pappso::PwizMsRunReader Class Reference

#include <pwizmsrunreader.h>

Inheritance diagram for pappso::PwizMsRunReader:

Public Member Functions
	PwizMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
virtual	~PwizMsRunReader ()
const pwiz::msdata::MSDataPtr	getMsDataPtr () const
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	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
const OboPsiModTerm	getOboPsiModTermNativeIDFormat () const
	get OboPsiModTerm corresponding to the nativeID format format of mz data
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::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.
virtual std::vector< double >	getRetentionTimeLine ()
	retention timeline get retention times along the MSrun in seconds
virtual Trace	getTicChromatogram ()
	get a TIC chromatogram
void	setMonoThread (bool is_mono_thread)
	set only one is_mono_thread to true
bool	isMonoThread () const

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

Static Protected Member Functions
static std::string	setGlobalLocaleToEnglish ()
static void	setGlobalLocaleToCurrentOs (const std::string &environment_locale)

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

Static Protected Attributes
static QMutex	m_mutex

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

Referenced by MsFileAccessor.

~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 733 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;
}

Referenced by MsFileAccessor.

acquireDevice()

bool pappso::PwizMsRunReader::acquireDevice ( )

overridevirtual

acquire data back end device

Returns

bool true if done

Implements pappso::MsRunReader.

Definition at line 1110 of file pwizmsrunreader.cpp.

{
  if(msp_msData == nullptr)
    {
      initialize();
    }
  return true;
}

References initialize(), and msp_msData.

Referenced by MsFileAccessor, readSpectrumCollectionByMsLevel(), readSpectrumCollectionWithMsrunReadConfig(), and spectrumStringIdentifier2SpectrumIndex().

getMsDataPtr()

const pwiz::msdata::MSDataPtr pappso::PwizMsRunReader::getMsDataPtr

(

)

const

Definition at line 170 of file pwizmsrunreader.cpp.

{
  return msp_msData;
}

References msp_msData.

Referenced by MsFileAccessor.

getOboPsiModTermInstrumentModelName()

const pappso::OboPsiModTerm pappso::PwizMsRunReader::getOboPsiModTermInstrumentModelName ( ) const

overrideprotectedvirtual

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

Velos Plus: Thermo Scientific second generation Velos.

LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite.

Orbitrap Fusion: Thermo Scientific Orbitrap Fusion.

LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite.

Q Exactive HF: Thermo Scientific Q Exactive.

LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite.

Exactive Plus: Thermo Scientific Exactive Plus MS.

Q Exactive Plus: Thermo Scientific Q Exactive Plus.

Orbitrap Fusion Lumos: Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.

Q Exactive HF-X: Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS.

Orbitrap Exploris 480: Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS.

Orbitrap Eclipse: Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.

Orbitrap Exploris 240: Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS.

Orbitrap Exploris 120: Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS.

LTQ Orbitrap Velos Pro: Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro.

Q Exactive UHMR: Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS.

TSQ Altis Plus: Thermo Scientific TSQ Altis Plus Triple Quadrupole MS.

Orbitrap Ascend: Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.

Orbitrap Astral: Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer.

Reimplemented from pappso::MsRunReader.

Definition at line 1206 of file pwizmsrunreader.cpp.

{
 
 
  pappso::OboPsiModTerm term;
 
  if(getOboPsiModTermNativeIDFormat().getAccession() == "MS:1000768")
    {
 
      pappso::FilterOboPsiModMap psims_map;
 
      pappso::OboPsiMs psims_file(psims_map);
      // it should be a Thermo instrument
      /*
       * [Term]
    id: MS:1000494
    name: Thermo Scientific instrument model
    def: "Thermo Scientific instrument model." [PSI:MS]
    is_a: MS:1000483 ! Thermo Fisher Scientific instrument model
 
      */
      term = psims_map.getOboPsiModTermWithAccession("MS:1000494");
 
      for(auto &param_group : msp_msData.get()->paramGroupPtrs)
        {
          for (const auto &cv_param : param_group.get()->cvParams) {
              if(cv_param.cvid == pwiz::cv::CVID::MS_Q_Exactive)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1001911");
                }
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Velos_Plus)
                {
                  /// Velos Plus: Thermo Scientific second generation Velos.
                  term = psims_map.getOboPsiModTermWithAccession("MS:1001909");
                }
              else if(cv_param.cvid == pwiz::cv::CVID::MS_LTQ_Orbitrap_Elite)
                {
                  /// LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred
                  /// to as the Orbitrap Elite.
 
                  term = psims_map.getOboPsiModTermWithAccession("MS:1001910");
                }
 
              /// Orbitrap Fusion: Thermo Scientific Orbitrap Fusion.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Fusion)
                {
                  /// LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred
                  /// to as the Orbitrap Elite.
 
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002416");
                }
              /// Q Exactive HF: Thermo Scientific Q Exactive.
              // MS_Q_Exactive_HF = 1002523,
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Q_Exactive_HF)
                {
                  /// LTQ Orbitrap Elite: Thermo Scientific LTQ Orbitrap Elite, often just referred
                  /// to as the Orbitrap Elite.
 
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002523");
                }
              //
              /// Exactive Plus: Thermo Scientific Exactive Plus MS.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Exactive_Plus)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002526");
                }
              /// Q Exactive Plus: Thermo Scientific Q Exactive Plus.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Q_Exactive_Plus)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002634");
                }
              /// Orbitrap Fusion Lumos: Thermo Scientific Orbitrap Fusion Lumos mass spectrometer
              /// with Tribrid architecture consisting of quadrupole mass filter, linear ion trap
              /// and Orbitrap mass analyzers.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Fusion_Lumos)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002732");
                }
              /// Q Exactive HF-X: Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Q_Exactive_HF_X)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1002877");
                }
              /// Orbitrap Exploris 480: Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap
              /// MS.
 
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Exploris_480)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003028");
                }
              /// Orbitrap Eclipse: Thermo Scientific Orbitrap Eclipse mass spectrometer with
              /// Tribrid architecture consisting of quadrupole mass filter, linear ion trap and
              /// Orbitrap mass analyzers.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Eclipse)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003029");
                }
              /// Orbitrap Exploris 240: Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap
              /// MS.
 
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Exploris_240)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003094");
                }
              /// Orbitrap Exploris 120: Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap
              /// MS.
 
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Exploris_120)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003095");
                }
              /// LTQ Orbitrap Velos Pro: Thermo Scientific LTQ Orbitrap Velos Pro, often just
              /// referred to as the Orbitrap Velos Pro.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_LTQ_Orbitrap_Velos_Pro)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003096");
                }
              /// Q Exactive UHMR: Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid
              /// Quadrupole Orbitrap MS.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Q_Exactive_UHMR)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003245");
                }
              /// TSQ Altis Plus: Thermo Scientific TSQ Altis Plus Triple Quadrupole MS.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_TSQ_Altis_Plus)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003292");
                }
              /// Orbitrap Ascend: Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid
              /// architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap
              /// mass analyzers.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Ascend)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003356");
                }
              /// Orbitrap Astral: Thermo Scientific Orbitrap Astral mass spectrometer contains
              /// three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral
              /// analyzer.
              else if(cv_param.cvid == pwiz::cv::CVID::MS_Orbitrap_Astral)
                {
                  term = psims_map.getOboPsiModTermWithAccession("MS:1003378");
                }
          }
        }
    }
  else
    {
 
      throw ExceptionNotFound(QObject::tr("instrument model name not found in %1")
                                .arg(mcsp_msRunId.get()->getFileName()));
    }
 
  return term;
}

References getOboPsiModTermNativeIDFormat(), pappso::FilterOboPsiModMap::getOboPsiModTermWithAccession(), pappso::MsRunReader::mcsp_msRunId, and msp_msData.

Referenced by MsFileAccessor.

getOboPsiModTermNativeIDFormat()

const OboPsiModTerm pappso::PwizMsRunReader::getOboPsiModTermNativeIDFormat

(

)

const

get OboPsiModTerm corresponding to the nativeID format format of mz data

Definition at line 176 of file pwizmsrunreader.cpp.

{
 
  OboPsiModTerm term;
 
  term.setAccession("MS:1000824");
  term.m_name = "no nativeID format";
  term.m_definition =
    "No nativeID format indicates that the file tagged with this term does "
    "not "
    "contain spectra that can have a nativeID format.";
 
 
  pwiz::cv::CVID cvid = pwiz::msdata::id::getDefaultNativeIDFormat(*(msp_msData.get()));
 
  switch(cvid)
    {
      case pwiz::cv::MS_Thermo_nativeID_format:
        term.setAccession("MS:1000768");
        term.m_name = "Thermo nativeID format";
        term.m_definition =
          "Native format defined by controllerType=xsd:nonNegativeInteger "
          "controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger.";
        break;
      default:
        break;
    }
  return term;
}

References pappso::OboPsiModTerm::m_definition, pappso::OboPsiModTerm::m_name, msp_msData, and pappso::OboPsiModTerm::setAccession().

Referenced by getOboPsiModTermInstrumentModelName(), and MsFileAccessor.

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 207 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 MsFileAccessor, qualifiedMassSpectrumFromPwizMSData(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().

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 1097 of file pwizmsrunreader.cpp.

{
  return m_hasScanNumbers;
}

References m_hasScanNumbers.

Referenced by MsFileAccessor.

initialize()

void pappso::PwizMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 67 of file pwizmsrunreader.cpp.

{
  std::string file_name_std = Utils::toUtf8StandardString(mcsp_msRunId->getFileName());
 
 
  // 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));
 
      throw(PappsoException(QString("Error reading file %1 in PwizMsRunReader, for msrun %2:\n%3")
                              .arg(mcsp_msRunId->getFileName())
                              .arg(mcsp_msRunId.get()->toString())
                              .arg(error.what())));
    }
 
  qDebug() << "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(const pwiz::msdata::MSDataPtr &msDataPtr : msDataPtrVector)
        {
          qDebug() << "msDataPtr->run.id=" << msDataPtr->run.id.c_str();
          qDebug() << "mcsp_msRunId->getRunId()=" << mcsp_msRunId->getRunId();
          qDebug() << "mcsp_msRunId->getXmlId()=" << mcsp_msRunId->getXmlId();
          qDebug() << "mcsp_msRunId->getSampleName()=" << mcsp_msRunId->getSampleName();
 
          if(msDataPtr->run.id == mcsp_msRunId->getRunId().toStdString())
            {
              msp_msData = msDataPtr;
 
              qDebug() << "Found the right MSDataPtr for run id.";
 
              break;
            }
        }
    }
 
  if(msp_msData == nullptr)
    {
      throw(ExceptionNotPossible(QString("Could not find a pwiz MSDataPtr "
                                         "matching the requested run id : %1")
                                   .arg(mcsp_msRunId.get()->toString())));
    }
 
 
  // 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()->getMsDataFormat() == Enums::MsDataFormat::mzXML)
    {
      m_hasScanNumbers = true;
    }
}

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

Referenced by PwizMsRunReader(), acquireDevice(), and MsFileAccessor.

massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 755 of file pwizmsrunreader.cpp.

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

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

Referenced by MsFileAccessor.

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 748 of file pwizmsrunreader.cpp.

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

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

Referenced by MsFileAccessor.

newXicCoordSPtrFromQualifiedMassSpectrum()

XicCoordSPtr pappso::PwizMsRunReader::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 1131 of file pwizmsrunreader.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(), and pappso::QualifiedMassSpectrum::getRtInSeconds().

Referenced by MsFileAccessor, and newXicCoordSPtrFromSpectrumIndex().

newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr pappso::PwizMsRunReader::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 1121 of file pwizmsrunreader.cpp.

{
 
  QualifiedMassSpectrum mass_spectrum = qualifiedMassSpectrum(spectrum_index, false);
 
  return newXicCoordSPtrFromQualifiedMassSpectrum(mass_spectrum, precision);
}

References newXicCoordSPtrFromQualifiedMassSpectrum(), and qualifiedMassSpectrum().

Referenced by MsFileAccessor.

processDriftTime()

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

protected

Definition at line 310 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 MsFileAccessor, and qualifiedMassSpectrumFromPwizSpectrumPtr().

processRetentionTime()

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

protected

Definition at line 247 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()->getMsDataFormat() == Enums::MsDataFormat::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, pappso::Enums::MGF, and pappso::QualifiedMassSpectrum::setRtInSeconds().

Referenced by MsFileAccessor, and 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 762 of file pwizmsrunreader.cpp.

{
 
  QualifiedMassSpectrum spectrum;
  bool ok = false;
 
  spectrum = qualifiedMassSpectrumFromPwizMSData(spectrum_index, want_binary_data, ok);
 
  if(mcsp_msRunId->getMsDataFormat() == Enums::MsDataFormat::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, pappso::Enums::MGF, and qualifiedMassSpectrumFromPwizMSData().

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

qualifiedMassSpectrumFromPwizMSData()

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

protected

Definition at line 689 of file pwizmsrunreader.cpp.

{
 
  std::string backup_env = setGlobalLocaleToEnglish();
 
  MassSpectrumId massSpectrumId(mcsp_msRunId);
 
  if(msp_msData == nullptr)
    {
      setGlobalLocaleToCurrentOs(backup_env);
      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())
    {
      setGlobalLocaleToCurrentOs(backup_env);
      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);
 
  setGlobalLocaleToCurrentOs(backup_env);
 
  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(), setGlobalLocaleToCurrentOs(), setGlobalLocaleToEnglish(), pappso::MassSpectrumId::setNativeId(), and pappso::MassSpectrumId::setSpectrumIndex().

Referenced by MsFileAccessor, and 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 375 of file pwizmsrunreader.cpp.

{
  // qDebug();
 
  if(spectrum_p == nullptr)
    qFatal("Spectrum pointer cannot be nullptr.");
 
  std::string backup_env = setGlobalLocaleToEnglish();
 
  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);
 
      if(!spectrum_p->scanList.scans[0].hasCVParam(pwiz::msdata::MS_peak_list_scans))
        {
 
          // qDebug() << spectrum_p->cvParam(pwiz::msdata::MS_peak_list_scans)
          //               .valueAs<double>();
          qualified_mass_spectrum.setParameterValue(
            QualifiedMassSpectrumParameter::ScanNumber,
            spectrum_p->cvParam(pwiz::msdata::MS_peak_list_scans).valueAs<double>());
        }
      // 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()->getMsDataFormat() == Enums::MsDataFormat::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()->getMsDataFormat() != Enums::MsDataFormat::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
              //<cvParam cvRef="MS" accession="MS:1000042"
              // value="910663.949707031" name="peak intensity"
              // unitAccession="MS:1000131" unitName="number of detector
              // counts" unitCvRef="MS" />
 
              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."));
          //}
        }
 
      // 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()->getMsDataFormat() == Enums::MsDataFormat::MGF)
            {
              // Sort peaks by mz
              spectrum.sortMz();
            }
 
          //  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()));
    }
 
  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, pappso::Enums::MGF, msp_msData, processDriftTime(), processRetentionTime(), pappso::PappsoException::qwhat(), pappso::ScanNumber, setGlobalLocaleToEnglish(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setPrecursorSpectrumIndex(), and pappso::MassSpectrum::sortMz().

Referenced by MsFileAccessor, qualifiedMassSpectrumFromPwizMSData(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().

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 786 of file pwizmsrunreader.cpp.

{
  try
    {
      readSpectrumCollectionByMsLevel(handler, 0);
    }
  catch(std::exception &error)
    {
      qDebug() << "Going to throw";
 
      throw pappso::PappsoException(
        QObject::tr("Error reading data (spectrum collection) using the "
                    "proteowizard library: %1")
          .arg(error.what()));
    }
}

References readSpectrumCollectionByMsLevel().

Referenced by MsFileAccessor.

readSpectrumCollection2()

void pappso::PwizMsRunReader::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 804 of file pwizmsrunreader.cpp.

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

References readSpectrumCollectionWithMsrunReadConfig().

Referenced by MsFileAccessor.

readSpectrumCollectionByMsLevel()

void pappso::PwizMsRunReader::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 824 of file pwizmsrunreader.cpp.

{
 
  acquireDevice();
  // 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 backup_env = setGlobalLocaleToEnglish();
 
  // 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.
      if(ms_level == 0)
        {
          handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
        }
      else
        {
          if(qualified_mass_spectrum.getMsLevel() == ms_level)
            {
              handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
            }
        }
    }
 
  setGlobalLocaleToCurrentOs(backup_env);
  // 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 acquireDevice(), pappso::QualifiedMassSpectrum::getMsLevel(), getPwizSpectrumPtr(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::SpectrumCollectionHandlerInterface::needPeakList(), qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), setGlobalLocaleToCurrentOs(), setGlobalLocaleToEnglish(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().

Referenced by MsFileAccessor, and readSpectrumCollection().

readSpectrumCollectionWithMsrunReadConfig()

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

protectedvirtual

Definition at line 954 of file pwizmsrunreader.cpp.

{
  acquireDevice();
  // qDebug();
 
  // 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 = config.needPeakList();
 
 
  std::string backup_env = setGlobalLocaleToEnglish();
 
  // qDebug();
  // 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.
 
  qDebug();
  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;
        }
 
      // qDebug();
      // 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);
      // qDebug();
      /*
       * 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*/);
 
      // qDebug();
      // 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;
        }
 
      // qDebug();
      // 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.
 
      // qDebug();
      if(config.acceptMsLevel(qualified_mass_spectrum.getMsLevel()))
        {
          if(config.acceptRetentionTimeInSeconds(qualified_mass_spectrum.getRtInSeconds()))
            {
              handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
            }
        }
    }
 
 
  qDebug();
  setGlobalLocaleToCurrentOs(backup_env);
  // End of
  // for(std::size_t iter = 0; iter < spectrum_list_size; iter++)
 
  // Now let the loading handler know that the loading of the data has ended.
  // The handler might need this "signal" to perform additional tasks or to
  // cleanup cruft.
 
  qDebug() << "Loading ended";
  handler.loadingEnded();
}

References pappso::MsRunReadConfig::acceptMsLevel(), pappso::MsRunReadConfig::acceptRetentionTimeInSeconds(), acquireDevice(), pappso::QualifiedMassSpectrum::getMsLevel(), getPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, msp_msData, pappso::MsRunReadConfig::needPeakList(), qualifiedMassSpectrumFromPwizSpectrumPtr(), pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), setGlobalLocaleToCurrentOs(), setGlobalLocaleToEnglish(), pappso::MassSpectrumId::setNativeId(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::SpectrumCollectionHandlerInterface::shouldStop(), and pappso::SpectrumCollectionHandlerInterface::spectrumListHasSize().

Referenced by MsFileAccessor, and readSpectrumCollection2().

releaseDevice()

bool pappso::PwizMsRunReader::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 1103 of file pwizmsrunreader.cpp.

{
  msp_msData = nullptr;
  return true;
}

References msp_msData.

Referenced by MsFileAccessor.

setGlobalLocaleToCurrentOs()

void pappso::PwizMsRunReader::setGlobalLocaleToCurrentOs ( const std::string & environment_locale )

staticprotected

Definition at line 1167 of file pwizmsrunreader.cpp.

{
  try
    {
#ifdef MXE
      // std::locale::global(std::locale("C")); // set locale to default
      // locale
      std::setlocale(LC_ALL, environment_locale.c_str());
#else
      std::locale::global(std::locale("")); // sets locale according to OS environment
#endif
    }
  catch(std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Error trying to set local to original system one %1 : %2")
          .arg(environment_locale.c_str())
          .arg(error.what()));
    }
}

Referenced by MsFileAccessor, qualifiedMassSpectrumFromPwizMSData(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().

setGlobalLocaleToEnglish()

std::string pappso::PwizMsRunReader::setGlobalLocaleToEnglish ( )

staticprotected

Definition at line 1143 of file pwizmsrunreader.cpp.

{
  std::string env_backup;
  try
    {
#ifdef MXE
      // std::locale::global(std::locale("C")); // set locale to default
      // locale
 
      std::string env_backup = std::setlocale(LC_ALL, nullptr);
      std::setlocale(LC_ALL, "C");
#else
      std::locale::global(std::locale("C")); // set locale to default locale
#endif
    }
  catch(std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("Error trying to set local to C : %1").arg(error.what()));
    }
  return env_backup;
}

Referenced by MsFileAccessor, qualifiedMassSpectrumFromPwizMSData(), qualifiedMassSpectrumFromPwizSpectrumPtr(), readSpectrumCollectionByMsLevel(), and readSpectrumCollectionWithMsrunReadConfig().

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 1091 of file pwizmsrunreader.cpp.

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

References msp_msData.

Referenced by MsFileAccessor.

spectrumStringIdentifier2SpectrumIndex()

std::size_t pappso::PwizMsRunReader::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 1189 of file pwizmsrunreader.cpp.

{
  acquireDevice();
  std::size_t spectrum_id =
    msp_msData->run.spectrumListPtr->find(spectrum_identifier.toStdString());
  if(spectrum_id == msp_msData->run.spectrumListPtr->size())
    {
      throw pappso::ExceptionNotFound(
        QObject::tr("Spectrum identifier %1 not found").arg(spectrum_identifier));
    }
  return spectrum_id;
}

References acquireDevice(), and msp_msData.

Referenced by MsFileAccessor.

Friends And Related Symbol Documentation

MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 47 of file pwizmsrunreader.h.

References PwizMsRunReader(), accept(), acquireDevice(), getMsDataPtr(), getOboPsiModTermInstrumentModelName(), getOboPsiModTermNativeIDFormat(), getPwizSpectrumPtr(), hasScanNumbers(), initialize(), massSpectrumCstSPtr(), massSpectrumSPtr(), MsFileAccessor, newXicCoordSPtrFromQualifiedMassSpectrum(), newXicCoordSPtrFromSpectrumIndex(), processDriftTime(), processRetentionTime(), qualifiedMassSpectrum(), qualifiedMassSpectrumFromPwizMSData(), qualifiedMassSpectrumFromPwizSpectrumPtr(), readSpectrumCollection(), readSpectrumCollection2(), readSpectrumCollectionByMsLevel(), readSpectrumCollectionWithMsrunReadConfig(), releaseDevice(), setGlobalLocaleToCurrentOs(), setGlobalLocaleToEnglish(), spectrumListSize(), and spectrumStringIdentifier2SpectrumIndex().

Referenced by MsFileAccessor.

Member Data Documentation

m_hasScanNumbers

bool pappso::PwizMsRunReader::m_hasScanNumbers = false

private

Definition at line 135 of file pwizmsrunreader.h.

Referenced by hasScanNumbers(), and initialize().

m_mutex

QMutex pappso::PwizMsRunReader::m_mutex

staticprotected

Definition at line 130 of file pwizmsrunreader.h.

msp_msData

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

protected

Definition at line 131 of file pwizmsrunreader.h.

Referenced by acquireDevice(), getMsDataPtr(), getOboPsiModTermInstrumentModelName(), getOboPsiModTermNativeIDFormat(), initialize(), qualifiedMassSpectrumFromPwizMSData(), qualifiedMassSpectrumFromPwizSpectrumPtr(), readSpectrumCollectionByMsLevel(), readSpectrumCollectionWithMsrunReadConfig(), releaseDevice(), spectrumListSize(), and spectrumStringIdentifier2SpectrumIndex().

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

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