base class to initialize mzCBOR file parsing More...

#include <mzcborreaderbase.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborReaderBase:

Public Member Functions
	MzcborReaderBase ()
virtual	~MzcborReaderBase ()
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
bool	isMzcbor () const
const QStringList &	getMsrunIdList () const
Public Member Functions inherited from pappso::cbor::CborStreamReaderInterface
	CborStreamReaderInterface ()
virtual	~CborStreamReaderInterface ()

Protected Member Functions
void	readRoot (pappso::UiMonitorInterface &monitor)
virtual void	readMsrun ()
virtual void	readReferenceableParamGroupList ()
std::map< QString, CvParam >	getCvParamsMap ()
	read the array containing cvParams to give accessions and values
Protected Member Functions inherited from pappso::cbor::CborStreamReaderInterface
bool	getExpectedString ()
void	initCborReader (QFile *pcborfile)
void	initCborReader (QIODevice *pcborfile)

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

Private Attributes
bool	m_isMzcbor = false
QStringList	m_msrunIdList

Detailed Description

base class to initialize mzCBOR file parsing

ensures stream read on regular file or any readable device

Definition at line 44 of file mzcborreaderbase.h.

Constructor & Destructor Documentation

◆ MzcborReaderBase()

pappso::cbor::mzcbor::MzcborReaderBase::MzcborReaderBase ( )

Default constructor

Definition at line 31 of file mzcborreaderbase.cpp.

32{

33}

◆ ~MzcborReaderBase()

pappso::cbor::mzcbor::MzcborReaderBase::~MzcborReaderBase ( )

virtual

Destructor

Definition at line 35 of file mzcborreaderbase.cpp.

36{

37}

Member Function Documentation

◆ close()

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

virtual

convenient function to clean pointer before leaving

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 40 of file mzcborreaderbase.cpp.

41{

42}

Referenced by pappso::MzcborMsRunReader::initialize(), and pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

◆ getCvParamsMap()

std::map< QString, pappso::cbor::mzcbor::CvParam > pappso::cbor::mzcbor::MzcborReaderBase::getCvParamsMap ( )

protected

read the array containing cvParams to give accessions and values

Definition at line 190 of file mzcborreaderbase.cpp.

{
  qDebug();
  std::map<QString, CvParam> accession_values;
  mpa_cborReader->enterContainer(); // start array
 
  while(mpa_cborReader->hasNext())
    {
 
      CvParam cv_param;
      cv_param.fromCbor(*mpa_cborReader);
      accession_values.insert({cv_param.accession, cv_param});
    }
 
  mpa_cborReader->leaveContainer(); // end array
  return accession_values;
}

References pappso::cbor::mzcbor::CvParam::accession, pappso::cbor::mzcbor::CvParam::fromCbor(), and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

Referenced by pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readScan().

◆ getMsrunIdList()

const QStringList & pappso::cbor::mzcbor::MzcborReaderBase::getMsrunIdList ( ) const

Definition at line 126 of file mzcborreaderbase.cpp.

{
  return m_msrunIdList;
}

References m_msrunIdList.

◆ isMzcbor()

bool pappso::cbor::mzcbor::MzcborReaderBase::isMzcbor ( ) const

Definition at line 120 of file mzcborreaderbase.cpp.

{
  return m_isMzcbor;
}

References m_isMzcbor.

◆ readCbor() [1/2]

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

virtual

read mzCBOR file

Parameters

cborp	file pointer
monitor	monitor read progress and messages

Reimplemented in pappso::cbor::mzcbor::MzcborBuildIndexReader.

Definition at line 45 of file mzcborreaderbase.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 pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

◆ readCbor() [2/2]

void pappso::cbor::mzcbor::MzcborReaderBase::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 59 of file mzcborreaderbase.cpp.

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

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

◆ readMsrun()

void pappso::cbor::mzcbor::MzcborReaderBase::readMsrun ( )

protectedvirtual

Reimplemented in pappso::cbor::mzcbor::MzcborBuildIndexReader, and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader.

Definition at line 169 of file mzcborreaderbase.cpp.

{
  mpa_cborReader->enterContainer();
 
  while(getExpectedString())
    {
      if(m_expectedString == "id")
        {
          getExpectedString();
          m_msrunIdList << m_expectedString;
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
  mpa_cborReader->leaveContainer();
}

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

Referenced by readRoot().

◆ readReferenceableParamGroupList()

void pappso::cbor::mzcbor::MzcborReaderBase::readReferenceableParamGroupList ( )

protectedvirtual

Definition at line 133 of file mzcborreaderbase.cpp.

{
  mpa_cborReader->enterContainer();
 
  while(getExpectedString())
    {
      if(m_expectedString == "referenceableParamGroup")
        {
          mpa_cborReader->next();
          /*
  mpa_cborReader->enterContainer();
 
  while(getExpectedString())
    {
      if(m_expectedString == "cvParam")
        {
          std::map<QString, pappso::cbor::mzcbor::CvParam> cvParamMap =
            CvParam::getCvParamsMapFromCbor(*mpa_cborReader);
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
  mpa_cborReader->leaveContainer();*/
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
  mpa_cborReader->leaveContainer();
}

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

Referenced by readRoot().

◆ readRoot()

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

protected

Definition at line 75 of file mzcborreaderbase.cpp.

{
  qDebug();
  mpa_cborReader->enterContainer();
 
  while(getExpectedString())
    {
 
      if(m_expectedString == "mzCBOR")
        {
          m_isMzcbor = true;
          mpa_cborReader->next();
        }
      else if(m_expectedString == "mzML")
        {
          m_isMzcbor = true;
          qDebug() << m_expectedString;
          mpa_cborReader->next();
 
          while(getExpectedString())
            {
              qDebug() << m_expectedString;
              if(m_expectedString == "run")
                {
                  readMsrun();
                }
              else if(m_expectedString == "referenceableParamGroupList")
                {
                  readReferenceableParamGroupList();
                }
              else
                {
                  mpa_cborReader->next();
                }
              if(m_stopParsing)
                break;
            }
        }
    }
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_isMzcbor, m_stopParsing, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, readMsrun(), and readReferenceableParamGroupList().

Referenced by pappso::cbor::mzcbor::MzcborBuildIndexReader::readCbor(), readCbor(), and readCbor().

Member Data Documentation

◆ m_isMzcbor

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

private

Definition at line 93 of file mzcborreaderbase.h.

Referenced by isMzcbor(), and readRoot().

◆ m_msrunIdList

QStringList pappso::cbor::mzcbor::MzcborReaderBase::m_msrunIdList

private

Definition at line 94 of file mzcborreaderbase.h.

Referenced by getMsrunIdList(), and readMsrun().

◆ m_stopParsing

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

protected

Definition at line 90 of file mzcborreaderbase.h.

Referenced by readRoot(), pappso::cbor::mzcbor::MzcborBuildIndexReader::readSpectrumListAndLeave(), and pappso::cbor::mzcbor::MzcborSpectrumCollectionReader::readSpectrumListAndLeave().

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

pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.h
pappsomspp/core/processing/cbor/mzcbor/mzcborreaderbase.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MzcborReaderBase()

◆ ~MzcborReaderBase()

Member Function Documentation

◆ close()

◆ getCvParamsMap()

◆ getMsrunIdList()

◆ isMzcbor()

◆ readCbor() [1/2]

◆ readCbor() [2/2]

◆ readMsrun()

◆ readReferenceableParamGroupList()

◆ readRoot()

Member Data Documentation

◆ m_isMzcbor

◆ m_msrunIdList

◆ m_stopParsing