pappso::TimsMsFileReader Class Reference

#include <timsmsfilereader.h>

Inheritance diagram for pappso::TimsMsFileReader:

Public Member Functions
	TimsMsFileReader (const QString &file_name)
virtual	~TimsMsFileReader ()
virtual Enums::MsDataFormat	getFileFormat () override
virtual std::vector< MsRunIdCstSPtr >	getMsRunIds (const QString &run_prefix) override
MsRunReader *	selectMsRunReader (const QString &file_name) const

Private Member Functions
virtual std::size_t	initialize ()
Private Member Functions inherited from pappso::MsFileReader
	MsFileReader (const QString &file_name)
virtual	~MsFileReader ()

Additional Inherited Members
Private Attributes inherited from pappso::MsFileReader
QString	m_fileName
Enums::MsDataFormat	m_fileFormat = Enums::MsDataFormat::unknown

Detailed Description

Todo

write docs

Definition at line 41 of file timsmsfilereader.h.

Constructor & Destructor Documentation

TimsMsFileReader()

pappso::TimsMsFileReader::TimsMsFileReader

(

const QString &

file_name

)

Definition at line 40 of file timsmsfilereader.cpp.

                                                           : MsFileReader(file_name)
{
  qDebug() << " " << m_fileName;
  initialize();
}

References pappso::MsFileReader::MsFileReader(), initialize(), and pappso::MsFileReader::m_fileName.

~TimsMsFileReader()

pappso::TimsMsFileReader::~TimsMsFileReader ( )

virtual

Definition at line 47 of file timsmsfilereader.cpp.

{
}

Member Function Documentation

getFileFormat()

Enums::MsDataFormat pappso::TimsMsFileReader::getFileFormat ( )

overridevirtual

Implements pappso::MsFileReader.

Definition at line 86 of file timsmsfilereader.cpp.

{
  return m_fileFormat;
}

References pappso::MsFileReader::m_fileFormat.

Referenced by pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr(), and pappso::MsFileAccessor::getMsRunIds().

getMsRunIds()

std::vector< MsRunIdCstSPtr > pappso::TimsMsFileReader::getMsRunIds ( const QString & run_prefix )

overridevirtual

Implements pappso::MsFileReader.

Definition at line 93 of file timsmsfilereader.cpp.

{
  std::vector<MsRunIdCstSPtr> ms_run_ids;
 
  if(!initialize())
    return ms_run_ids;
 
  // Finally create the MsRunId with the file name.
  MsRunId ms_run_id(m_fileName);
  ms_run_id.setMsDataFormat(m_fileFormat);
 
  // We need to set the unambiguous xmlId string.
  ms_run_id.setXmlId(QString("%1a1").arg(run_prefix));
 
  ms_run_id.setRunId("a1");
 
  // Now set the sample name to the run id:
 
  ms_run_id.setSampleName(QFileInfo(m_fileName).baseName());
 
  qDebug() << "Current ms_run_id:" << ms_run_id.toString();
 
  // Finally make a shared pointer out of it and append it to the vector.
  ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
 
  return ms_run_ids;
}

References initialize(), pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, pappso::MsRunId::setMsDataFormat(), pappso::MsRunId::setRunId(), pappso::MsRunId::setSampleName(), pappso::MsRunId::setXmlId(), and pappso::MsRunId::toString().

Referenced by pappso::MsFileAccessor::buildTimsMsRunReaderMs2SPtr(), and pappso::MsFileAccessor::getMsRunIds().

initialize()

std::size_t pappso::TimsMsFileReader::initialize ( )

privatevirtual

Definition at line 53 of file timsmsfilereader.cpp.

{
 
  m_fileFormat = Enums::MsDataFormat::unknown;
  try
    {
      TimsData tims_data(m_fileName);
      m_fileFormat = Enums::MsDataFormat::brukerTims;
    }
 
  catch(ExceptionNotRecognized &error)
    {
      qWarning() << "tims data not recognized initializing TimsData object:\n" << error.qwhat();
 
      throw pappso::ExceptionNotRecognized(
        QObject::tr("Bruker tims data file not recognized in %1 :\n%2")
          .arg(m_fileName)
          .arg(error.qwhat()));
      return 0;
    }
  catch(PappsoException &error)
    {
      m_fileFormat = Enums::MsDataFormat::brukerTims;
      throw pappso::PappsoException(QObject::tr("Error reading Bruker tims data in %1 :\n%2")
                                      .arg(m_fileName)
                                      .arg(error.qwhat()));
    }
 
  return 1;
}

References pappso::Enums::brukerTims, pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, pappso::PappsoException::qwhat(), and pappso::Enums::unknown.

Referenced by TimsMsFileReader(), and getMsRunIds().

selectMsRunReader()

MsRunReader * pappso::TimsMsFileReader::selectMsRunReader

(

const QString &

file_name

)

const

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

• pappsomspp/core/msfile/timsmsfilereader.h
• pappsomspp/core/msfile/timsmsfilereader.cpp