pappso::MsFileAccessor Class Reference

#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
MzFormat	getFileFormat () const
	get the raw format of mz data More...
void	setPreferedFileReaderType (MzFormat format, FileReaderType reader_type)
	given an mz format, explicitly set the prefered reader More...
std::vector< MsRunIdCstSPtr >	getMsRunIds ()
MsRunReaderSPtr	msRunReaderSp (MsRunIdCstSPtr ms_run_id)
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...

Private Attributes
QString	m_fileName
const QString	m_xmlPrefix
MzFormat	m_fileFormat = MzFormat::unknown
FileReaderType	m_fileReaderType
std::map< MzFormat, FileReaderType >	m_preferedFileReaderTypeMap

Detailed Description

Definition at line 34 of file msfileaccessor.h.

Constructor & Destructor Documentation

MsFileAccessor() [1/2]

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

Definition at line 28 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())));
}

MsFileAccessor() [2/2]

pappso::MsFileAccessor::MsFileAccessor

(

const MsFileAccessor &

other

)

Definition at line 39 of file msfileaccessor.cpp.

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

~MsFileAccessor()

pappso::MsFileAccessor::~MsFileAccessor ( )

virtual

Definition at line 47 of file msfileaccessor.cpp.

{
}

Member Function Documentation

buildMsRunReaderSPtr()

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

Definition at line 223 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())));
 
  MzFormat file_format = ms_run_id.get()->getMzFormat();
 
  if(file_format == MzFormat::xy)
    {
      qDebug() << "Returning a XyMsRunReader.";
 
      return std::make_shared<XyMsRunReader>(ms_run_id);
    }
  else if(file_format == MzFormat::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 == MzFormat::brukerTims)
    {
      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);
    }
}

buildTimsMsRunReaderMs2SPtr()

TimsMsRunReaderMs2SPtr pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr

(

)

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

Definition at line 142 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::pwiz.

getFileFormat()

MzFormat pappso::MsFileAccessor::getFileFormat

(

)

const

get the raw format of mz data

Definition at line 60 of file msfileaccessor.cpp.

{
  return m_fileFormat;
}

References m_fileFormat.

getFileName()

const QString & pappso::MsFileAccessor::getFileName

(

)

const

Definition at line 53 of file msfileaccessor.cpp.

{
  return m_fileName;
}

References m_fileName.

getMsRunIds()

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

(

)

Definition at line 67 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_fileReaderType = FileReaderType::pwiz;
 
      m_fileFormat = pwiz_ms_file_reader.getFileFormat();
 
      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_fileReaderType = FileReaderType::tims;
      m_fileFormat     = tims_file_reader.getFileFormat();
      m_fileName       = tims_dir;
 
 
      auto pref = m_preferedFileReaderTypeMap.find(m_fileFormat);
      if(pref != m_preferedFileReaderTypeMap.end())
        {
          m_fileReaderType = pref->second;
        }
 
      return ms_run_ids;
    }
 
  // qDebug() << "The Tims 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::PwizMsFileReader::getFileFormat(), pappso::TimsMsFileReader::getFileFormat(), pappso::XyMsFileReader::getFileFormat(), pappso::PwizMsFileReader::getMsRunIds(), pappso::TimsMsFileReader::getMsRunIds(), pappso::XyMsFileReader::getMsRunIds(), m_fileFormat, m_fileName, m_fileReaderType, m_preferedFileReaderTypeMap, and m_xmlPrefix.

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

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 260 of file msfileaccessor.cpp.

{
  qDebug() << "GGGGGGGGG1";
  std::vector<MsRunIdCstSPtr> run_list = getMsRunIds();
  MsRunReaderSPtr reader_sp;
  qDebug() << "GGGGGGGGG";
  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 msRunReaderSp(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 msRunReaderSp(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, msRunReaderSp(), and pappso::MsRunId::setXmlId().

msRunReaderSp()

MsRunReaderSPtr pappso::MsFileAccessor::msRunReaderSp

(

MsRunIdCstSPtr

ms_run_id

)

Definition at line 174 of file msfileaccessor.cpp.

{
  if(m_fileName != ms_run_id->getFileName())
    throw(ExceptionNotPossible(
      QObject::tr("The MsRunId instance must have the name file name as the "
                  "MsFileAccessor.")));
 
  if(m_fileReaderType == FileReaderType::pwiz)
    {
      qDebug() << "Returning a PwizMsRunReader.";
 
      return std::make_shared<PwizMsRunReader>(ms_run_id);
    }
  else if(m_fileReaderType == FileReaderType::xy)
    {
      qDebug() << "Returning a XyMsRunReader.";
 
      return std::make_shared<XyMsRunReader>(ms_run_id);
    }
 
  else if(m_fileReaderType == FileReaderType::tims)
    {
      qDebug() << "Returning a TimsMsRunReader.";
 
      return std::make_shared<TimsMsRunReader>(ms_run_id);
    }
  else if(m_fileReaderType == FileReaderType::tims_ms2)
    {
      qDebug() << "Returning a TimsMsRunReaderMs2.";
 
      return std::make_shared<TimsMsRunReaderMs2>(ms_run_id);
    }
 
  if(m_fileFormat == MzFormat::unknown)
    {
      if(ms_run_id.get()->getMzFormat() == MzFormat::xy)
        {
          return std::make_shared<XyMsRunReader>(ms_run_id);
        }
      else
        {
          return std::make_shared<PwizMsRunReader>(ms_run_id);
        }
    }
 
  return nullptr;
}

References m_fileFormat, m_fileName, m_fileReaderType, and pappso::pwiz.

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

setPreferedFileReaderType()

void pappso::MsFileAccessor::setPreferedFileReaderType	(	MzFormat	format,
		FileReaderType	reader_type
	)

given an mz format, explicitly set the prefered reader

Definition at line 298 of file msfileaccessor.cpp.

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

References m_preferedFileReaderTypeMap.

Referenced by pappso::TandemWrapperRun::convertOrginalMsData2mzXmlData().

Member Data Documentation

m_fileFormat

MzFormat pappso::MsFileAccessor::m_fileFormat = MzFormat::unknown

private

Definition at line 82 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getFileFormat(), getMsRunIds(), and msRunReaderSp().

m_fileName

QString pappso::MsFileAccessor::m_fileName

private

Definition at line 76 of file msfileaccessor.h.

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

m_fileReaderType

FileReaderType pappso::MsFileAccessor::m_fileReaderType

private

Definition at line 85 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), getMsRunIds(), and msRunReaderSp().

m_preferedFileReaderTypeMap

std::map<MzFormat, FileReaderType> pappso::MsFileAccessor::m_preferedFileReaderTypeMap

private

Definition at line 87 of file msfileaccessor.h.

Referenced by getMsRunIds(), and setPreferedFileReaderType().

m_xmlPrefix

const QString pappso::MsFileAccessor::m_xmlPrefix

private

Definition at line 80 of file msfileaccessor.h.

Referenced by buildTimsMsRunReaderMs2SPtr(), and getMsRunIds().

---

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

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