pappso::BafAsciiMsRunReader Class Reference

#include <bafasciimsrunreader.h>

Inheritance diagram for pappso::BafAsciiMsRunReader:

Public Member Functions
	BafAsciiMsRunReader (MsRunIdCstSPtr &msrun_id_csp)
virtual	~BafAsciiMsRunReader ()
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 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 More...
virtual pappso::XicCoordSPtr	newXicCoordSPtrFromQualifiedMassSpectrum (const pappso::QualifiedMassSpectrum &mass_spectrum, pappso::PrecisionPtr precision) const override
	get a xic coordinate object from a given spectrum More...
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 More...
virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data file More...
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 More...
virtual bool	acquireDevice () override
	acquire data back end device More...
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 More...
Public Member Functions inherited from pappso::MsRunReader
	MsRunReader (const MsRunIdCstSPtr &ms_run_id)
	MsRunReader (const MsRunReader &other)
virtual	~MsRunReader ()
const MsRunIdCstSPtr &	getMsRunId () const
virtual MassSpectrumSPtr	massSpectrumSPtr (std::size_t spectrum_index)=0
	get a MassSpectrumSPtr class given its spectrum index More...
virtual MassSpectrumCstSPtr	massSpectrumCstSPtr (std::size_t spectrum_index)=0
virtual QualifiedMassSpectrum	qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const =0
	get a QualifiedMassSpectrum class given its scan number More...
virtual XicCoordSPtr	newXicCoordSPtrFromSpectrumIndex (std::size_t spectrum_index, PrecisionPtr precision) const =0
	get a xic coordinate object from a given spectrum index More...
virtual XicCoordSPtr	newXicCoordSPtrFromQualifiedMassSpectrum (const QualifiedMassSpectrum &mass_spectrum, PrecisionPtr precision) const =0
	get a xic coordinate object from a given spectrum More...
virtual std::size_t	spectrumListSize () const =0
	get the totat number of spectrum conained in the MSrun data file More...
virtual void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler)=0
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
virtual void	readSpectrumCollection2 (const MsRunReadConfig &config, SpectrumCollectionHandlerInterface &handler)=0
virtual void	readSpectrumCollectionByMsLevel (SpectrumCollectionHandlerInterface &handler, unsigned int ms_level)=0
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler by Ms Levels More...
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...
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 More...
virtual std::size_t	spectrumStringIdentifier2SpectrumIndex (const QString &spectrum_identifier)=0
	if possible, get the spectrum index given a string identifier throw a not found exception if spectrum identifier is not found More...
virtual bool	releaseDevice ()=0
	release data back end device if a the data back end is released, the developper has to use acquireDevice before using the msrunreader object More...
virtual bool	acquireDevice ()=0
	acquire data back end device More...
virtual std::vector< double >	getRetentionTimeLine ()
	retention timeline get retention times along the MSrun in seconds More...
virtual Trace	getTicChromatogram ()
	get a TIC chromatogram More...
void	setMonoThread (bool is_mono_thread)
	set only one is_mono_thread to true More...
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 More...

Protected Member Functions
QString	craftLineParserRegExpPattern () const
QRegularExpression	craftLineParserRegExp (QString &pattern) const
bool	parseMassSpectrumLine (QString &line, MassSpectrumLineData &ms_line_data, QRegularExpression &line_regexp) const
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...
QualifiedMassSpectrum	qualifiedMassSpectrumFromBafAsciiMSDataFile (std::size_t spectrum_index, bool want_binary_data) const
virtual void	initialize ()=0
virtual bool	accept (const QString &file_name) const =0
	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...

Protected Attributes
QString	m_fileName
std::size_t	m_spectrumCount = 0
Protected Attributes inherited from pappso::MsRunReader
MsRunIdCstSPtr	mcsp_msRunId
MsRunReaderScanNumberMultiMap *	mpa_multiMapScanNumber = nullptr

Friends
class	MsFileAccessor

Detailed Description

Definition at line 23 of file bafasciimsrunreader.h.

Constructor & Destructor Documentation

BafAsciiMsRunReader()

pappso::BafAsciiMsRunReader::BafAsciiMsRunReader

(

MsRunIdCstSPtr &

msrun_id_csp

)

Definition at line 27 of file bafasciimsrunreader.cpp.

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

References initialize().

~BafAsciiMsRunReader()

pappso::BafAsciiMsRunReader::~BafAsciiMsRunReader ( )

virtual

Definition at line 52 of file bafasciimsrunreader.cpp.

{
}

Member Function Documentation

accept()

bool pappso::BafAsciiMsRunReader::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 220 of file bafasciimsrunreader.cpp.

{
  qDebug();
 
  // Here we just test all the lines of the file to check that they comply with
  // the BafAscii format (ascii export from Baf file using the Bruker
  // DataAnalysis/Compass software)..
 
  // The format of the file, for MS1 data only is the following:
  // <rt time in min>,+,ESI,ms1,-,profile,<m/z range start>-<m/z range
  // end>,512704,<m/z> <int>,<m/z> <int>,.. One such line per retention time
  // value.
 
  QString line_regexp_pattern    = craftLineParserRegExpPattern();
  QRegularExpression line_regexp = craftLineParserRegExp(line_regexp_pattern);
 
  if(!line_regexp.isValid())
    {
      qDebug() << "Failed to craft the regular expresssion";
 
      return false;
    }
 
  QFile file(file_name);
 
  if(!file.open(QFile::ReadOnly | QFile::Text))
    {
      qDebug() << "Failed to open file" << file_name;
 
      return false;
    }
 
  MassSpectrumLineData ms_line_data;
 
  while(!file.atEnd())
    {
      QString line = file.readLine().trimmed();
 
      if(!parseMassSpectrumLine(line, ms_line_data, line_regexp))
        {
          qDebug() << "Failed to parse a line.";
 
          file.close();
          return false;
        }
 
      ++m_spectrumCount;
    }
 
  file.close();
 
  if(m_spectrumCount >= 1)
    {
      qDebug() << "The file seems indeed to be BafAscii.";
      return true;
    }
 
  qDebug() << "The file does not seem to be BafAscii.";
  return false;
}

References craftLineParserRegExp(), craftLineParserRegExpPattern(), line, m_spectrumCount, and parseMassSpectrumLine().

Referenced by initialize().

acquireDevice()

bool pappso::BafAsciiMsRunReader::acquireDevice ( )

overridevirtual

acquire data back end device

Returns

bool true if done

Implements pappso::MsRunReader.

Definition at line 663 of file bafasciimsrunreader.cpp.

{
  return true;
}

craftLineParserRegExp()

QRegularExpression pappso::BafAsciiMsRunReader::craftLineParserRegExp ( QString &  pattern ) const

protected

Definition at line 99 of file bafasciimsrunreader.cpp.

{
  QRegularExpression regexp = QRegularExpression(pattern);
 
  if(!regexp.isValid())
    {
      qDebug() << "The regular expression is not valid:" << regexp.errorString();
      return QRegularExpression();
    }
 
  return QRegularExpression(pattern);
}

Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().

craftLineParserRegExpPattern()

QString pappso::BafAsciiMsRunReader::craftLineParserRegExpPattern ( ) const

protected

Definition at line 57 of file bafasciimsrunreader.cpp.

{
 
  // Construct the regular expression pattern, piecemeal...
 
  // The retention time as the very first value in the line.
  QString regexp_pattern =
    QString("^(%1)").arg(Utils::unsignedDoubleNumberNoExponentialRegExp.pattern());
 
  // The ionization mode (positive or negative)
  regexp_pattern += QString(",([+-])");
 
  // The ion source type.
  regexp_pattern += QString(",(ESI|MALDI)");
 
  // The MS level (ms1 for full scan mass spectrum)
  regexp_pattern += QString(",ms(\\d)");
 
  // Do no know what this is for.
  regexp_pattern += QString(",(-)");
 
  // The type of peak (profile or centroid).
  regexp_pattern += QString(",(profile|line)");
 
  // The m/z range of the mass spectrum.
  regexp_pattern += QString(",(%1-%2)")
                      .arg(Utils::unsignedDoubleNumberNoExponentialRegExp.pattern())
                      .arg(Utils::unsignedDoubleNumberNoExponentialRegExp.pattern());
 
  // The count of peaks following this element in the remaining of the line.
  regexp_pattern += QString(",(\\d+)");
 
  // Finally the whole set of ,<mz><space><intensity> pairs to
  // then end of the line.
  regexp_pattern += QString("(.*$)");
 
  // qDebug() << "The full regexp_pattern:" << regexp_pattern;
 
  return regexp_pattern;
}

References pappso::Utils::unsignedDoubleNumberNoExponentialRegExp.

Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().

initialize()

void pappso::BafAsciiMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 37 of file bafasciimsrunreader.cpp.

{
  // Use the accept function to parse the whole file, check its
  // contents validity and also count the number of spectra (that is,
  // of lines).
  if(!accept(mcsp_msRunId->getFileName()))
    {
      throw(pappso::ExceptionNotRecognized(QString("Failed to initialize reading of file %1 "
                                                   "in BafAsciiMsRunReader, for MS run %2:\n")
                                             .arg(mcsp_msRunId->getFileName())
                                             .arg(mcsp_msRunId.get()->toString())));
    }
}

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

Referenced by BafAsciiMsRunReader().

massSpectrumCstSPtr()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 290 of file bafasciimsrunreader.cpp.

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

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

massSpectrumSPtr()

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

overridevirtual

get a MassSpectrumSPtr class given its spectrum index

Implements pappso::MsRunReader.

Definition at line 283 of file bafasciimsrunreader.cpp.

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

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

newXicCoordSPtrFromQualifiedMassSpectrum()

XicCoordSPtr pappso::BafAsciiMsRunReader::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 678 of file bafasciimsrunreader.cpp.

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

newXicCoordSPtrFromSpectrumIndex()

XicCoordSPtr pappso::BafAsciiMsRunReader::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 669 of file bafasciimsrunreader.cpp.

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

parseMassSpectrumLine()

bool pappso::BafAsciiMsRunReader::parseMassSpectrumLine ( QString &  line, MassSpectrumLineData &  ms_line_data, QRegularExpression &  line_regexp  ) const

protected

Definition at line 113 of file bafasciimsrunreader.cpp.

{
  // We get a line from the file, exactly as is and we have to
  // parse it using regexp to extract all the data out of it,
  // which are then set to ms_line_data.
 
  line = line.trimmed();
 
  // qDebug() << "Current brukerBafAscii format line " << line_count << ": "
  //          << line.left(30) << " ... " << line.right(30);
 
  QRegularExpressionMatch regexp_match = line_regexp.match(line);
  bool ok                              = false;
 
  if(regexp_match.hasMatch())
    {
      // qDebug() << "The match succeeded.";
 
      double retention_time = regexp_match.captured(1).toDouble(&ok);
      if(!ok)
        {
          qDebug() << "Failed to extract the retention time of the mass spectrum.";
          return false;
        }
      ms_line_data.retentionTime = retention_time;
 
 
      ms_line_data.ionizationMode = regexp_match.captured(2);
      ms_line_data.ionSourceType  = regexp_match.captured(3);
 
      int ms_level = regexp_match.captured(4).toInt(&ok);
      if(!ok)
        {
          qDebug() << "Failed to extract the MS level of the mass spectrum.";
          return false;
        }
      ms_line_data.msLevel = ms_level;
 
      QString dash      = regexp_match.captured(5);
      ms_line_data.dash = dash;
 
      ms_line_data.peakShapeType = regexp_match.captured(6);
 
      QString mz_range = regexp_match.captured(7);
 
      double mz_range_start = mz_range.left(mz_range.indexOf("-")).toDouble(&ok);
      if(!ok)
        {
          qDebug() << "Failed to extract the start of the m/z range.";
          return false;
        }
      double mz_range_end = mz_range.right(mz_range.indexOf("-") + 1).toDouble(&ok);
      if(!ok)
        {
          qDebug() << "Failed to extract the end of the m/z range.";
          return false;
        }
      ms_line_data.mz_range = std::pair<double, double>(mz_range_start, mz_range_end);
 
      // qDebug() << qSetRealNumberPrecision(10)
      //          << "mz_range_start: " << mz_range_start
      //          << "mz_range_end: " << mz_range_end;
 
      std::size_t peak_count = regexp_match.captured(8).toULongLong(&ok);
      if(!ok)
        {
          qDebug() << "Failed to extract the number of peaks in the mass "
                      "spectrum.";
          return false;
        }
      ms_line_data.peakCount = peak_count;
 
      QString peaks         = regexp_match.captured(9);
      ms_line_data.peakList = peaks.split(",", Qt::SkipEmptyParts);
 
      // qDebug() << "The number of peaks:" << ms_line_data.peakList.size();
 
      // Sanity check:
      if(static_cast<std::size_t>(ms_line_data.peakList.size()) != ms_line_data.peakCount)
        {
          qDebug() << "The number of peaks in the mass spectrum does not "
                      "match the advertised one.";
          return false;
        }
 
      // qDebug() << "The retention time:" << retention_time
      //          << "the ionization mode: " << ionization_mode
      //          << "the source type: " << source_type
      //          << "MS level is:" << ms_level
      //          << "peak shape type: " << peak_shape_type
      //          << "m/z range: " << mz_range << "peak count: " <<
      //          peak_count
      //          << "and peaks: " << peaks.left(100) << " ... "
      //          << peaks.right(100) << "";
    }
  else
    {
      qDebug() << "The match failed.";
      return false;
    }
 
  return true;
}

References pappso::MassSpectrumLineData::dash, pappso::MassSpectrumLineData::ionizationMode, pappso::MassSpectrumLineData::ionSourceType, line, pappso::MassSpectrumLineData::msLevel, pappso::MassSpectrumLineData::mz_range, pappso::MassSpectrumLineData::peakCount, pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::peakShapeType, and pappso::MassSpectrumLineData::retentionTime.

Referenced by accept(), qualifiedMassSpectrumFromBafAsciiMSDataFile(), and readSpectrumCollectionByMsLevel().

qualifiedMassSpectrum()

QualifiedMassSpectrum pappso::BafAsciiMsRunReader::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 445 of file bafasciimsrunreader.cpp.

{
  // qDebug();
 
  QualifiedMassSpectrum qualified_mass_spectrum =
    qualifiedMassSpectrumFromBafAsciiMSDataFile(spectrum_index, want_binary_data);
 
  // qDebug() << "qualified mass spectrum has size:"
  //          << qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
  return qualified_mass_spectrum;
}

References qualifiedMassSpectrumFromBafAsciiMSDataFile().

Referenced by massSpectrumCstSPtr(), and massSpectrumSPtr().

qualifiedMassSpectrumFromBafAsciiMSDataFile()

QualifiedMassSpectrum pappso::BafAsciiMsRunReader::qualifiedMassSpectrumFromBafAsciiMSDataFile ( std::size_t  spectrum_index, bool  want_binary_data  ) const

protected

Definition at line 297 of file bafasciimsrunreader.cpp.

{
  // qDebug();
 
  // Each line holds the data of one mass spectrum. There are other
  // metadata at the beginning of the line.
 
  QString file_name = mcsp_msRunId->getFileName();
 
  QFile file(file_name);
 
  if(!file.open(QFile::ReadOnly | QFile::Text))
    {
      throw(PappsoException(QString("%1-%2 Error reading file %3 in "
                                    "BafAsciiMsRunReader, for MS run %4:\n")
                              .arg(__FILE__)
                              .arg(__LINE__)
                              .arg(mcsp_msRunId->getFileName())
                              .arg(mcsp_msRunId.get()->toString())));
    }
 
  // The format of the file, for MS1 data only is the following:
  // <rt time in min>,+,ESI,ms1,-,profile,<m/z range start>-<m/z range
  // end>,512704,<m/z> <int>,<m/z> <int>,.. One such line per retention time
  // value.
 
  QString line_regexp_pattern    = craftLineParserRegExpPattern();
  QRegularExpression line_regexp = craftLineParserRegExp(line_regexp_pattern);
 
  if(!line_regexp.isValid())
    {
      throw(PappsoException(QString("%1-%2 Failed to craft the regular expresssion while reading "
                                    "file %3 in BafAsciiMsRunReader, for MS run %4:")
                              .arg(__FILE__)
                              .arg(__LINE__)
                              .arg(mcsp_msRunId->getFileName())
                              .arg(mcsp_msRunId.get()->toString())));
    }
 
  QualifiedMassSpectrum qualified_mass_spectrum;
  MassSpectrumLineData ms_line_data;
  std::size_t mass_spectrum_index = 0;
 
  while(!file.atEnd())
    {
      if(mass_spectrum_index < spectrum_index)
        continue;
 
 
      QString line = file.readLine().trimmed();
 
      if(!parseMassSpectrumLine(line, ms_line_data, line_regexp))
        {
          file.close();
 
          throw(PappsoException(QString("%1-%2 Failed to parse line while reading file %3 "
                                        "in BafAsciiMsRunReader, for MS run %4:\n")
                                  .arg(__FILE__)
                                  .arg(__LINE__)
                                  .arg(mcsp_msRunId->getFileName())
                                  .arg(mcsp_msRunId.get()->toString())));
        }
 
      // At this point we have all the data inside the ms_line_data structure.
      // If the user wants the binary data, that is, the mass spectrometric
      // data, we need to prepare these.
 
      MassSpectrumId mass_spectrum_id(mcsp_msRunId, mass_spectrum_index);
 
      qualified_mass_spectrum.setMassSpectrumId(mass_spectrum_id);
      qualified_mass_spectrum.setMsLevel(ms_line_data.msLevel);
      qualified_mass_spectrum.setRtInSeconds(ms_line_data.retentionTime * 60);
 
      // Should we create the peak list?
 
      if(want_binary_data)
        {
          // qDebug() << "The binary data are wanted.";
 
          MassSpectrum mass_spectrum;
          bool ok = false;
 
          for(int iter = 0; iter < ms_line_data.peakList.size(); ++iter)
            {
              QString pair_string = ms_line_data.peakList.at(iter);
 
              // qDebug() << "The pair string:" << pair_string;
 
              QStringList mz_and_intensity_list = pair_string.split(" ", Qt::SkipEmptyParts);
 
              double mz = mz_and_intensity_list.first().toDouble(&ok);
              if(!ok)
                {
                  file.close();
 
                  throw(PappsoException(QString("%1-%2 Failed to parse line while reading file %3 "
                                                "in BafAsciiMsRunReader, for MS run %4:\n")
                                          .arg(__FILE__)
                                          .arg(__LINE__)
                                          .arg(mcsp_msRunId->getFileName())
                                          .arg(mcsp_msRunId.get()->toString())));
                }
 
              // qDebug() << qSetRealNumberPrecision(10) << "m/z:" << mz;
 
              double intensity = mz_and_intensity_list.last().toDouble(&ok);
              if(!ok)
                {
                  file.close();
 
                  throw(PappsoException(QString("%1-%2 Failed to parse line while reading file %3 "
                                                "in BafAsciiMsRunReader, for MS run %4:\n")
                                          .arg(__FILE__)
                                          .arg(__LINE__)
                                          .arg(mcsp_msRunId->getFileName())
                                          .arg(mcsp_msRunId.get()->toString())));
                }
 
              // qDebug() << qSetRealNumberPrecision(10)
              //          << "intensity:" << intensity;
 
              // qDebug() << "Emplacing back with:" << mz << "-" << intensity;
 
              mass_spectrum.emplace_back(mz, intensity);
            }
 
          MassSpectrumSPtr spectrum_sp = mass_spectrum.makeMassSpectrumSPtr();
          qualified_mass_spectrum.setMassSpectrumSPtr(spectrum_sp);
        }
      else
        qualified_mass_spectrum.setMassSpectrumSPtr(nullptr);
 
      // qDebug() << "qualified mass spectrum has size:"
      //          << qualified_mass_spectrum.getMassSpectrumSPtr()->size();
 
      break;
    }
  // End of
  // while(!file.atEnd())
 
  file.close();
 
  return qualified_mass_spectrum;
}

References craftLineParserRegExp(), craftLineParserRegExpPattern(), line, pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::MassSpectrumLineData::msLevel, pappso::mz, parseMassSpectrumLine(), pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::retentionTime, pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), and pappso::QualifiedMassSpectrum::setRtInSeconds().

Referenced by qualifiedMassSpectrum().

readSpectrumCollection()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 460 of file bafasciimsrunreader.cpp.

{
  readSpectrumCollectionByMsLevel(handler, 0);
}

References readSpectrumCollectionByMsLevel().

Referenced by readSpectrumCollection2().

readSpectrumCollection2()

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

overridevirtual

Implements pappso::MsRunReader.

Definition at line 644 of file bafasciimsrunreader.cpp.

{
  return readSpectrumCollection(handler);
}

References readSpectrumCollection().

readSpectrumCollectionByMsLevel()

void pappso::BafAsciiMsRunReader::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 467 of file bafasciimsrunreader.cpp.

{
  qDebug();
 
  // Each line holds the data of one mass spectrum. There are other
  // metadata at the beginning of the line.
 
  // 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();
 
  QString file_name = mcsp_msRunId->getFileName();
 
  QFile file(file_name);
 
  if(!file.open(QFile::ReadOnly | QFile::Text))
    {
      throw(PappsoException(QString("%1-%2 Error reading file %3 in "
                                    "BafAsciiMsRunReader, for MS run %4:\n")
                              .arg(__FILE__)
                              .arg(__LINE__)
                              .arg(mcsp_msRunId->getFileName())
                              .arg(mcsp_msRunId.get()->toString())));
    }
 
  // The format of the file, for MS1 data only is the following:
  // <rt time in min>,+,ESI,ms1,-,profile,<m/z range start>-<m/z range
  // end>,512704,<m/z> <int>,<m/z> <int>,.. One such line per retention time
  // value.
 
  QString line_regexp_pattern    = craftLineParserRegExpPattern();
  QRegularExpression line_regexp = craftLineParserRegExp(line_regexp_pattern);
 
  if(!line_regexp.isValid())
    {
      throw(PappsoException(
        QString("%1-%2 Failed to craft the regular expresssion while reading file %3 "
                "in BafAsciiMsRunReader, for MS run %4:\n")
          .arg(__FILE__)
          .arg(__LINE__)
          .arg(mcsp_msRunId->getFileName())
          .arg(mcsp_msRunId.get()->toString())));
    }
 
  MassSpectrumLineData ms_line_data;
  std::size_t mass_spectrum_index = 0;
 
  while(!file.atEnd())
    {
      // qDebug() << "Iterating at line index:" << mass_spectrum_index;
 
      // 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;
        }
 
      QString line = file.readLine().trimmed();
 
      if(!parseMassSpectrumLine(line, ms_line_data, line_regexp))
        {
          file.close();
 
          throw(PappsoException(QString("%1-%2 Failed to parse line whilereading file %3 "
                                        "in BafAsciiMsRunReader, for MS run %4:\n")
                                  .arg(__FILE__)
                                  .arg(__LINE__)
                                  .arg(mcsp_msRunId->getFileName())
                                  .arg(mcsp_msRunId.get()->toString())));
        }
 
      // qDebug() << "The size of the peaks string list:"
      //          << ms_line_data.peakList.size();
 
      // At this point we have all the data inside the ms_line_data structure.
      // If the user wants the binary data, that is, the mass spectrometric
      // data, we need to prepare these.
 
      MassSpectrumId mass_spectrum_id(mcsp_msRunId, mass_spectrum_index);
 
      QualifiedMassSpectrum qualified_mass_spectrum(mass_spectrum_id);
 
      qualified_mass_spectrum.setMsLevel(ms_line_data.msLevel);
      qualified_mass_spectrum.setRtInSeconds(ms_line_data.retentionTime * 60);
 
      // Should we create the peak list?
 
      if(want_binary_data)
        {
          // qDebug() << "The binary data are wanted.";
 
          MassSpectrum mass_spectrum;
          bool ok = false;
 
          for(int iter = 0; iter < ms_line_data.peakList.size(); ++iter)
            {
              QString pair_string = ms_line_data.peakList.at(iter);
 
              // qDebug() << "The pair string:" << pair_string;
 
              QStringList mz_and_intensity_list = pair_string.split(" ", Qt::SkipEmptyParts);
 
              double mz = mz_and_intensity_list.first().toDouble(&ok);
              if(!ok)
                {
                  file.close();
 
                  throw(PappsoException(QString("%1-%2 Failed to parse line while reading file %3 "
                                                "in BafAsciiMsRunReader, for MS run %4:\n")
                                          .arg(__FILE__)
                                          .arg(__LINE__)
                                          .arg(mcsp_msRunId->getFileName())
                                          .arg(mcsp_msRunId.get()->toString())));
                }
 
              // qDebug() << qSetRealNumberPrecision(10) << "m/z:" << mz;
 
              double intensity = mz_and_intensity_list.last().toDouble(&ok);
              if(!ok)
                {
                  file.close();
 
                  throw(PappsoException(QString("%1-%2 Failed to parse line while reading file %3 "
                                                "in BafAsciiMsRunReader, for MS run %4:\n")
                                          .arg(__FILE__)
                                          .arg(__LINE__)
                                          .arg(mcsp_msRunId->getFileName())
                                          .arg(mcsp_msRunId.get()->toString())));
                }
 
              // qDebug() << qSetRealNumberPrecision(10)
              //          << "intensity:" << intensity;
 
              // qDebug() << "Emplacing back with:" << mz << "-" << intensity;
 
              mass_spectrum.emplace_back(mz, intensity);
            }
 
          MassSpectrumSPtr spectrum_sp = mass_spectrum.makeMassSpectrumSPtr();
          qualified_mass_spectrum.setMassSpectrumSPtr(spectrum_sp);
        }
      else
        qualified_mass_spectrum.setMassSpectrumSPtr(nullptr);
 
      // 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.
      // Only hand over the mass spectrum to the handler if the
      // requested ms_level matches: if ms_level is 0, then any
      // mass spectrum of any msLevel will be ok. If ms_level is not 0,
      // then we only hand over the mass spectrum if its msLevel is
      // exactly equal to ms_level.
      if(ms_level == 0 || qualified_mass_spectrum.getMsLevel() == ms_level)
        {
          handler.setQualifiedMassSpectrum(qualified_mass_spectrum);
        }
 
      // This is and index of the spectrum in the file, not a count
      // of the mass spectra actually handed over to the handler.
      ++mass_spectrum_index;
    }
  // End of
  // while(!file.atEnd())
 
  file.close();
 
  qDebug() << "Loading ended";
  handler.loadingEnded();
}

References craftLineParserRegExp(), craftLineParserRegExpPattern(), pappso::QualifiedMassSpectrum::getMsLevel(), line, pappso::SpectrumCollectionHandlerInterface::loadingEnded(), pappso::MassSpectrum::makeMassSpectrumSPtr(), pappso::MsRunReader::mcsp_msRunId, pappso::MassSpectrumLineData::msLevel, pappso::mz, pappso::SpectrumCollectionHandlerInterface::needPeakList(), parseMassSpectrumLine(), pappso::MassSpectrumLineData::peakList, pappso::MassSpectrumLineData::retentionTime, pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::SpectrumCollectionHandlerInterface::setQualifiedMassSpectrum(), pappso::QualifiedMassSpectrum::setRtInSeconds(), and pappso::SpectrumCollectionHandlerInterface::shouldStop().

Referenced by readSpectrumCollection().

releaseDevice()

bool pappso::BafAsciiMsRunReader::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 657 of file bafasciimsrunreader.cpp.

{
  return true;
}

spectrumListSize()

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

overridevirtual

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

Implements pappso::MsRunReader.

Definition at line 651 of file bafasciimsrunreader.cpp.

{
  return m_spectrumCount;
}

References m_spectrumCount.

spectrumStringIdentifier2SpectrumIndex()

std::size_t pappso::BafAsciiMsRunReader::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 687 of file bafasciimsrunreader.cpp.

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

Friends And Related Function Documentation

MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 25 of file bafasciimsrunreader.h.

Member Data Documentation

m_fileName

QString pappso::BafAsciiMsRunReader::m_fileName

protected

Definition at line 65 of file bafasciimsrunreader.h.

m_spectrumCount

std::size_t pappso::BafAsciiMsRunReader::m_spectrumCount = 0

mutableprotected

Definition at line 68 of file bafasciimsrunreader.h.

Referenced by accept(), and spectrumListSize().

---

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

• pappsomspp/msrun/bafasciimsrunreader.h
• pappsomspp/msrun/bafasciimsrunreader.cpp