pappso::MsRunXicExtractorDiskBuffer Class Reference

#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 ()
virtual XicCstSPtr	getXicCstSPtr (const MzRange &mz_range, pappso::pappso_double rt_begin, pappso::pappso_double rt_end) override
	get a XIC on this MsRun at the given mass range More...
virtual std::vector< XicCstSPtr >	getXicCstSPtrList (const std::vector< MzRange > &mz_range_list) override
	extract a list of XIC given a list of mass to extract More...
Public Member Functions inherited from pappso::MsRunXicExtractor
	MsRunXicExtractor (const MsRunXicExtractor &other)
virtual	~MsRunXicExtractor ()
Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (XicExtractMethod method)
	set the XIC extraction method More...
virtual XicCstSPtr	getXicCstSPtr (const MzRange &mz_range) final
	get a XIC on this MsRun at the given mass range More...
const MsRunIdCstSPtr &	getMsRunId () const

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 More...
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)
void	prepareExtractor ()
void	serializeMsRun ()
void	appendSliceOnDisk (unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
	append a slice on disk (in a file) More...
std::vector< MsRunSliceSPtr >	acquireSlices (const MzRange &mz_range)
	retrieve all the slices corresponding to a given mz_range More...
MsRunSliceSPtr	unserializeSlice (unsigned int slice_number)
	get one slice from disk by her slice number (dalton) More...
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 More...
	MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)
virtual	~MsRunXicExtractorInterface ()

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
XicExtractMethod	m_xicExtractMethod = XicExtractMethod::max

Private Attributes
friend	MsRunXicExtractorFactory

Detailed Description

Definition at line 42 of file msrunxicextractordiskbuffer.h.

Constructor & Destructor Documentation

MsRunXicExtractorDiskBuffer() [1/2]

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

protected

Definition at line 59 of file msrunxicextractordiskbuffer.cpp.

{
 
  m_bufferSize++;

References m_bufferSize.

MsRunXicExtractorDiskBuffer() [2/2]

pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer

(

const MsRunXicExtractorDiskBuffer &

other

)

Definition at line 67 of file msrunxicextractordiskbuffer.cpp.

    {
      appendSliceInBuffer(msrun_slice.first, msrun_slice.second, ipos);
    }
 
  if(m_bufferSize == m_bufferMaxSize)
    {
      flushBufferOnDisk();

References appendSliceInBuffer().

~MsRunXicExtractorDiskBuffer()

pappso::MsRunXicExtractorDiskBuffer::~MsRunXicExtractorDiskBuffer ( )

virtual

Definition at line 75 of file msrunxicextractordiskbuffer.cpp.

Member Function Documentation

appendSliceInBuffer()

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

protected

Definition at line 97 of file msrunxicextractordiskbuffer.cpp.

        { // 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() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
 
 
void
MsRunXicExtractorDiskBuffer::flushBufferOnDisk()
{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
  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())

Referenced by MsRunXicExtractorDiskBuffer().

endPwizRead()

void pappso::MsRunXicExtractorDiskBuffer::endPwizRead ( )

overrideprotectedvirtual

Reimplemented from pappso::MsRunXicExtractorDisk.

Definition at line 227 of file msrunxicextractordiskbuffer.cpp.

flushBufferOnDisk()

void pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk ( )

protected

Definition at line 151 of file msrunxicextractordiskbuffer.cpp.

                    {
                      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() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}
 
 
void
MsRunXicExtractorDiskBuffer::endPwizRead()
{
  flushBufferOnDisk();
 
  m_sliceBufferMap.clear();
}
} // namespace pappso

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 80 of file msrunxicextractordiskbuffer.cpp.

{
  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
  if(ipos < 0)
    return;
  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()));

References m_sliceBufferMap.

Member Data Documentation

m_bufferMaxSize

std::size_t pappso::MsRunXicExtractorDiskBuffer::m_bufferMaxSize = 150

protected

Definition at line 50 of file msrunxicextractordiskbuffer.h.

m_bufferSize

std::size_t pappso::MsRunXicExtractorDiskBuffer::m_bufferSize = 0

protected

Definition at line 49 of file msrunxicextractordiskbuffer.h.

Referenced by MsRunXicExtractorDiskBuffer().

m_sliceBufferMap

std::map<unsigned int, QByteArray> pappso::MsRunXicExtractorDiskBuffer::m_sliceBufferMap

protected

Definition at line 47 of file msrunxicextractordiskbuffer.h.

Referenced by storeSlices().

MsRunXicExtractorFactory

friend pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorFactory

private

Definition at line 44 of file msrunxicextractordiskbuffer.h.

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

• pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.h
• pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.cpp