#include <xymsrunreader.h>

Inheritance diagram for pappso::XyMsRunReader:

Public Member Functions
	XyMsRunReader (MsRunIdCstSPtr &msrun_id_csp)

virtual	~XyMsRunReader ()

virtual MassSpectrumSPtr	massSpectrumSPtr (std::size_t spectrum_index) override
	get a MassSpectrumSPtr class given its spectrum index

virtual MassSpectrumCstSPtr	massSpectrumCstSPtr (std::size_t spectrum_index) override

virtual QualifiedMassSpectrum	qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override
	get a QualifiedMassSpectrum class given its scan number

virtual void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler

virtual void	readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler) override

virtual pappso::XicCoordSPtr	newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, pappso::PrecisionPtr precision) const override
	get a xic coordinate object from a given spectrum index

virtual pappso::XicCoordSPtr	newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
	get a xic coordinate object from a given spectrum

virtual void	readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels

virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data file

virtual bool	releaseDevice () override
	release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object

virtual bool	acquireDevice () override
	acquire data back end device

virtual std::size_t	spectrumStringIdentifier2SpectrumIndex (const QString &spectrum_identifier) override
	if possible, get the spectrum index given a string identifier throw a not found exception if spectrum identifier is not found

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 bool	hasScanNumbers () const
	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 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

virtual const OboPsiModTerm	getOboPsiModTermInstrumentModelName () const
	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

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

QualifiedMassSpectrum	qualifiedMassSpectrumFromXyMSDataFile (MassSpectrumId mass_spectrum_id) const

Protected Attributes
QString	m_fileName

Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId

MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Friends
class	MsFileAccessor

Detailed Description

Definition at line 10 of file xymsrunreader.h.

Constructor & Destructor Documentation

◆ XyMsRunReader()

pappso::XyMsRunReader::XyMsRunReader ( MsRunIdCstSPtr & msrun_id_csp )

Definition at line 26 of file xymsrunreader.cpp.

                                                         : pappso::MsRunReader(msrun_id_csp)
{
  // Run the initialization function that checks that the file exists!
 
  initialize();
}

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

Referenced by MsFileAccessor.

◆ ~XyMsRunReader()

pappso::XyMsRunReader::~XyMsRunReader ( )

virtual

Definition at line 46 of file xymsrunreader.cpp.

47{

48}

Member Function Documentation

◆ accept()

bool pappso::XyMsRunReader::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 52 of file xymsrunreader.cpp.

{
 
  // Here we just test all the lines of the file to check that they comply with
  // the xy format.
 
  std::size_t line_count = 0;
 
  QFile file(file_name);
 
  if(!file.open(QFile::ReadOnly | QFile::Text))
    {
      qDebug() << __FILE__ << __LINE__ << "Failed to open file" << file_name;
 
      return false;
    }
 
  QRegularExpressionMatch regExpMatch;
 
  QString line;
  bool file_reading_failed = false;
 
  while(!file.atEnd())
    {
      line = file.readLine();
      ++line_count;
 
      if(line.startsWith('#') || line.isEmpty() || Utils::endOfLineRegExp.match(line).hasMatch())
        continue;
 
      // qDebug() << __FILE__ << __LINE__ << "Current xy format line:" << line;
 
      if(Utils::xyMassDataFormatRegExp.match(line).hasMatch())
        continue;
      else
        {
          file_reading_failed = true;
          break;
        }
    }
 
  file.close();
 
  if(!file_reading_failed && line_count >= 1)
    return true;
 
  return false;
}

References pappso::Utils::endOfLineRegExp, line, and pappso::Utils::xyMassDataFormatRegExp.

◆ acquireDevice()

bool pappso::XyMsRunReader::acquireDevice ( )

overridevirtual

acquire data back end device

Returns: bool true if done

Implements pappso::MsRunReader.

Definition at line 308 of file xymsrunreader.cpp.

{
  return true;
}

Referenced by MsFileAccessor.

◆ initialize()

void pappso::XyMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 35 of file xymsrunreader.cpp.

{
  // qDebug();
 
  if(!QFileInfo(mcsp_msRunId->getFileName()).exists())
    throw ExceptionNotFound(
      QObject::tr("Xy MS file %1 not found\n").arg(mcsp_msRunId->getFileName()));
  // qDebug();
}

References pappso::MsRunReader::mcsp_msRunId.

Referenced by XyMsRunReader().

◆ massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 110 of file xymsrunreader.cpp.

{
  return qualifiedMassSpectrum(spectrum_index).getMassSpectrumCstSPtr();
}

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

Referenced by MsFileAccessor.

◆ massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 103 of file xymsrunreader.cpp.

{
  return qualifiedMassSpectrum(spectrum_index).getMassSpectrumSPtr();
}

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

Referenced by MsFileAccessor.

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

XicCoordSPtr pappso::XyMsRunReader::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 323 of file xymsrunreader.cpp.

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

Referenced by MsFileAccessor.

◆ newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr pappso::XyMsRunReader::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 314 of file xymsrunreader.cpp.

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

Referenced by MsFileAccessor.

◆ qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::XyMsRunReader::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 209 of file xymsrunreader.cpp.

{
  // qDebug();
 
  // In reality there is only one mass spectrum in the file, so we do not use
  // spectrum_index, but use 0 instead.
 
  MassSpectrumId massSpectrumId(mcsp_msRunId, 0);
 
  QualifiedMassSpectrum qualified_mass_spectrum =
    qualifiedMassSpectrumFromXyMSDataFile(massSpectrumId);
 
  // qDebug() << "qualified mass spectrum has size:"
  //<< qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
  // We also do not abide by the want_binary_data parameter because in this XY
  // mass spec data file loading process we actually want the data.
  if(!want_binary_data)
    {
      // qualified_mass_spectrum.setMassSpectrumSPtr(nullptr);
    }
 
  return qualified_mass_spectrum;
}

References pappso::MsRunReader::mcsp_msRunId, and qualifiedMassSpectrumFromXyMSDataFile().

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

◆ qualifiedMassSpectrumFromXyMSDataFile()

QualifiedMassSpectrum pappso::XyMsRunReader::qualifiedMassSpectrumFromXyMSDataFile ( MassSpectrumId mass_spectrum_id ) const

protected

Definition at line 117 of file xymsrunreader.cpp.

{
  // qDebug();
 
  // This is a file that contains a single spectrum. Just iterate in the various
  // lines and convert them to DataPoint objects that are fed to the mass
  // spectrum.
 
  QualifiedMassSpectrum qualified_mass_spectrum(mass_spectrum_id);
 
  // Set manually data that are necessary for the correct use of this mass
  // spectrum in the MS data set tree node.
  qualified_mass_spectrum.setMsLevel(1);
  qualified_mass_spectrum.setRtInSeconds(0);
 
  MassSpectrum mass_spectrum;
 
  QFile file(mcsp_msRunId->getFileName());
 
  if(!file.exists())
    {
      // qDebug() << "File" << mcsp_msRunId->getFileName() << "does not exist.";
 
      return qualified_mass_spectrum;
    }
 
  if(!file.open(QFile::ReadOnly | QFile::Text))
    {
      // qDebug() << "Failed to open file" << mcsp_msRunId->getFileName();
 
      return qualified_mass_spectrum;
    }
 
  QRegularExpressionMatch regExpMatch;
 
  QString line;
 
  while(!file.atEnd())
    {
      line = file.readLine();
 
      if(line.startsWith('#') || line.isEmpty() || Utils::endOfLineRegExp.match(line).hasMatch())
        continue;
 
      if(Utils::xyMassDataFormatRegExp.match(line).hasMatch())
        {
          pappso_double x = -1;
          pappso_double y = -1;
 
          QRegularExpressionMatch regExpMatch = Utils::xyMassDataFormatRegExp.match(line);
 
          if(!regExpMatch.hasMatch())
            throw ExceptionNotPossible(
              QObject::tr("Failed to create data point with line %1.\n").arg(line));
 
          bool ok = false;
 
          x = regExpMatch.captured(1).toDouble(&ok);
 
          if(!ok)
            throw ExceptionNotPossible(
              QObject::tr("Failed to create data point with line %1.\n").arg(line));
 
          // Note that group 2 is the separator group.
 
          y = regExpMatch.captured(3).toDouble(&ok);
 
          if(!ok)
            throw ExceptionNotPossible(
              QObject::tr("Failed to create data point with line %1.\n").arg(line));
 
          // FIXME: what is this data point for if we use emplace_back
          // right below ?
          DataPoint data_point(x, y);
 
          mass_spectrum.emplace_back(x, y);
        }
    }
 
  file.close();
 
  MassSpectrumSPtr spectrum_sp = mass_spectrum.makeMassSpectrumSPtr();
  qualified_mass_spectrum.setMassSpectrumSPtr(spectrum_sp);
 
  // qDebug() << "the qualified mass spectrum has size:"
  //<< qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
  return qualified_mass_spectrum;
}

References pappso::Utils::endOfLineRegExp, line, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::x, pappso::Utils::xyMassDataFormatRegExp, and pappso::y.

Referenced by qualifiedMassSpectrum(), readSpectrumCollection(), and readSpectrumCollectionByMsLevel().

◆ readSpectrumCollection()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 237 of file xymsrunreader.cpp.

{
  // qDebug();
 
  // In reality there is only one mass spectrum in the file.
 
  MassSpectrumId massSpectrumId(mcsp_msRunId, 0 /* spectrum index*/);
 
  QualifiedMassSpectrum qualified_mass_spectrum =
    qualifiedMassSpectrumFromXyMSDataFile(massSpectrumId);
 
  // qDebug() << "qualified mass spectrum has size:"
  //<< qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
  // 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);
 
  // qDebug() << "Loading ended";
  handler.loadingEnded();
}

References pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, qualifiedMassSpectrumFromXyMSDataFile(), and pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum().

Referenced by MsFileAccessor, and readSpectrumCollection2().

◆ readSpectrumCollection2()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 289 of file xymsrunreader.cpp.

{
  return readSpectrumCollection(handler);
}

References readSpectrumCollection().

Referenced by MsFileAccessor.

◆ readSpectrumCollectionByMsLevel()

void pappso::XyMsRunReader::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 261 of file xymsrunreader.cpp.

{
  // qDebug();
 
  // In reality there is only one mass spectrum in the file.
 
  MassSpectrumId massSpectrumId(mcsp_msRunId, 0 /* spectrum index*/);
 
  QualifiedMassSpectrum qualified_mass_spectrum =
    qualifiedMassSpectrumFromXyMSDataFile(massSpectrumId);
 
  // qDebug() << "qualified mass spectrum has size:"
  //<< qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
  // The handler will receive the index of the mass spectrum in the
  // current run via the mass spectrum id member datum.
 
  if(qualified_mass_spectrum.getMsLevel() == ms_level)
    {
      handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
    }
 
  // qDebug() << "Loading ended";
  handler.loadingEnded();
}

References pappso::QualifiedMassSpectrum::getMsLevel(), pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MsRunReader::mcsp_msRunId, qualifiedMassSpectrumFromXyMSDataFile(), and pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum().

Referenced by MsFileAccessor.

◆ releaseDevice()

bool pappso::XyMsRunReader::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 302 of file xymsrunreader.cpp.

{
  return true;
}

Referenced by MsFileAccessor.

◆ spectrumListSize()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 296 of file xymsrunreader.cpp.

{
  return 1;
}

Referenced by MsFileAccessor.

◆ spectrumStringIdentifier2SpectrumIndex()

std::size_t pappso::XyMsRunReader::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 333 of file xymsrunreader.cpp.

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

Referenced by MsFileAccessor.

Friends And Related Symbol Documentation

◆ MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 12 of file xymsrunreader.h.

References XyMsRunReader(), acquireDevice(), massSpectrumCstSPtr(), massSpectrumSPtr(), MsFileAccessor, newXicCoordSPtrFromQualifiedMassSpectrum(), newXicCoordSPtrFromSpectrumIndex(), qualifiedMassSpectrum(), readSpectrumCollection(), readSpectrumCollection2(), readSpectrumCollectionByMsLevel(), releaseDevice(), spectrumListSize(), and spectrumStringIdentifier2SpectrumIndex().

Referenced by MsFileAccessor.

Member Data Documentation

◆ m_fileName

QString pappso::XyMsRunReader::m_fileName

protected

Definition at line 52 of file xymsrunreader.h.

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

pappsomspp/core/msrun/xymsrunreader.h
pappsomspp/core/msrun/xymsrunreader.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ XyMsRunReader()

◆ ~XyMsRunReader()

Member Function Documentation

◆ accept()

◆ acquireDevice()

◆ initialize()

◆ massSpectrumCstSPtr()

◆ massSpectrumSPtr()

◆ newXicCoordSPtrFromQualifiedMassSpectrum()

◆ newXicCoordSPtrFromSpectrumIndex()

◆ qualifiedMassSpectrum()

◆ qualifiedMassSpectrumFromXyMSDataFile()

◆ readSpectrumCollection()

◆ readSpectrumCollection2()

◆ readSpectrumCollectionByMsLevel()

◆ releaseDevice()

◆ spectrumListSize()

◆ spectrumStringIdentifier2SpectrumIndex()

Friends And Related Symbol Documentation

◆ MsFileAccessor

Member Data Documentation

◆ m_fileName