pappso::cbor::mzcbor::MzcborCopyReplaceBase Class Reference

base class to transform mzCBOR stream in a new mzCBOR output stream More...

#include <mzcborcopyreplacebase.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborCopyReplaceBase:

Public Member Functions
	MzcborCopyReplaceBase (CborStreamWriter *cbor_output_p, const QString &operation)
virtual	~MzcborCopyReplaceBase ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR file
virtual void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
	read mzCBOR from any device (memory buffer or else)
virtual void	close ()
	convenient function to clean pointer before leaving
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
void	readRoot (pappso::UiMonitorInterface &monitor)
void	readCbor (pappso::UiMonitorInterface &monitor)
void	readRun (pappso::UiMonitorInterface &monitor)
void	readSpectrumList (pappso::UiMonitorInterface &monitor)
virtual void	processQcborSpectrum (SpectrumTube &spectrum_tube, QcborSpectrum &cbor_spectrum)
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

Protected Attributes
bool	m_stopParsing = false
CborStreamWriter *	mp_cborOutput
QString	m_operation
Protected Attributes inherited from pappso::cbor::CborStreamReaderInterface
CborStreamReader *	mpa_cborReader = nullptr
QString	m_expectedString
QByteArray	m_data

Private Attributes
bool	m_isMzcbor = false
QString	m_uuid

Detailed Description

base class to transform mzCBOR stream in a new mzCBOR output stream

ensures stream read on regular file or any readable device

Definition at line 46 of file mzcborcopyreplacebase.h.

Constructor & Destructor Documentation

MzcborCopyReplaceBase()

pappso::cbor::mzcbor::MzcborCopyReplaceBase::MzcborCopyReplaceBase	(	CborStreamWriter *	cbor_output_p,
		const QString &	operation )

Default constructor

Definition at line 43 of file mzcborcopyreplacebase.cpp.

{
 
  mp_cborOutput = cbor_output_p;
  m_operation   = operation;
}

References m_operation, and mp_cborOutput.

Referenced by pappso::cbor::mzcbor::MzcborPrecursorFinder::MzcborPrecursorFinder().

~MzcborCopyReplaceBase()

pappso::cbor::mzcbor::MzcborCopyReplaceBase::~MzcborCopyReplaceBase ( )

virtual

Destructor

Definition at line 50 of file mzcborcopyreplacebase.cpp.

{
}

Member Function Documentation

close()

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::close ( )

virtual

convenient function to clean pointer before leaving

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 55 of file mzcborcopyreplacebase.cpp.

{
}

processQcborSpectrum()

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::processQcborSpectrum ( SpectrumTube & spectrum_tube, QcborSpectrum & cbor_spectrum )

protectedvirtual

Reimplemented in pappso::cbor::mzcbor::MzcborPrecursorFinder.

Definition at line 337 of file mzcborcopyreplacebase.cpp.

{
  qDebug() << cbor_spectrum.getId() << " mslevel=" << cbor_spectrum.getMsLevel();
  cbor_spectrum.setId(QString("%1 oliv=%2").arg(cbor_spectrum.getId()).arg("cc"));
  if(cbor_spectrum.getMsLevel() == 2)
    {
      spectrum_tube.push_back(cbor_spectrum);
    }
}

References pappso::cbor::mzcbor::QcborSpectrum::getId(), pappso::cbor::mzcbor::QcborSpectrum::getMsLevel(), pappso::cbor::mzcbor::SpectrumTube::push_back(), and pappso::cbor::mzcbor::QcborSpectrum::setId().

Referenced by readSpectrumList().

readCbor() [1/3]

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readCbor ( pappso::UiMonitorInterface & monitor )

protected

Definition at line 158 of file mzcborcopyreplacebase.cpp.

{
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap old_informations;
 
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      // mode
      //  informations
      //  log
      //  parameter_map
      getExpectedString();
      qDebug() << m_expectedString;
      if(m_expectedString == "mode")
        {
          mp_cborOutput->append("mode");
          mp_cborOutput->append(mpa_cborReader->toInteger());
          mpa_cborReader->next();
        }
      else if(m_expectedString == "informations")
        {
 
          mpa_cborReader->readCborMap(old_informations);
          mp_cborOutput->writeInformations(
            "libpappsomspp", Utils::getVersion(), "mzCBOR", m_operation);
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR").arg(m_expectedString));
        }
    }
 
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::Utils::getVersion(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_operation, mp_cborOutput, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

readCbor() [2/3]

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readCbor ( QFile * cborp, pappso::UiMonitorInterface & monitor )

virtual

read mzCBOR file

Parameters

cborp	file pointer
monitor	monitor read progress and messages

Definition at line 60 of file mzcborcopyreplacebase.cpp.

{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

References pappso::cbor::CborStreamReaderInterface::initCborReader(), pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readRoot().

Referenced by readRoot().

readCbor() [3/3]

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readCbor ( QIODevice * cborp, pappso::UiMonitorInterface & monitor )

virtual

read mzCBOR from any device (memory buffer or else)

Parameters

cborp	device pointer
monitor	monitor read progress and messages

Definition at line 74 of file mzcborcopyreplacebase.cpp.

{
  qDebug();
  initCborReader(cborp);
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

References pappso::cbor::CborStreamReaderInterface::initCborReader(), pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readRoot().

readRoot()

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readRoot ( pappso::UiMonitorInterface & monitor )

protected

Definition at line 88 of file mzcborcopyreplacebase.cpp.

{
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
 
 
  getExpectedString();
  if(m_expectedString == "mzCBOR")
    {
      mp_cborOutput->append("mzCBOR");
      qDebug() << m_expectedString;
      readCbor(monitor);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting mzCBOR element");
    }
 
 
  QCborMap tmp_map;
  getExpectedString();
  if(m_expectedString == "mzML")
    {
      mp_cborOutput->append("mzML");
 
      mpa_cborReader->readCborMap(tmp_map);
      mp_cborOutput->writeCborMap(tmp_map);
    }
  else
    {
      throw pappso::PappsoException("ERROR: expecting mzML element");
    }
 
 
  QStringList copy_tags;
  copy_tags << "cvList"
            << "fileDescription" << "referenceableParamGroupList" << "softwareList"
            << "instrumentConfigurationList" << "dataProcessingList";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborMap(tmp_map);
          mp_cborOutput->writeCborMap(tmp_map);
        }
      else if(m_expectedString == "run")
        {
 
          mp_cborOutput->append("run");
          qDebug() << m_expectedString;
          readRun(monitor);
        }
 
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR root").arg(m_expectedString));
        }
    }
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, mp_cborOutput, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, readCbor(), and readRun().

Referenced by readCbor(), and readCbor().

readRun()

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readRun ( pappso::UiMonitorInterface & monitor )

protected

Definition at line 198 of file mzcborcopyreplacebase.cpp.

{
 
  // <run
  //       id="20120906_balliau_extract_1_A01_urnb-1"
  //       defaultInstrumentConfigurationRef="IC1"
  //       startTimeStamp="2012-09-06T16:17:42.762Z"
  //       defaultSourceFileRef="RAW1"
  //   >
  //   <spectrumList
  //           count="3"
  //           defaultDataProcessingRef="ThermoRawFileParserProcessing"
  //       >
  //
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap tmp_map;
 
  QStringList copy_tags;
  copy_tags << "id" << "defaultInstrumentConfigurationRef" << "startTimeStamp"
            << "defaultSourceFileRef";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          getExpectedString();
          qDebug() << m_expectedString;
          mp_cborOutput->append(m_expectedString);
        }
 
      else if(m_expectedString == "spectrumList")
        {
          mp_cborOutput->append(m_expectedString);
          readSpectrumList(monitor);
        }
      else if(m_expectedString == "chromatogramList")
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborMap(tmp_map);
          mp_cborOutput->writeCborMap(tmp_map);
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR run").arg(m_expectedString));
        }
    }
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, mp_cborOutput, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrumList().

Referenced by readRoot().

readSpectrumList()

void pappso::cbor::mzcbor::MzcborCopyReplaceBase::readSpectrumList ( pappso::UiMonitorInterface & monitor )

protected

Definition at line 257 of file mzcborcopyreplacebase.cpp.

{
 
  //   <spectrumList
  //           count="3"
  //           defaultDataProcessingRef="ThermoRawFileParserProcessing"
  //       >
  //
  mp_cborOutput->startMap();
  mpa_cborReader->enterContainer();
  QCborMap tmp_map;
  QCborValue tmp_value;
  QcborSpectrum cbor_spectrum;
 
  SpectrumTube spectrum_tube;
 
  QStringList copy_tags;
  copy_tags << "defaultDataProcessingRef";
  while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
    {
      getExpectedString();
      qDebug() << m_expectedString;
 
 
      if(copy_tags.contains(m_expectedString))
        {
          mp_cborOutput->append(m_expectedString);
          mpa_cborReader->readCborValue(tmp_value);
          mp_cborOutput->writeCborValue(tmp_value);
        }
      else if(m_expectedString == "count")
        {
          if(mpa_cborReader->isInteger())
            {
              monitor.setStatus(
                QObject::tr("original spectrumList count=%1").arg(mpa_cborReader->toInteger()));
              monitor.setTotalSteps(mpa_cborReader->toInteger());
            }
          mpa_cborReader->next();
        }
      else if(m_expectedString == "spectrum")
        {
          qDebug() << m_expectedString;
 
          // this is an array
          mpa_cborReader->enterContainer();
          while(!mpa_cborReader->lastError() && mpa_cborReader->hasNext())
            {
              mpa_cborReader->readCborMap(cbor_spectrum);
              monitor.count();
              processQcborSpectrum(spectrum_tube, cbor_spectrum);
            }
 
 
          mpa_cborReader->leaveContainer();
 
 
          monitor.setStatus(QObject::tr("new spectrumList count=%1").arg(spectrum_tube.size()));
          mp_cborOutput->append("count");
          mp_cborOutput->append((quint64)spectrum_tube.size());
          mp_cborOutput->append(m_expectedString);
          mp_cborOutput->startArray();
 
          spectrum_tube.flush(mp_cborOutput);
 
          mp_cborOutput->endArray();
        }
      else
        {
          throw pappso::PappsoException(
            QObject::tr("ERROR: %1 not expected in mzCBOR spectrumList").arg(m_expectedString));
        }
    }
 
 
  mp_cborOutput->endMap();
  mpa_cborReader->leaveContainer();
}

References pappso::UiMonitorInterface::count(), pappso::cbor::mzcbor::SpectrumTube::flush(), pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, mp_cborOutput, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, processQcborSpectrum(), pappso::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::setTotalSteps(), and pappso::cbor::mzcbor::SpectrumTube::size().

Referenced by readRun().

Member Data Documentation

m_isMzcbor

bool pappso::cbor::mzcbor::MzcborCopyReplaceBase::m_isMzcbor = false

private

Definition at line 91 of file mzcborcopyreplacebase.h.

m_operation

QString pappso::cbor::mzcbor::MzcborCopyReplaceBase::m_operation

protected

Definition at line 88 of file mzcborcopyreplacebase.h.

Referenced by MzcborCopyReplaceBase(), and readCbor().

m_stopParsing

bool pappso::cbor::mzcbor::MzcborCopyReplaceBase::m_stopParsing = false

protected

Definition at line 86 of file mzcborcopyreplacebase.h.

m_uuid

QString pappso::cbor::mzcbor::MzcborCopyReplaceBase::m_uuid

private

Definition at line 92 of file mzcborcopyreplacebase.h.

mp_cborOutput

CborStreamWriter* pappso::cbor::mzcbor::MzcborCopyReplaceBase::mp_cborOutput

protected

Definition at line 87 of file mzcborcopyreplacebase.h.

Referenced by MzcborCopyReplaceBase(), readCbor(), readRoot(), readRun(), and readSpectrumList().

---

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

• pappsomspp/core/processing/cbor/mzcbor/copyreplace/mzcborcopyreplacebase.h
• pappsomspp/core/processing/cbor/mzcbor/copyreplace/mzcborcopyreplacebase.cpp