pappso::cbor::mzcbor::MzcborReaderBase Class Reference

#include <mzcborreaderbase.h>

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

Public Member Functions
	MzcborReaderBase ()
virtual	~MzcborReaderBase ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor)
virtual void	readCbor (QIODevice *cborp, pappso::UiMonitorInterface &monitor)
virtual void	close ()
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

Todo:

write docs

Definition at line 42 of file mzcborreaderbase.h.

Constructor & Destructor Documentation

MzcborReaderBase()

pappso::cbor::mzcbor::MzcborReaderBase::MzcborReaderBase

(

)

Default constructor

Definition at line 32 of file mzcborreaderbase.cpp.

{
}

~MzcborReaderBase()

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

virtual

Destructor

Definition at line 36 of file mzcborreaderbase.cpp.

{
}

Member Function Documentation

close()

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

virtual

Reimplemented from pappso::cbor::CborStreamReaderInterface.

Definition at line 41 of file mzcborreaderbase.cpp.

{
}

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 191 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, and pappso::cbor::mzcbor::CvParam::fromCbor().

getMsrunIdList()

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

(

)

const

Definition at line 127 of file mzcborreaderbase.cpp.

{
  return m_msrunIdList;
}

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

isMzcbor()

bool pappso::cbor::mzcbor::MzcborReaderBase::isMzcbor

(

)

const

Definition at line 121 of file mzcborreaderbase.cpp.

{
  return m_isMzcbor;
}

readCbor() [1/2]

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

virtual

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

Definition at line 46 of file mzcborreaderbase.cpp.

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

Referenced by pappso::MzcborMsRunReader::readSpectrumCollectionWithMsrunReadConfig().

readCbor() [2/2]

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

virtual

Definition at line 60 of file mzcborreaderbase.cpp.

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

readMsrun()

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

protectedvirtual

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

Definition at line 170 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();
}

readReferenceableParamGroupList()

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

protectedvirtual

Definition at line 134 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();
}

readRoot()

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

protected

Definition at line 76 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();
}

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

Member Data Documentation

m_isMzcbor

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

private

Definition at line 78 of file mzcborreaderbase.h.

m_msrunIdList

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

private

Definition at line 79 of file mzcborreaderbase.h.

m_stopParsing

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

protected

Definition at line 75 of file mzcborreaderbase.h.

Referenced by pappso::cbor::mzcbor::MzcborBuildIndexReader::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