pappso::MzcborMsFileReader Class Reference

#include <mzcbormsfilereader.h>

Inheritance diagram for pappso::MzcborMsFileReader:

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

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

Private Attributes
std::vector< pwiz::msdata::MSDataPtr >	m_msDataPtrVector
pappso::cbor::mzcbor::MzcborReaderBase	m_mzcborReaderBase
pappso::cbor::mzcbor::MzcborIndexReader	m_mzcborIndexReader
Private Attributes inherited from pappso::MsFileReader
QString	m_fileName
Enums::MsDataFormat	m_fileFormat = Enums::MsDataFormat::unknown

Detailed Description

Todo:

write docs

Definition at line 21 of file mzcbormsfilereader.h.

Constructor & Destructor Documentation

MzcborMsFileReader()

pappso::MzcborMsFileReader::MzcborMsFileReader

(

const QString &

file_name

)

Definition at line 10 of file mzcbormsfilereader.cpp.

                                                               : MsFileReader{file_name}
{
  m_fileFormat = pappso::Enums::MsDataFormat::unknown;
  initialize();
}

References initialize(), pappso::MsFileReader::m_fileFormat, and pappso::Enums::unknown.

~MzcborMsFileReader()

pappso::MzcborMsFileReader::~MzcborMsFileReader ( )

virtual

Definition at line 17 of file mzcbormsfilereader.cpp.

{
}

Member Function Documentation

getFileFormat()

Enums::MsDataFormat pappso::MzcborMsFileReader::getFileFormat ( )

overridevirtual

Implements pappso::MsFileReader.

Definition at line 23 of file mzcbormsfilereader.cpp.

{
  // std::cout << __FILE__ << " @ " << __LINE__ << " " << __FUNCTION__ << " () "
  //        << std::setprecision(15) << "m_fileFormat: " << (int)m_fileFormat
  //      << std::endl;
 
  return m_fileFormat;
}

References pappso::MsFileReader::m_fileFormat.

Referenced by pappso::MsFileAccessor::getMsRunIds().

getMsRunIds()

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

overridevirtual

Implements pappso::MsFileReader.

Definition at line 79 of file mzcbormsfilereader.cpp.

{
  std::vector<MsRunIdCstSPtr> ms_run_ids;
 
 
  if(m_fileFormat == pappso::Enums::MsDataFormat::mzcbor)
    {
 
      if(m_mzcborIndexReader.getRunIdList().size() > 0)
        {
          qDebug();
          std::size_t iter = 0;
          for(auto &msrun_id_str : m_mzcborIndexReader.getRunIdList())
            {
              MsRunId ms_run_id(m_fileName, msrun_id_str);
 
 
              // Set the MS data format as determined in initialize().
              ms_run_id.setMsDataFormat(m_fileFormat);
 
              // We need to set the unambiguous xmlId string.
              ms_run_id.setXmlId(
                QString("%1%2").arg(run_prefix).arg(Utils::getLexicalOrderedString(iter)));
 
              // Now set the sample name to the run id : we can not do that, this is not the use
              // sample name ms_run_id.setSampleName(QString::fromStdString(ms_data_ptr->run.id));
 
              // And if it is possible, the real sample name because this one is for the
              // end user to recognize his sample:
              ms_run_id.setSampleName(msrun_id_str);
 
 
              ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
              iter++;
            }
        }
      else
        {
 
          std::size_t iter = 0;
          for(auto &msrun_id_str : m_mzcborReaderBase.getMsrunIdList())
            {
              MsRunId ms_run_id(m_fileName, msrun_id_str);
 
 
              // Set the MS data format as determined in initialize().
              ms_run_id.setMsDataFormat(m_fileFormat);
 
              // We need to set the unambiguous xmlId string.
              ms_run_id.setXmlId(
                QString("%1%2").arg(run_prefix).arg(Utils::getLexicalOrderedString(iter)));
 
              // Now set the sample name to the run id : we can not do that, this is not the use
              // sample name ms_run_id.setSampleName(QString::fromStdString(ms_data_ptr->run.id));
 
              // And if it is possible, the real sample name because this one is for the
              // end user to recognize his sample:
              ms_run_id.setSampleName(msrun_id_str);
 
 
              ms_run_ids.push_back(std::make_shared<MsRunId>(ms_run_id));
              iter++;
            }
        }
    }
 
  return ms_run_ids;
}

References pappso::Utils::getLexicalOrderedString(), pappso::cbor::mzcbor::MzcborReaderBase::getMsrunIdList(), pappso::cbor::mzcbor::MzcborIndexReader::getRunIdList(), pappso::MsFileReader::m_fileFormat, pappso::MsFileReader::m_fileName, m_mzcborIndexReader, m_mzcborReaderBase, pappso::Enums::mzcbor, pappso::MsRunId::setMsDataFormat(), pappso::MsRunId::setSampleName(), and pappso::MsRunId::setXmlId().

Referenced by pappso::MsFileAccessor::getMsRunIds().

initialize()

std::size_t pappso::MzcborMsFileReader::initialize ( )

privatevirtual

Definition at line 33 of file mzcbormsfilereader.cpp.

{
 
  pappso::UiMonitorVoid monitor;
  QString str_index_file = m_fileName;
  QFileInfo mzcbor_index_fileinfo(str_index_file.append(".idx"));
  if(mzcbor_index_fileinfo.exists())
    {
      qDebug() << "mzcbor_index_fileinfo.exists()";
      QFile mzcbor_index_file(mzcbor_index_fileinfo.absoluteFilePath());
      mzcbor_index_file.open(QIODevice::ReadOnly);
 
      m_mzcborIndexReader.readCbor(&mzcbor_index_file);
      if(m_mzcborIndexReader.isMzcborIndex())
        {
          m_fileFormat = pappso::Enums::MsDataFormat::mzcbor;
        }
      m_mzcborIndexReader.close();
      mzcbor_index_file.close();
 
      qDebug() << m_mzcborIndexReader.getRunIdList().size();
 
      return m_mzcborIndexReader.getRunIdList().size();
    }
  else
    {
      qDebug();
      QFile mzcbor_file(m_fileName);
      mzcbor_file.open(QIODevice::ReadOnly);
 
      m_mzcborReaderBase.readCbor(&mzcbor_file, monitor);
      if(m_mzcborReaderBase.isMzcbor())
        {
          m_fileFormat = pappso::Enums::MsDataFormat::mzcbor;
        }
      m_mzcborReaderBase.close();
      mzcbor_file.close();
 
      qDebug() << m_mzcborReaderBase.getMsrunIdList().join(" ");
 
      return m_mzcborReaderBase.getMsrunIdList().size();
    }
}

References pappso::Enums::mzcbor.

Referenced by MzcborMsFileReader().

Member Data Documentation

m_msDataPtrVector

std::vector<pwiz::msdata::MSDataPtr> pappso::MzcborMsFileReader::m_msDataPtrVector

private

Definition at line 36 of file mzcbormsfilereader.h.

m_mzcborIndexReader

pappso::cbor::mzcbor::MzcborIndexReader pappso::MzcborMsFileReader::m_mzcborIndexReader

private

Definition at line 39 of file mzcbormsfilereader.h.

Referenced by getMsRunIds().

m_mzcborReaderBase

pappso::cbor::mzcbor::MzcborReaderBase pappso::MzcborMsFileReader::m_mzcborReaderBase

private

Definition at line 38 of file mzcbormsfilereader.h.

Referenced by getMsRunIds().

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

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