:" << massSpectrumId.getSpectrumIndex()
               //<< "msLevel:" << msLevel
               //<< "with number of precursors:" << precursor_list_size;
 
      if(precursor_list_size > 0)
        {
 
          // Sanity check
          if(msLevel < 2)
            {
              qDebug() << "Going to throw: msLevel cannot be less than two for "
                          "a spectrum that has items in its Precursor list.";
 
              throw(ExceptionNotPossible(
                "msLevel cannot be less than two for "
                "a spectrum that has items in its Precursor list."));
            }
 
          // See what is the first precursor in the list.
 
          for(auto &precursor : spectrum_p->precursors)
            {
 
              // Set this variable ready as we need that default value in
              // certain circumstances.
 
              std::size_t precursor_spectrum_index =
                std::numeric_limits<std::size_t>::max();
 
              // The spectrum ID of the precursor might be empty.
 
              if(precursor.spectrumID.empty())
                {
                  // qDebug() << "The precursor's spectrum ID is empty.";
 
                  if(mcsp_msRunId.get()->getMzFormat() == MzFormat::MGF)
                    {
                      // qDebug()
                      //<< "Format is MGF, precursor's spectrum ID can be
                      // empty.";
                    }
                  else
                    {
                      // When performing Lumos Fusion fragmentation experiments
                      // in Tune mode and with recording, the first spectrum of
                      // the list is a fragmentation spectrum (ms level 2) that
                      // has no identity for the precursor spectrum because
                      // there is no full scan accquisition.
                    }
                }
              // End of
              // if(precursor.spectrumID.empty())
              else
                {
                  // We could get a native precursor spectrum id, so convert
                  // that native id to a spectrum index.
 
                  qualified_mass_spectrum.setPrecursorNativeId(
                    QString::fromStdString(precursor.spectrumID));
 
                  if(qualified_mass_spectrum.getPrecursorNativeId().isEmpty())
                    {
                      // qDebug() << "The native id of the precursor spectrum is
                      // empty.";
                    }
 
                  //  Get the spectrum index of the spectrum that contained the
                  //  precursor ion.
 
                  precursor_spectrum_index =
                    msp_msData->run.spectrumListPtr->find(precursor.spectrumID);
 
                  // Note that the Mascot MGF format has a peculiar handling of
                  // the precursor ion stuff so we cannot throw.
                  if(precursor_spectrum_index ==
                     msp_msData->run.spectrumListPtr->size())
                    {
                      if(mcsp_msRunId.get()->getMzFormat() != MzFormat::MGF)
                        {
                          throw(ExceptionNotPossible(
                            "Failed to find the index of the "
                            "precursor ion's spectrum."));
                        }
                    }
 
                  qualified_mass_spectrum.setPrecursorSpectrumIndex(
                    precursor_spectrum_index);
 
                  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ <<
                  // "()"
                  //<< "Set the precursor spectrum index to:"
                  //<< qualified_mass_spectrum.getPrecursorSpectrumIndex()
                  //<< "for qualified mass spectrum:"
                  //<< &qualified_mass_spectrum;
                }
 
              if(!precursor.selectedIons.size())
                {
                  qDebug()
                    << "Going to throw The spectrum has msLevel > 1 but the "
                       "precursor ions's selected ions list is empty..";
 
                  throw(
                    ExceptionNotPossible("The spectrum has msLevel > 1 but the "
                                         "precursor ions's selected ions "
                                         "list is empty."));
                }
 
              pwiz::msdata::SelectedIon &ion =
                *(precursor.selectedIons.begin());
 
              // selected ion m/z
 
              pappso_double selected_ion_mz =
                QString(
                  ion.cvParam(pwiz::cv::MS_selected_ion_m_z).value.c_str())
                  .toDouble();
 
              // selected ion peak intensity
 
              pappso_double selected_ion_peak_intensity =
                QString(ion.cvParam(pwiz::cv::MS_peak_intensity).value.c_str())
                  .toDouble();
 
              // charge state
 
              unsigned int selected_ion_charge_state =
                QString(ion.cvParam(pwiz::cv::MS_charge_state).value.c_str())
                  .toUInt();
 
              // At this point we can craft a new PrecursorIonData instance and
              // push it back to the vector.
 
              PrecursorIonData precursor_ion_data(selected_ion_mz,
                                                  selected_ion_charge_state,
                                                  selected_ion_peak_intensity);
 
              qualified_mass_spectrum.appendPrecursorIonData(
                precursor_ion_data);
 
              // General sum-up
 
              //qDebug()
                //<< "Appended new PrecursorIonData:"
                //<< "mz:"
                //<< qualified_mass_spectrum.getPrecursorIonData().back().mz
                //<< "charge:"
                //<< qualified_mass_spectrum.getPrecursorIonData().back().charge
                //<< "intensity:"
                //<< qualified_mass_spectrum.getPrecursorIonData()
                     //.back()
                     //.intensity;
            }
          // End of
          // for(auto &precursor : spectrum_p->precursors)
        }
      // End of
      // if(precursor_list_size > 0)
      else
        {
          // Sanity check
 
          // Unfortunately, logic here is defeated by some vendors that have
          // files with MS2 spectra without <precursorList>. Thus we have
          // spectrum_p->precursors.size() == 0 and msLevel > 1.
 
          // if(msLevel != 1)
          //{
          // throw(
          // ExceptionNotPossible("msLevel cannot be different than 1 if "
          //"there is not a single precursor ion."));
          //}
        }
 
      qDebug();
 
      // Sanity check.
 
      if(precursor_list_size !=
         qualified_mass_spectrum.getPrecursorIonData().size())
        {
          qDebug() << "Going to throw The number of precursors in the file is "
                      "different from the number of precursors in memory.";
 
          throw pappso::PappsoException(
            QObject::tr("The number of precursors in the file is different "
                        "from the number of precursors in memory."));
        }
 
      //if(precursor_list_size == 1)
        //{
          //qDebug() << "Trying to get the mz value of the unique precursor ion:"
                   //<< qualified_mass_spectrum.getPrecursorMz();
        //}
 
      processRetentionTime(spectrum_p, qualified_mass_spectrum);
 
      processDriftTime(spectrum_p, qualified_mass_spectrum);
 
      // for(pwiz::data::CVParam cv_param : ion.cvParams)
      //{
      // pwiz::msdata::CVID param_id = cv_param.cvid;
      // qDebug() << param_id;
      // qDebug() << cv_param.cvid.c_str();
      // qDebug() << cv_param.name().c_str();
      // qDebug() << cv_param.value.c_str();
      //}
 
      if(want_binary_data)
        {
 
          // Fill-in MZIntensityPair vector for convenient access to binary
          // data
 
          std::vector<pwiz::msdata::MZIntensityPair> pairs;
          spectrum_p->getMZIntensityPairs(pairs);
 
          MassSpectrum spectrum;
          double tic = 0;
          // std::size_t iterCount = 0;
 
          // Iterate through the m/z-intensity pairs
          for(std::vector<pwiz::msdata::MZIntensityPair>::const_iterator
                it  = pairs.begin(),
                end = pairs.end();
              it != end;
              ++it)
            {
              //++iterCount;
 
              // qDebug() << "it->mz " << it->mz << " it->intensity" <<
              // it->intensity;
              if(it->intensity)
                {
                  spectrum.push_back(DataPoint(it->mz, it->intensity));
                  tic += it->intensity;
                }
            }
 
          if(mcsp_msRunId.get()->getMzFormat() == MzFormat::MGF)
            {
              // Sort peaks by mz
              spectrum.sortMz();
            }
 
          // lc = localeconv ();
          // qDebug() << " env=" << localeconv () << " lc->decimal_point "
          // << lc->decimal_point;
          //  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()
          //  "<< spectrum.size();
          MassSpectrumSPtr spectrum_sp = spectrum.makeMassSpectrumSPtr();
          qualified_mass_spectrum.setMassSpectrumSPtr(spectrum_sp);
 
          // double sumY =
          // qualified_mass_spectrum.getMassSpectrumSPtr()->sumY(); qDebug()
          // <<
          // __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
          //<< "iterCount:" << iterCount << "Spectrum size "
          //<< spectrum.size() << "with tic:" << tic
          //<< "and sumY:" << sumY;
        }
      else
        qualified_mass_spectrum.setMassSpectrumSPtr(nullptr);
    }
  catch(PappsoException &errorp)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data using the proteowizard library: %1")
          .arg(errorp.qwhat()));
    }
  catch(std::exception &error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data using the proteowizard library: %1")
          .arg(error.what()));
    }
 
  // setlocale(LC_ALL, env.c_str());
 
  ok = true;
 
  // qDebug() << "QualifiedMassSpectrum: " <<
  // qualified_mass_spectrum.toString();
  return qualified_mass_spectrum;
}

References pappso::QualifiedMassSpectrum::appendPrecursorIonData(), pappso::QualifiedMassSpectrum::getPrecursorIonData(), pappso::QualifiedMassSpectrum::getPrecursorNativeId(), pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, msp_msData, processDriftTime(), processRetentionTime(), pappso::PappsoException::qwhat(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), and pappso::MassSpectrum::sortMz().

Referenced by qualifiedMassSpectrumFromPwizMSData(), and readSpectrumCollection().

readSpectrumCollection()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 781 of file pwizmsrunreader.cpp.

{
 
  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";
 
  // We want to iterate in the pwiz-spectrum-list and for each pwiz-spectrum
  // create a pappso-spectrum (QualifiedMassSpectrum). Once the pappso mass
  // spectrum has been fully qualified (that is, the member data have been
  // set), it is transferred to the handler passed as parameter to this
  // function for the consumer to do what it wants with it.
 
  // Does the handler consuming the mass spectra read from file want these
  // mass spectra to hold the binary data arrays (mz/i vectors)?
 
  const bool want_binary_data = handler.needPeakList();
 
 
  std::string env;
  env = setlocale(LC_ALL, "");
  setlocale(LC_ALL, "C");
 
 
  // We access the pwiz-mass-spectra via the spectrumListPtr that sits in the
  // run member of msp_msData.
 
  pwiz::msdata::SpectrumListPtr spectrum_list_p =
    msp_msData->run.spectrumListPtr;
 
  // We'll need it to perform the looping in the spectrum list.
  std::size_t spectrum_list_size = spectrum_list_p.get()->size();
 
  // 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.
 
  for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
    {
 
      // 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;
        }
 
      // Get the native pwiz-spectrum from the spectrum list.
      // Note that this pointer is a shared pointer from pwiz.
 
      pwiz::msdata::SpectrumPtr native_pwiz_spectrum_sp =
        getPwizSpectrumPtr(spectrum_list_p.get(), iter, want_binary_data);
 
      /*
       * we want to load metadata of the spectrum even if it does not contain
       peaks
 
       * if(!native_pwiz_spectrum_sp->hasBinaryData())
              {
                // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ <<
       "
       ()"
                //<< "native pwiz spectrum is empty, continuing.";
                continue;
              }
              */
 
      // Instantiate the mass spectrum id that will hold critical information
      // like the the native id string and the spectrum index.
 
      MassSpectrumId massSpectrumId(mcsp_msRunId, iter /* spectrum index*/);
 
      // Get the spectrum native id as a QString to store it in the mass
      // spectrum id class. This is will allow later to refer to the same
      // spectrum starting back from the file.
 
      QString native_id = QString::fromStdString(native_pwiz_spectrum_sp->id);
      massSpectrumId.setNativeId(native_id);
 
      // Finally, instantiate the qualified mass spectrum with its id. This
      // function will continue performing pappso-spectrum detailed
      // qualification.
 
      bool ok = false;
 
      QualifiedMassSpectrum qualified_mass_spectrum =
        qualifiedMassSpectrumFromPwizSpectrumPtr(
          massSpectrumId, native_pwiz_spectrum_sp.get(), want_binary_data, ok);
 
      if(!ok)
        {
          // qDebug() << "Encountered a mass spectrum for which the returned "
          //"status is bad.";
          continue;
        }
 
      // Before handing the mass spectrum out to the handler, see if the
      // native mass spectrum was empty or not.
 
      // if(!native_pwiz_spectrum_sp->defaultArrayLength)
      // qDebug() << "The mass spectrum has not defaultArrayLength";
 
      qualified_mass_spectrum.setEmptyMassSpectrum(
        !native_pwiz_spectrum_sp->defaultArrayLength);
 
      // The handler will receive the index of the mass spectrum in the
      // current run via the mass spectrum id member datum.
      handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
    }
 
  setlocale(LC_ALL, env.c_str());
  // 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 getPwizSpectrumPtr(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().

spectrumListSize()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 909 of file pwizmsrunreader.cpp.

{
  return msp_msData->run.spectrumListPtr.get()->size();
}

References msp_msData.

Friends And Related Function Documentation

MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 47 of file pwizmsrunreader.h.

Member Data Documentation

m_hasScanNumbers

bool pappso::PwizMsRunReader::m_hasScanNumbers = false

private

Definition at line 95 of file pwizmsrunreader.h.

Referenced by hasScanNumbers(), and initialize().

msp_msData

pwiz::msdata::MSDataPtr pappso::PwizMsRunReader::msp_msData = nullptr

protected

Definition at line 70 of file pwizmsrunreader.h.

Referenced by initialize(), qualifiedMassSpectrumFromPwizMSData(), qualifiedMassSpectrumFromPwizSpectrumPtr(), readSpectrumCollection(), and spectrumListSize().

---

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

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