#include <msfileaccessor.h>

Public Member Functions
	MsFileAccessor (const QString &file_name, const QString &xml_prefix)

	MsFileAccessor (const MsFileAccessor &other)

virtual	~MsFileAccessor ()

const QString &	getFileName () const

MsDataFormat	getFileFormat () const
	get the raw format of mz data More...

const OboPsiModTerm	getOboPsiModTermFileFormat () const
	get OboPsiModTerm corresponding to the raw format of mz data More...

const OboPsiModTerm &	getOboPsiModTermNativeIDFormat () const
	get OboPsiModTerm corresponding to the nativeID format format of mz data More...

FileReaderType	getFileReaderType () const
	get the file reader type More...

void	setPreferredFileReaderType (MsDataFormat format, FileReaderType reader_type)
	given an mz format, explicitly set the preferred reader More...

FileReaderType	getpreferredFileReaderType (MsDataFormat format)

std::vector< MsRunIdCstSPtr >	getMsRunIds ()

void	setSelectedMsRunId (MsRunIdCstSPtr ms_run_id_csp)

MsRunIdCstSPtr	getSelectedMsRunId () const

MsRunReaderSPtr	msRunReaderSPtr (MsRunIdCstSPtr ms_run_id)

MsRunReaderSPtr	msRunReaderSPtr (std::size_t ms_run_id_index)

MsRunReaderSPtr	msRunReaderSPtrForSelectedMsRunId ()

MsRunReaderSPtr	getMsRunReaderSPtrByRunId (const QString &run_id, const QString &xml_id)
	get an msrun reader by finding the run_id in file More...

TimsMsRunReaderMs2SPtr	buildTimsMsRunReaderMs2SPtr ()
	if possible, builds directly a dedicated Tims TOF tdf file reader More...

Static Public Member Functions
static MsRunReaderSPtr	buildMsRunReaderSPtr (MsRunIdCstSPtr ms_run_id)
	get an MsRunReader directly from a valid MsRun ID More...

static MsRunReaderSPtr	buildMsRunReaderSPtr (MsRunIdCstSPtr ms_run_id, pappso::FileReaderType preferred_file_reader_type)
	get an MsRunReader directly from a valid MsRun ID More...

Private Attributes
QString	m_fileName

const QString	m_xmlPrefix

MsDataFormat	m_fileFormat = MsDataFormat::unknown

FileReaderType	m_fileReaderType

std::map< MsDataFormat, FileReaderType >	m_preferredFileReaderTypeMap

MsRunIdCstSPtr	mcsp_selectedMsRunId = nullptr

OboPsiModTerm	m_oboPsiModTermNativeIDFormat

Detailed Description

Definition at line 27 of file msfileaccessor.h.

Constructor & Destructor Documentation

◆ MsFileAccessor() [1/2]

pappso::MsFileAccessor::MsFileAccessor	(	const QString &	file_name,
		const QString &	xml_prefix
	)

Definition at line 35 of file msfileaccessor.cpp.

  : m_fileName(file_name), m_xmlPrefix(xml_prefix)
{
  QFile file(file_name);
  if(!file.exists())
    throw(ExceptionNotFound(
      QObject::tr("File %1 not found.").arg(QFileInfo(file_name).absoluteFilePath())));
 
 
  m_oboPsiModTermNativeIDFormat.setAccession("MS:1000824");
  m_oboPsiModTermNativeIDFormat.m_name = "no nativeID format";
  m_oboPsiModTermNativeIDFormat.m_definition =
    "No nativeID format indicates that the file tagged with this term does not "
    "contain spectra that can have a nativeID format.";
}

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

◆ MsFileAccessor() [2/2]

pappso::MsFileAccessor::MsFileAccessor ( const MsFileAccessor & other )

Definition at line 52 of file msfileaccessor.cpp.

  : m_fileName(other.m_fileName),
    m_xmlPrefix(other.m_xmlPrefix),
    m_fileFormat(other.m_fileFormat),
    m_fileReaderType(other.m_fileReaderType)
{
  m_oboPsiModTermNativeIDFormat = other.m_oboPsiModTermNativeIDFormat;
}

References m_oboPsiModTermNativeIDFormat.

◆ ~MsFileAccessor()

pappso::MsFileAccessor::~MsFileAccessor ( )

virtual

Definition at line 61 of file msfileaccessor.cpp.

62{

63}

Member Function Documentation

◆ buildMsRunReaderSPtr() [1/2]

MsRunReaderSPtr pappso::MsFileAccessor::buildMsRunReaderSPtr ( MsRunIdCstSPtr ms_run_id )

static

get an MsRunReader directly from a valid MsRun ID

no need to check the file format or filename : all is already part of the msrunid

Parameters

ms_run_id msrun identifier

Returns: msrun reader shared pointer

Definition at line 497 of file msfileaccessor.cpp.

{
  return buildMsRunReaderSPtr(ms_run_id, pappso::FileReaderType::tims);
}

References buildMsRunReaderSPtr(), and pappso::tims.

Referenced by buildMsRunReaderSPtr().

◆ buildMsRunReaderSPtr() [2/2]

MsRunReaderSPtr pappso::MsFileAccessor::buildMsRunReaderSPtr	(	MsRunIdCstSPtr	ms_run_id,
		pappso::FileReaderType	preferred_file_reader_type
	)

static

get an MsRunReader directly from a valid MsRun ID

no need to check the file format or filename : all is already part of the msrunid

Parameters

ms_run_id	msrun identifier
preferred_file_reader_type	the preferred file reader type to use (depending on the mz format)

Returns: msrun reader shared pointer

Definition at line 503 of file msfileaccessor.cpp.

{
  QFile file(ms_run_id.get()->getFileName());
  if(!file.exists())
    throw(ExceptionNotFound(QObject::tr("unable to build a reader : file %1 not found.")
                              .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
 
  MsDataFormat file_format = ms_run_id.get()->getMsDataFormat();
 
  if(file_format == MsDataFormat::xy)
    {
      // qDebug() << "Returning a XyMsRunReader.";
 
      return std::make_shared<XyMsRunReader>(ms_run_id);
    }
  else if(file_format == MsDataFormat::brukerBafAscii)
    {
      // qDebug() << "Returning a XyMsRunReader.";
 
      return std::make_shared<BafAsciiMsRunReader>(ms_run_id);
    }
  else if(file_format == MsDataFormat::unknown)
    {
      throw(PappsoException(QObject::tr("unable to build a reader for %1 : unknown file format")
                              .arg(QFileInfo(ms_run_id.get()->getFileName()).absoluteFilePath())));
    }
 
  else if(file_format == MsDataFormat::brukerTims)
    {
      if(preferred_file_reader_type == pappso::FileReaderType::tims)
        {
          return std::make_shared<TimsMsRunReader>(ms_run_id);
        }
      else if(preferred_file_reader_type == pappso::FileReaderType::tims_ms2)
        {
          return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
        }
      else if(preferred_file_reader_type == pappso::FileReaderType::tims_frames)
        {
          qDebug() << "returning std::make_shared<TimsFramesMsRunReader>(ms_run_id).";
          return std::make_shared<TimsFramesMsRunReader>(ms_run_id);
        }
      // qDebug() << "by default, build a TimsMsRunReader.";
      return std::make_shared<TimsMsRunReader>(ms_run_id);
    }
  else
    {
      // qDebug() << "Returning a PwizMsRunReader .";
      return std::make_shared<PwizMsRunReader>(ms_run_id);
    }
}

References pappso::brukerBafAscii, pappso::brukerTims, pappso::tims, pappso::tims_frames, pappso::tims_ms2, pappso::unknown, and pappso::xy.

◆ buildTimsMsRunReaderMs2SPtr()

TimsMsRunReaderMs2SPtr pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr ( )

if possible, builds directly a dedicated Tims TOF tdf file reader

Definition at line 368 of file msfileaccessor.cpp.

{
  // try TimsData reader
  QString tims_dir = m_fileName;
  if(!QFileInfo(tims_dir).isDir())
    {
      tims_dir = QFileInfo(m_fileName).absolutePath();
    }
  TimsMsFileReader tims_file_reader(tims_dir);
 
  std::vector<MsRunIdCstSPtr> ms_run_ids = tims_file_reader.getMsRunIds(m_xmlPrefix);
 
  if(ms_run_ids.size())
    {
      // qDebug() << "Might well be handled using the Bruker code";
      m_fileReaderType = FileReaderType::tims_ms2;
      m_fileFormat     = tims_file_reader.getFileFormat();
      m_fileName       = tims_dir;
 
      return std::make_shared<TimsMsRunReaderMs2>(ms_run_ids.front());
    }
  else
    {
      throw(ExceptionNotPossible(
        QObject::tr("Unable to read mz data directory %1 with TimsTOF reader.").arg(tims_dir)));
    }
}

References pappso::TimsMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_xmlPrefix, and pappso::tims_ms2.

◆ getFileFormat()

MsDataFormat pappso::MsFileAccessor::getFileFormat ( ) const

get the raw format of mz data

Definition at line 74 of file msfileaccessor.cpp.

{
  return m_fileFormat;
}

References m_fileFormat.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and pappso::masschroq::JsonInput::readMzDataFiles().

◆ getFileName()

const QString & pappso::MsFileAccessor::getFileName ( ) const

Definition at line 67 of file msfileaccessor.cpp.

{
  return m_fileName;
}

References m_fileName.

◆ getFileReaderType()

FileReaderType pappso::MsFileAccessor::getFileReaderType ( ) const

get the file reader type

Definition at line 348 of file msfileaccessor.cpp.

{
  return m_fileReaderType;
}

References m_fileReaderType.

◆ getMsRunIds()

std::vector< MsRunIdCstSPtr > pappso::MsFileAccessor::getMsRunIds ( )

Definition at line 194 of file msfileaccessor.cpp.

{
  // qDebug();
 
  // Try the PwizMsFileReader
 
  PwizMsFileReader pwiz_ms_file_reader(m_fileName);
 
  std::vector<MsRunIdCstSPtr> ms_run_ids = pwiz_ms_file_reader.getMsRunIds(m_xmlPrefix);
  if(ms_run_ids.size())
    {
      qDebug() << "Might well be handled using the Pwiz code.";
 
      m_fileFormat     = pwiz_ms_file_reader.getFileFormat();
      m_fileReaderType = FileReaderType::pwiz;
 
      // But the user might have configured one preferred reader type.
 
      auto pref = m_preferredFileReaderTypeMap.find(m_fileFormat);
      if(pref != m_preferredFileReaderTypeMap.end())
        {
          m_fileReaderType = pref->second;
        }
 
      return ms_run_ids;
    }
 
  qDebug() << "The Pwiz reader did not work.";
 
  // Try the TimsData reader
 
  QString tims_dir = m_fileName;
  if(!QFileInfo(tims_dir).isDir())
    {
      tims_dir = QFileInfo(m_fileName).absolutePath();
    }
 
  TimsMsFileReader tims_file_reader(tims_dir);
 
  ms_run_ids = tims_file_reader.getMsRunIds(m_xmlPrefix);
 
  if(ms_run_ids.size())
    {
      qDebug() << "Might well be handled using the Bruker code";
 
      m_fileName       = tims_dir;
      m_fileFormat     = tims_file_reader.getFileFormat();
      m_fileReaderType = FileReaderType::tims;
 
      auto pref = m_preferredFileReaderTypeMap.find(m_fileFormat);
      if(pref != m_preferredFileReaderTypeMap.end())
        {
          m_fileReaderType = pref->second;
        }
 
      qDebug() << "Returning Bruker::tims ms run(s)."
               << "with preferred reader type:" << Utils::fileReaderTypeAsString(m_fileReaderType);
 
      return ms_run_ids;
    }
 
  qDebug() << "The Tims reader did not work.";
 
  // Try the Baf->ascii export format from Bruker Compass
 
  try
    {
      ms_run_ids.clear();
      BafAsciiFileReader baf_ascii_ms_file_reader(m_fileName);
 
      ms_run_ids = baf_ascii_ms_file_reader.getMsRunIds(m_xmlPrefix);
 
      if(ms_run_ids.size())
        {
          qDebug() << "Might well be handled using the BafAscii code";
 
          m_fileReaderType = FileReaderType::bafascii;
 
          m_fileFormat = baf_ascii_ms_file_reader.getFileFormat();
 
          if(m_fileFormat == MsDataFormat::unknown)
            {
              ms_run_ids.clear();
            }
          else
            {
              return ms_run_ids;
            }
        }
    }
  catch(const pappso::PappsoException &error)
    {
      qDebug() << "This is not a BafAscii code file" << error.qwhat();
    }
 
 
  qDebug() << "The BafAscii reader did not work.";
 
  // At this point try the XyMsFileReader
 
  XyMsFileReader xy_ms_file_reader(m_fileName);
 
  ms_run_ids = xy_ms_file_reader.getMsRunIds(m_xmlPrefix);
 
  if(ms_run_ids.size())
    {
      qDebug() << "Might well be handled using the XY code";
 
      m_fileReaderType = FileReaderType::xy;
 
      m_fileFormat = xy_ms_file_reader.getFileFormat();
 
      return ms_run_ids;
    }
 
  qDebug() << "The XY reader did not work.";
 
  return ms_run_ids;
}

References pappso::bafascii, pappso::Utils::fileReaderTypeAsString(), pappso::BafAsciiFileReader::getFileFormat(), pappso::PwizMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getFileFormat(), pappso::XyMsFileReader::getFileFormat(), pappso::BafAsciiFileReader::getMsRunIds(), pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), pappso::XyMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_preferredFileReaderTypeMap, m_xmlPrefix, pappso::pwiz, pappso::PappsoException::qwhat(), pappso::tims, pappso::unknown, and pappso::xy.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), getMsRunReaderSPtrByRunId(), msRunReaderSPtr(), and pappso::masschroq::JsonInput::readMzDataFiles().

◆ getMsRunReaderSPtrByRunId()

MsRunReaderSPtr pappso::MsFileAccessor::getMsRunReaderSPtrByRunId	(	const QString &	run_id,
		const QString &	xml_id
	)

get an msrun reader by finding the run_id in file

Parameters

run_id	identifier within file of the MSrun
xml_id	XML identifier given by the user to identify this MSrun in our experiment (not in the file)

Definition at line 558 of file msfileaccessor.cpp.

{
  std::vector<MsRunIdCstSPtr> run_list = getMsRunIds();
  MsRunReaderSPtr reader_sp;
  for(MsRunIdCstSPtr &original_run_id : run_list)
    {
      if(original_run_id.get()->getRunId() == run_id)
        {
          MsRunId new_run_id(*original_run_id.get());
          new_run_id.setXmlId(xml_id);
 
          return msRunReaderSPtr(std::make_shared<MsRunId>(new_run_id));
        }
    }
 
  if((run_id.isEmpty()) && (run_list.size() == 1))
    {
      MsRunId new_run_id(*run_list[0].get());
      new_run_id.setXmlId(xml_id);
 
      return msRunReaderSPtr(std::make_shared<MsRunId>(new_run_id));
    }
 
 
  if(reader_sp == nullptr)
    {
      throw(ExceptionNotFound(QObject::tr("run id %1 not found in file %2")
                                .arg(run_id)
                                .arg(QFileInfo(m_fileName).absoluteFilePath())));
    }
  return reader_sp;
}

References getMsRunIds(), m_fileName, msRunReaderSPtr(), and pappso::MsRunId::setXmlId().

Referenced by pappso::masschroq::JsonInput::readMzDataFiles().

◆ getOboPsiModTermFileFormat()

const OboPsiModTerm pappso::MsFileAccessor::getOboPsiModTermFileFormat ( ) const

get OboPsiModTerm corresponding to the raw format of mz data

Definition at line 80 of file msfileaccessor.cpp.

{
  OboPsiModTerm term;
 
  // is_a: MS:1000560 ! mass spectrometer file format
  switch(m_fileFormat)
    {
      case MsDataFormat::abSciexT2D:
        term.setAccession("MS:1001560");
        term.m_name = "SCIEX TOF/TOF T2D format";
        term.m_definition =
          "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument "
          "export format.";
        break;
      case MsDataFormat::abSciexWiff:
        term.setAccession("MS:1000562");
        term.m_name       = "ABI WIFF format";
        term.m_definition = "Applied Biosystems WIFF file format.";
        break;
      case MsDataFormat::agilentMassHunter:
        term.setAccession("MS:1001509");
        term.m_name = "Agilent MassHunter format";
        term.m_definition =
          "A data file format found in an Agilent MassHunter directory which "
          "contains raw data acquired by an Agilent mass spectrometer.";
        break;
      case MsDataFormat::brukerBaf:
        break;
      case MsDataFormat::brukerFid:
        term.setAccession("MS:1000825");
        term.m_name       = "Bruker FID format";
        term.m_definition = "Bruker FID file format.";
        break;
      case MsDataFormat::brukerTims:
        term.setAccession("MS:1002817");
        term.m_name       = "Bruker TDF format";
        term.m_definition = "Bruker TDF raw file format.";
        break;
      case MsDataFormat::brukerYep:
        term.setAccession("MS:1000567");
        term.m_name       = "Bruker/Agilent YEP format";
        term.m_definition = "Bruker/Agilent YEP file format.";
        break;
      case MsDataFormat::MGF:
        term.setAccession("MS:1001062");
        term.m_name       = "Mascot MGF format";
        term.m_definition = "Mascot MGF file format.";
        break;
      case MsDataFormat::msn:
        break;
      case MsDataFormat::mz5:
        term.setAccession("MS:1001881");
        term.m_name       = "mz5 format";
        term.m_definition = "mz5 file format, modelled after mzML.";
        break;
      case MsDataFormat::mzML:
        term.setAccession("MS:1000584");
        term.m_name       = "mzML format";
        term.m_definition = "Proteomics Standards Inititative mzML file format.";
        break;
      case MsDataFormat::mzXML:
        term.setAccession("MS:1000566");
        term.m_name       = "ISB mzXML format";
        term.m_definition = "Institute of Systems Biology mzXML file format.";
        break;
      case MsDataFormat::SQLite3:
        break;
      case MsDataFormat::thermoRaw:
 
        term.setAccession("MS:1000563");
        term.m_name       = "Thermo RAW format";
        term.m_definition = "Thermo Scientific RAW file format.";
        break;
      case MsDataFormat::unknown:
        break;
      case MsDataFormat::watersRaw:
        term.setAccession("MS:1000526");
        term.m_name = "Waters raw format";
        term.m_definition =
          "Waters data file format found in a Waters RAW directory, generated "
          "from an MS acquisition.";
        break;
      case MsDataFormat::brukerBafAscii:
        term.setAccession("MS:1001369");
        term.m_name = "BafAscii text format";
        term.m_definition =
          "Simple text file format obtained by exporting Bruker Baf to ascii "
          "using Bruker software";
        break;
      case MsDataFormat::xy:
        term.setAccession("MS:1001369");
        term.m_name = "text format";
        term.m_definition =
          "Simple text file format of \"m/z<separator>intensity\" value pairs "
          "for a single mass spectrum, a PMF (or single MS2) search.";
        break;
      default:
        break;
    }
 
  return term;
}

References pappso::abSciexT2D, pappso::abSciexWiff, pappso::agilentMassHunter, pappso::brukerBaf, pappso::brukerBafAscii, pappso::brukerFid, pappso::brukerTims, pappso::brukerYep, pappso::OboPsiModTerm::m_definition, m_fileFormat, pappso::OboPsiModTerm::m_name, pappso::MGF, pappso::msn, pappso::mz5, pappso::mzML, pappso::mzXML, pappso::OboPsiModTerm::setAccession(), pappso::SQLite3, pappso::thermoRaw, pappso::unknown, pappso::watersRaw, and pappso::xy.

◆ getOboPsiModTermNativeIDFormat()

const OboPsiModTerm & pappso::MsFileAccessor::getOboPsiModTermNativeIDFormat ( ) const

get OboPsiModTerm corresponding to the nativeID format format of mz data

Definition at line 185 of file msfileaccessor.cpp.

{
 
 
  return m_oboPsiModTermNativeIDFormat;
}

References m_oboPsiModTermNativeIDFormat.

◆ getpreferredFileReaderType()

FileReaderType pappso::MsFileAccessor::getpreferredFileReaderType ( MsDataFormat format )

Definition at line 332 of file msfileaccessor.cpp.

{
  // qDebug();
 
  auto ret = m_preferredFileReaderTypeMap.find(format);
 
  if(ret != m_preferredFileReaderTypeMap.end())
    {
      return ret->second;
    }
 
  return m_fileReaderType;
}

References m_fileReaderType, and m_preferredFileReaderTypeMap.

Referenced by msRunReaderSPtr().

◆ getSelectedMsRunId()

MsRunIdCstSPtr pappso::MsFileAccessor::getSelectedMsRunId ( ) const

Definition at line 362 of file msfileaccessor.cpp.

{
  return mcsp_selectedMsRunId;
}

References mcsp_selectedMsRunId.

◆ msRunReaderSPtr() [1/2]

MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtr ( MsRunIdCstSPtr ms_run_id )

Definition at line 398 of file msfileaccessor.cpp.

{
  // qDebug();
 
  // We want to return a MsRunReader that accounts for the configuration that
  // the user might have set.
 
  if(m_fileName != ms_run_id->getFileName())
    throw(
      ExceptionNotPossible(QObject::tr("The MsRunId instance must have the name file name as the "
                                       "MsFileAccessor.")));
 
  if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::pwiz)
    {
      // qDebug() << "Returning a PwizMsRunReader.";
      auto pwiz_reader              = std::make_shared<PwizMsRunReader>(ms_run_id);
      m_oboPsiModTermNativeIDFormat = pwiz_reader->getOboPsiModTermNativeIDFormat();
      return pwiz_reader;
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::xy)
    {
      // qDebug() << "Returning a XyMsRunReader.";
 
      return std::make_shared<XyMsRunReader>(ms_run_id);
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::tims)
    {
      // qDebug() << "Returning a TimsMsRunReader.";
 
      return std::make_shared<TimsMsRunReader>(ms_run_id);
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::tims_frames)
    {
      // qDebug() << "Returning a TimsFramesMsRunReader.";
 
      return std::make_shared<TimsFramesMsRunReader>(ms_run_id);
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::tims_ms2)
    {
      // qDebug() << "Returning a TimsMsRunReaderMs2.";
 
      return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::tims_dia)
    {
      // qDebug() << "Returning a TimsMsRunReaderMs2.";
 
      // qInfo() << "std::make_shared<TimsMsRunReaderDia>(ms_run_id);";
      return std::make_shared<TimsMsRunReaderDia>(ms_run_id);
    }
  else if(getpreferredFileReaderType(m_fileFormat) == FileReaderType::bafascii)
    {
      // qDebug() << "Returning a BafAsciiMsRunReader.";
 
      return std::make_shared<BafAsciiMsRunReader>(ms_run_id);
    }
  if(m_fileFormat == MsDataFormat::unknown)
    {
      if(ms_run_id.get()->getMsDataFormat() == MsDataFormat::xy)
        {
          return std::make_shared<XyMsRunReader>(ms_run_id);
        }
      else
        {
          auto pwiz_reader              = std::make_shared<PwizMsRunReader>(ms_run_id);
          m_oboPsiModTermNativeIDFormat = pwiz_reader->getOboPsiModTermNativeIDFormat();
          return pwiz_reader;
        }
    }
  else
    {
      throw PappsoException(QObject::tr("No file format was found."));
    }
 
  return nullptr;
}

References pappso::bafascii, getpreferredFileReaderType(), m_fileFormat, m_fileName, m_oboPsiModTermNativeIDFormat, pappso::pwiz, pappso::tims, pappso::tims_dia, pappso::tims_frames, pappso::tims_ms2, pappso::unknown, and pappso::xy.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), getMsRunReaderSPtrByRunId(), msRunReaderSPtr(), and msRunReaderSPtrForSelectedMsRunId().

◆ msRunReaderSPtr() [2/2]

MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtr ( std::size_t ms_run_id_index )

Definition at line 477 of file msfileaccessor.cpp.

{
  std::vector<MsRunIdCstSPtr> ms_run_ids = getMsRunIds();
  if(ms_run_id_index >= ms_run_ids.size())
    throw PappsoException(QObject::tr("MsRunId request out-of-bound error."));
 
  return msRunReaderSPtr(ms_run_ids.at(ms_run_id_index));
}

References getMsRunIds(), and msRunReaderSPtr().

◆ msRunReaderSPtrForSelectedMsRunId()

MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSPtrForSelectedMsRunId ( )

Definition at line 488 of file msfileaccessor.cpp.

{
  // qDebug();
 
  return msRunReaderSPtr(mcsp_selectedMsRunId);
}

References mcsp_selectedMsRunId, and msRunReaderSPtr().

◆ setPreferredFileReaderType()

void pappso::MsFileAccessor::setPreferredFileReaderType	(	MsDataFormat	format,
		FileReaderType	reader_type
	)

given an mz format, explicitly set the preferred reader

Definition at line 316 of file msfileaccessor.cpp.

{
  // qDebug();
 
  auto ret = m_preferredFileReaderTypeMap.insert(
    std::pair<MsDataFormat, FileReaderType>(format, reader_type));
 
  if(!ret.second)
    {
      // replace
      ret.first->second = reader_type;
    }
}

References m_preferredFileReaderTypeMap.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData(), and pappso::masschroq::JsonInput::readMzDataFiles().

◆ setSelectedMsRunId()

void pappso::MsFileAccessor::setSelectedMsRunId ( MsRunIdCstSPtr ms_run_id_csp )

Definition at line 355 of file msfileaccessor.cpp.

{
  mcsp_selectedMsRunId = ms_run_id_csp;
}

References mcsp_selectedMsRunId.

Member Data Documentation

◆ m_fileFormat

MsDataFormat pappso::MsFileAccessor::m_fileFormat = MsDataFormat::unknown

private

Definition at line 115 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getFileFormat(), getMsRunIds(), getOboPsiModTermFileFormat(), and msRunReaderSPtr().

◆ m_fileName

QString pappso::MsFileAccessor::m_fileName

private

Definition at line 109 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getFileName(), getMsRunIds(), getMsRunReaderSPtrByRunId(), and msRunReaderSPtr().

◆ m_fileReaderType

FileReaderType pappso::MsFileAccessor::m_fileReaderType

private

Definition at line 118 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getFileReaderType(), getMsRunIds(), and getpreferredFileReaderType().

◆ m_oboPsiModTermNativeIDFormat

OboPsiModTerm pappso::MsFileAccessor::m_oboPsiModTermNativeIDFormat

private

Definition at line 124 of file msfileaccessor.h.

Referenced by MsFileAccessor(), getOboPsiModTermNativeIDFormat(), and msRunReaderSPtr().

◆ m_preferredFileReaderTypeMap

std::map<MsDataFormat, FileReaderType> pappso::MsFileAccessor::m_preferredFileReaderTypeMap

private

Definition at line 120 of file msfileaccessor.h.

Referenced by getMsRunIds(), getpreferredFileReaderType(), and setPreferredFileReaderType().

◆ m_xmlPrefix

const QString pappso::MsFileAccessor::m_xmlPrefix

private

Definition at line 113 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), and getMsRunIds().

◆ mcsp_selectedMsRunId

MsRunIdCstSPtr pappso::MsFileAccessor::mcsp_selectedMsRunId = nullptr

private

Definition at line 122 of file msfileaccessor.h.

Referenced by getSelectedMsRunId(), msRunReaderSPtrForSelectedMsRunId(), and setSelectedMsRunId().

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

pappsomspp/msfile/msfileaccessor.h
pappsomspp/msfile/msfileaccessor.cpp

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsFileAccessor() [1/2]

◆ MsFileAccessor() [2/2]

◆ ~MsFileAccessor()

Member Function Documentation

◆ buildMsRunReaderSPtr() [1/2]

◆ buildMsRunReaderSPtr() [2/2]

◆ buildTimsMsRunReaderMs2SPtr()

◆ getFileFormat()

◆ getFileName()

◆ getFileReaderType()

◆ getMsRunIds()

◆ getMsRunReaderSPtrByRunId()

◆ getOboPsiModTermFileFormat()

◆ getOboPsiModTermNativeIDFormat()

◆ getpreferredFileReaderType()

◆ getSelectedMsRunId()

◆ msRunReaderSPtr() [1/2]

◆ msRunReaderSPtr() [2/2]

◆ msRunReaderSPtrForSelectedMsRunId()

◆ setPreferredFileReaderType()

◆ setSelectedMsRunId()

Member Data Documentation

◆ m_fileFormat

◆ m_fileName

◆ m_fileReaderType

◆ m_oboPsiModTermNativeIDFormat

◆ m_preferredFileReaderTypeMap

◆ m_xmlPrefix

◆ mcsp_selectedMsRunId