#include <mzcborbuildindexreader.h>

Inheritance diagram for pappso::cbor::mzcbor::MzcborBuildIndexReader:

Public Member Functions
	MzcborBuildIndexReader (const MsRunIdCstSPtr &msrun_id)
virtual	~MzcborBuildIndexReader ()
virtual void	readCbor (QFile *cborp, pappso::UiMonitorInterface &monitor) override
	read mzCBOR file
const std::vector< qint64 > &	getSpectrumIndexPositionInFile () const
const std::map< QString, std::size_t > &	getNativeId2SpectrumIndexMap () const
Public Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
	MzcborReaderBase ()
virtual	~MzcborReaderBase ()
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
virtual void	readMsrun () override
	read only the targeted msrun
void	readSpectrumListAndLeave ()
	only the spectrum list of targeted msrun, then stop parsing
void	readSpectrum (qint64 position_of_spectrum_in_file, std::size_t index_count)
	read each spectrum in the targeted msrun (msrunId)
Protected Member Functions inherited from pappso::cbor::mzcbor::MzcborReaderBase
void	readRoot (pappso::UiMonitorInterface &monitor)
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)

Private Attributes
MsRunIdCstSPtr	mcsp_msRunId
QString	m_xmlMzMlRunId
std::vector< qint64 >	m_spectrumIndexPositionInFile
std::map< QString, std::size_t >	m_nativeId2SpectrumIndexMap

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

Detailed Description

Todo: write docs

Definition at line 45 of file mzcborbuildindexreader.h.

Constructor & Destructor Documentation

◆ MzcborBuildIndexReader()

pappso::cbor::mzcbor::MzcborBuildIndexReader::MzcborBuildIndexReader ( const MsRunIdCstSPtr & msrun_id )

Default constructor

Definition at line 39 of file mzcborbuildindexreader.cpp.

  : mcsp_msRunId(msrun_id)
{
  m_xmlMzMlRunId = msrun_id.get()->getRunId();
}

References m_xmlMzMlRunId, and mcsp_msRunId.

◆ ~MzcborBuildIndexReader()

pappso::cbor::mzcbor::MzcborBuildIndexReader::~MzcborBuildIndexReader ( )

virtual

Destructor

Definition at line 45 of file mzcborbuildindexreader.cpp.

46{

47}

Member Function Documentation

◆ getNativeId2SpectrumIndexMap()

const std::map< QString, std::size_t > & pappso::cbor::mzcbor::MzcborBuildIndexReader::getNativeId2SpectrumIndexMap ( ) const

Definition at line 76 of file mzcborbuildindexreader.cpp.

{
  return m_nativeId2SpectrumIndexMap;
}

References m_nativeId2SpectrumIndexMap.

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

◆ getSpectrumIndexPositionInFile()

const std::vector< qint64 > & pappso::cbor::mzcbor::MzcborBuildIndexReader::getSpectrumIndexPositionInFile ( ) const

Definition at line 70 of file mzcborbuildindexreader.cpp.

{
  return m_spectrumIndexPositionInFile;
}

References m_spectrumIndexPositionInFile.

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

◆ readCbor()

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

overridevirtual

read mzCBOR file

Parameters

cborp	file pointer
monitor	monitor read progress and messages

Reimplemented from pappso::cbor::mzcbor::MzcborReaderBase.

Definition at line 51 of file mzcborbuildindexreader.cpp.

{
  qDebug();
  initCborReader((QIODevice *)cborp);
 
  if(mpa_cborReader->device() == nullptr)
    {
      throw pappso::PappsoException(QObject::tr("device is null"));
    }
 
  qDebug();
  if(mpa_cborReader->isMap())
    {
      readRoot(monitor);
    }
  qDebug();
}

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

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

◆ readMsrun()

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

overrideprotectedvirtual

read only the targeted msrun

Reimplemented from pappso::cbor::mzcbor::MzcborReaderBase.

Definition at line 81 of file mzcborbuildindexreader.cpp.

{
  // qDebug();
 
  mpa_cborReader->enterContainer();
  bool ms_run_to_read = false;
 
  while(getExpectedString())
    {
      if(m_expectedString == "id")
        {
          getExpectedString();
 
          if((m_expectedString == m_xmlMzMlRunId) || (m_xmlMzMlRunId.isEmpty()))
            {
              ms_run_to_read = true;
            }
        }
      else if(m_expectedString == "spectrumList")
        {
          if(ms_run_to_read)
            {
              readSpectrumListAndLeave();
            }
          else
            {
              mpa_cborReader->next();
            }
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
  mpa_cborReader->leaveContainer();
}

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

◆ readSpectrum()

void pappso::cbor::mzcbor::MzcborBuildIndexReader::readSpectrum	(	qint64	position_of_spectrum_in_file,
		std::size_t	index_count )

protected

read each spectrum in the targeted msrun (msrunId)

Definition at line 178 of file mzcborbuildindexreader.cpp.

{
  qDebug();
  mpa_cborReader->enterContainer();
  //<spectrum id="controllerType=0 controllerNumber=1 scan=1" index="0" defaultArrayLength="1552">
  QString native_id;
  std::size_t given_index = 0;
  std::map<QString, CvParam> spectrum_parameters;
  std::map<QString, CvParam> scan_parameters;
 
 
  while(getExpectedString())
    {
      qDebug() << m_expectedString;
      if(m_expectedString == "id")
        {
          getExpectedString();
          native_id = m_expectedString;
          qDebug() << m_expectedString;
        }
      else if(m_expectedString == "index")
        {
          if(mpa_cborReader->isUnsignedInteger())
            {
              given_index = mpa_cborReader->toUnsignedInteger();
              mpa_cborReader->next();
 
              qDebug() << given_index;
              // qFatal();
            }
          else
            {
            }
        }
      else if(m_expectedString == "cvParam")
        {
 
          mpa_cborReader->next();
          // spectrum_parameters = getCvParamsMap();
        }
      else if(m_expectedString == "scanList")
        {
          mpa_cborReader->next();
        }
      else if(m_expectedString == "binaryDataArray")
        {
          mpa_cborReader->next();
        }
      else
        {
          mpa_cborReader->next();
        }
    }
  if((given_index != index_count) || (index_count != m_spectrumIndexPositionInFile.size()))
    {
      throw pappso::PappsoException(QObject::tr("index inconsistency %1 %2 %3")
                                      .arg(given_index)
                                      .arg(index_count)
                                      .arg(m_spectrumIndexPositionInFile.size()));
    }
  m_spectrumIndexPositionInFile.push_back(position_of_spectrum_in_file);
 
  m_nativeId2SpectrumIndexMap.insert({native_id, given_index});
 
  mpa_cborReader->leaveContainer();
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, m_nativeId2SpectrumIndexMap, m_spectrumIndexPositionInFile, and pappso::cbor::CborStreamReaderInterface::mpa_cborReader.

Referenced by readSpectrumListAndLeave().

◆ readSpectrumListAndLeave()

void pappso::cbor::mzcbor::MzcborBuildIndexReader::readSpectrumListAndLeave ( )

protected

only the spectrum list of targeted msrun, then stop parsing

Definition at line 121 of file mzcborbuildindexreader.cpp.

{
 
  mpa_cborReader->enterContainer();
 
 
  // qDebug();
 
  // We'll need it to perform the looping in the spectrum list.
  std::size_t spectrum_list_size = 0;
 
  // qDebug() << "The spectrum list has size:" << spectrum_list_size;
 
  while(getExpectedString())
    {
 
      qDebug() << m_expectedString;
      if(m_expectedString == "count")
        {
          if(mpa_cborReader->isUnsignedInteger())
            {
              spectrum_list_size = mpa_cborReader->toUnsignedInteger();
              mpa_cborReader->next();
              qDebug() << "spectrum count=" << spectrum_list_size;
            }
        }
      else if(m_expectedString == "spectrum")
        {
 
          mpa_cborReader->enterContainer(); // start array
          qint64 pos = mpa_cborReader->currentOffset();
 
          std::size_t index_count = 0;
          while(mpa_cborReader->hasNext())
            {
              qDebug();
              qDebug();
              readSpectrum(pos, index_count);
              index_count++;
              pos = mpa_cborReader->currentOffset();
            }
 
          mpa_cborReader->leaveContainer(); // stop array
        }
      else
        {
          mpa_cborReader->next();
        }
    }
 
 
  mpa_cborReader->leaveContainer();
  m_stopParsing = true;
}

References pappso::cbor::CborStreamReaderInterface::getExpectedString(), pappso::cbor::CborStreamReaderInterface::m_expectedString, pappso::cbor::mzcbor::MzcborReaderBase::m_stopParsing, pappso::cbor::CborStreamReaderInterface::mpa_cborReader, and readSpectrum().

Referenced by readMsrun().

Member Data Documentation

◆ m_nativeId2SpectrumIndexMap

std::map<QString, std::size_t> pappso::cbor::mzcbor::MzcborBuildIndexReader::m_nativeId2SpectrumIndexMap

private

Definition at line 86 of file mzcborbuildindexreader.h.

Referenced by getNativeId2SpectrumIndexMap(), and readSpectrum().

◆ m_spectrumIndexPositionInFile

std::vector<qint64> pappso::cbor::mzcbor::MzcborBuildIndexReader::m_spectrumIndexPositionInFile

private

Definition at line 85 of file mzcborbuildindexreader.h.

Referenced by getSpectrumIndexPositionInFile(), and readSpectrum().

◆ m_xmlMzMlRunId

QString pappso::cbor::mzcbor::MzcborBuildIndexReader::m_xmlMzMlRunId

private

Definition at line 83 of file mzcborbuildindexreader.h.

Referenced by MzcborBuildIndexReader(), and readMsrun().

◆ mcsp_msRunId

MsRunIdCstSPtr pappso::cbor::mzcbor::MzcborBuildIndexReader::mcsp_msRunId

private

Definition at line 82 of file mzcborbuildindexreader.h.

Referenced by MzcborBuildIndexReader().

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

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

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MzcborBuildIndexReader()

◆ ~MzcborBuildIndexReader()

Member Function Documentation

◆ getNativeId2SpectrumIndexMap()

◆ getSpectrumIndexPositionInFile()

◆ readCbor()

◆ readMsrun()

◆ readSpectrum()

◆ readSpectrumListAndLeave()

Member Data Documentation

◆ m_nativeId2SpectrumIndexMap

◆ m_spectrumIndexPositionInFile

◆ m_xmlMzMlRunId

◆ mcsp_msRunId