#include <msrunxicextractordiskbuffer.h>

Inheritance diagram for pappso::MsRunXicExtractorDiskBuffer:

Public Member Functions
	MsRunXicExtractorDiskBuffer (const MsRunXicExtractorDiskBuffer &other)

virtual	~MsRunXicExtractorDiskBuffer ()

Public Member Functions inherited from pappso::MsRunXicExtractorDisk
	MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader)

	MsRunXicExtractorDisk (const MsRunXicExtractorDisk &other)

virtual	~MsRunXicExtractorDisk ()

Public Member Functions inherited from pappso::MsRunXicExtractor
	MsRunXicExtractor (const MsRunXicExtractor &other)

virtual	~MsRunXicExtractor ()

Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (Enums::XicExtractMethod method)
	set the XIC extraction method

void	setRetentionTimeAroundTarget (double range_in_seconds)
	set the retention time range in seconds around the target rt

virtual void	extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
	extract a list of XIC given a list of xic coordinates to extract

virtual void	extractXicCoordSPtrListParallelized (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) final
	multithreaded XIC extraction

const MsRunIdCstSPtr &	getMsRunId () const

const MsRunReaderSPtr &	getMsRunReaderSPtr () const
	get the msrunreader currently used for XIC extraction

void	setPostExtractionTraceFilterCstSPtr (pappso::FilterInterfaceCstSPtr &filter)
	filter interface to apply just after XIC extration on each trace

Protected Member Functions
	MsRunXicExtractorDiskBuffer (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)

virtual void	storeSlices (std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override
	store MassSpectrum slices (by daltons) for a given retention time

void	appendSliceInBuffer (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)

void	flushBufferOnDisk ()

virtual void	endPwizRead () override

Protected Member Functions inherited from pappso::MsRunXicExtractorDisk
	MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)

virtual void	protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override

void	prepareExtractor ()

void	serializeMsRun ()

void	appendSliceOnDisk (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
	append a slice on disk (in a file)

std::vector< MsRunSliceSPtr >	acquireSlices (const MzRange &mz_range)
	retrieve all the slices corresponding to a given mz_range

MsRunSliceSPtr	unserializeSlice (unsigned int slice_number)
	get one slice from disk by her slice number (dalton)

Protected Member Functions inherited from pappso::MsRunXicExtractor
	MsRunXicExtractor (MsRunReaderSPtr &msrun_reader)

virtual void	getXicFromPwizMSDataFile (std::vector< Xic * > &xic_list, const std::vector< MzRange > &mass_range_list, pappso::pappso_double rt_begin, pappso::pappso_double rt_end)

Protected Member Functions inherited from pappso::MsRunXicExtractorInterface
	MsRunXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
	constructor is private, use the MsRunXicExtractorFactory

	MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)

virtual	~MsRunXicExtractorInterface ()

virtual void	postExtractionProcess (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)
	possible post extraction process, eventually trace filters

Protected Attributes
std::map< unsigned int, QByteArray >	m_sliceBufferMap

std::size_t	m_bufferSize = 0

std::size_t	m_bufferMaxSize = 150

Protected Attributes inherited from pappso::MsRunXicExtractorDisk
QString	m_temporaryDirectory

QTemporaryDir *	mpa_temporaryDirectory = nullptr

std::vector< pappso::pappso_double >	m_retentionTimeList

pappso::pappso_double	m_maxMz = 0

pappso::pappso_double	m_minMz = 5000

std::size_t	m_rtSize = 0

std::deque< MsRunSliceSPtr >	m_msRunSliceListCache

QMutex	m_mutex

Protected Attributes inherited from pappso::MsRunXicExtractor
std::vector< MsRunXicExtractorPoints >	m_msrun_points

Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr	msp_msrun_reader

Enums::XicExtractMethod	m_xicExtractMethod = Enums::XicExtractMethod::max

double	m_retentionTimeAroundTarget = std::numeric_limits<double>::max()

pappso::FilterInterfaceCstSPtr	mcsp_postExtractionTraceFilter = nullptr

Private Attributes
friend	MsRunXicExtractorFactory

Detailed Description

Definition at line 43 of file msrunxicextractordiskbuffer.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorDiskBuffer() [1/2]

pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer ( const MsRunXicExtractorDiskBuffer & other )

Definition at line 48 of file msrunxicextractordiskbuffer.cpp.

  : MsRunXicExtractorDisk(other)
{
 
  m_sliceBufferMap.clear();
}

References pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), MsRunXicExtractorDiskBuffer(), and m_sliceBufferMap.

Referenced by MsRunXicExtractorDiskBuffer().

◆ ~MsRunXicExtractorDiskBuffer()

pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer ( )

virtual

Definition at line 56 of file msrunxicextractordiskbuffer.cpp.

57{

58}

◆ MsRunXicExtractorDiskBuffer() [2/2]

pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer	(	MsRunReaderSPtr &	msrun_reader,
		const QDir &	temporary_dir )

protected

Definition at line 40 of file msrunxicextractordiskbuffer.cpp.

  : MsRunXicExtractorDisk(msrun_reader, temporary_dir)
{
 
  m_sliceBufferMap.clear();
}

References pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), and m_sliceBufferMap.

Member Function Documentation

◆ appendSliceInBuffer()

void pappso::MsRunXicExtractorDiskBuffer::appendSliceInBuffer	(	unsigned int	slice_number,
		MassSpectrum &	spectrum,
		std::size_t	ipos )

protected

Definition at line 78 of file msrunxicextractordiskbuffer.cpp.

{
  //qDebug();
 
  std::size_t spectrum_size = spectrum.size();
 
  if(spectrum_size == 0)
    return;
  try
    {
      std::pair<std::map<unsigned int, QByteArray>::iterator, bool> ret =
        m_sliceBufferMap.insert(
          std::pair<unsigned int, QByteArray>(slice_number, QByteArray()));
 
 
      if(ret.second)
        { // new buffer
          ret.first->second.resize(0);
          QDataStream outstream(&ret.first->second, QIODevice::WriteOnly);
          outstream << (quint32)ipos;
          outstream << spectrum;
        }
      else
        {
          QDataStream outstream(&ret.first->second,
                                QIODevice::WriteOnly | QIODevice::Append);
          outstream << (quint32)ipos;
          outstream << spectrum;
        }
    }
  catch(PappsoException &error_pappso)
    {
      throw pappso::PappsoException(
        QObject::tr("appendSliceInBuffer : error ipos=%1 :\n%2")
          .arg(ipos)
          .arg(error_pappso.qwhat()));
    }
  catch(std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("appendSliceInBuffer slice_number=%1 ipos=%2 error :\n%3")
          .arg(slice_number)
          .arg(ipos)
          .arg(error.what()));
    }
  //qDebug();
}

References m_sliceBufferMap, and pappso::PappsoException::qwhat().

Referenced by storeSlices().

◆ endPwizRead()

void pappso::MsRunXicExtractorDiskBuffer::endPwizRead ( )

overrideprotectedvirtual

Reimplemented from pappso::MsRunXicExtractorDisk.

Definition at line 206 of file msrunxicextractordiskbuffer.cpp.

{
  flushBufferOnDisk();
 
  m_sliceBufferMap.clear();
 
  msp_msrun_reader.get()->releaseDevice();
}

References flushBufferOnDisk(), m_sliceBufferMap, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.

◆ flushBufferOnDisk()

void pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk ( )

protected

Definition at line 130 of file msrunxicextractordiskbuffer.cpp.

{
  qDebug();
 
  try
    {
      for(auto &buffer_pair : m_sliceBufferMap)
        {
 
          if(buffer_pair.second.size() > 0)
            {
              QFile slice_file(QString("%1/%2")
                                 .arg(mpa_temporaryDirectory->path())
                                 .arg(buffer_pair.first));
              bool new_file = false;
              if(!slice_file.exists())
                {
                  new_file = true;
 
                  if(!slice_file.open(QIODevice::WriteOnly))
                    {
                      throw pappso::PappsoException(
                        QObject::tr("unable to open file %1")
                          .arg(slice_file.fileName()));
                    }
                }
              else
                {
                  if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append))
                    {
                      throw pappso::PappsoException(
                        QObject::tr("unable to open file %1")
                          .arg(slice_file.fileName()));
                    }
                }
 
              QDataStream stream(&slice_file);
 
              if(new_file)
                {
                  stream << (quint32)buffer_pair.first;
                  stream << (quint32)m_rtSize;
                  stream.writeRawData(buffer_pair.second.constData(),
                                      buffer_pair.second.size());
                }
              else
                {
                  stream.writeRawData(buffer_pair.second.constData(),
                                      buffer_pair.second.size());
                }
 
 
              slice_file.flush();
              slice_file.close();
            }
          // buffer_pair.second = std::vector<MassSpectrum>();
        }
 
      m_bufferSize = 0;
      m_sliceBufferMap.clear();
    }
  catch(PappsoException &error_pappso)
    {
      throw pappso::PappsoException(
        QObject::tr("flushBufferOnDisk error :\n%1").arg(error_pappso.qwhat()));
    }
  catch(std::exception &error)
    {
      throw pappso::PappsoException(
        QObject::tr("flushBufferOnDisk error :\n%1").arg(error.what()));
    }
  qDebug();
}

References m_bufferSize, pappso::MsRunXicExtractorDisk::m_rtSize, m_sliceBufferMap, pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory, and pappso::PappsoException::qwhat().

Referenced by endPwizRead(), and storeSlices().

◆ storeSlices()

void pappso::MsRunXicExtractorDiskBuffer::storeSlices	(	std::map< unsigned int, MassSpectrum > &	slice_vector,
		std::size_t	ipos )

overrideprotectedvirtual

store MassSpectrum slices (by daltons) for a given retention time

Parameters

slice_vector	mass spectrum chunks (by daltons)
ipos	the position in the retention time vector

Reimplemented from pappso::MsRunXicExtractorDisk.

Definition at line 61 of file msrunxicextractordiskbuffer.cpp.

{
 
  m_bufferSize++;
  for(auto &&msrun_slice : slice_vector)
    {
      appendSliceInBuffer(msrun_slice.first, msrun_slice.second, ipos);
    }
 
  if(m_bufferSize == m_bufferMaxSize)
    {
      flushBufferOnDisk();
    }
}