pappso::XyMsRunReader Class Reference

#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 More...
virtual MassSpectrumCstSPtr	massSpectrumCstSPtr (std::size_t spectrum_index) override
virtual QualifiedMassSpectrum	qualifiedMassSpectrum (std::size_t spectrum_index, bool want_binary_data=true) const override
	get a QualifiedMassSpectrum class given its scan number More...
virtual void	readSpectrumCollection (SpectrumCollectionHandlerInterface &handler) override
	function to visit an MsRunReader and get each Spectrum in a spectrum collection handler More...
virtual std::size_t	spectrumListSize () const override
	get the totat number of spectrum conained in the MSrun data file More...
Public Member Functions inherited from pappso::MsRunReader
	MsRunReader (MsRunIdCstSPtr &ms_run_id)
	MsRunReader (const MsRunReader &other)
virtual	~MsRunReader ()
const MsRunIdCstSPtr &	getMsRunId () const
virtual std::size_t	scanNumber2SpectrumIndex (std::size_t scan_number)
	if possible, converts a scan number into a spectrum index This is a convenient function to help transition from the old scan number (not implemented by all vendors) to more secure spectrum index (not vendor dependant). It is better to not rely on this function. More...
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...

Protected Member Functions
virtual void	initialize () override
virtual bool	accept (const QString &file_name) const override
	tells if the reader is able to handle this file must be implemented by private MS run reader, specific of one or more file format More...
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 25 of file xymsrunreader.cpp.

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

References initialize().

~XyMsRunReader()

pappso::XyMsRunReader::~XyMsRunReader ( )

virtual

Definition at line 43 of file xymsrunreader.cpp.

{
}

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 49 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, and pappso::Utils::xyMassDataFormatRegExp.

initialize()

void pappso::XyMsRunReader::initialize ( )

overrideprotectedvirtual

Implements pappso::MsRunReader.

Definition at line 35 of file xymsrunreader.cpp.

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

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 108 of file xymsrunreader.cpp.

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

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

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 101 of file xymsrunreader.cpp.

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

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

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 205 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(), and massSpectrumSPtr().

qualifiedMassSpectrumFromXyMSDataFile()

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

protected

Definition at line 115 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.open(QFile::ReadOnly | QFile::Text))
    {
      qDebug() << __FILE__ << __LINE__ << "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));
 
          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, 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(), and readSpectrumCollection().

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 233 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().

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 258 of file xymsrunreader.cpp.

{
  return 1;
}

Friends And Related Function Documentation

MsFileAccessor

friend class MsFileAccessor

friend

Definition at line 12 of file xymsrunreader.h.

Member Data Documentation

m_fileName

QString pappso::XyMsRunReader::m_fileName

protected

Definition at line 33 of file xymsrunreader.h.

---

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

• pappsomspp/msrun/xymsrunreader.h
• pappsomspp/msrun/xymsrunreader.cpp