#include <msrunxicextractordisk.h>

Inheritance diagram for pappso::MsRunXicExtractorDisk:

Public Member Functions
	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
	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 ()

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

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)

virtual void	endPwizRead ()

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
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 Member Functions
void	extractOneXicCoord (XicCoord &xic_coord)

Private Attributes
friend	MsRunXicExtractorFactory

Detailed Description

Definition at line 44 of file msrunxicextractordisk.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorDisk() [1/3]

pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk ( MsRunReaderSPtr & msrun_reader )

References MsRunXicExtractorDisk().

Referenced by MsRunXicExtractorDisk(), MsRunXicExtractorDisk(), pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer(), and pappso::MsRunXicExtractorDiskBuffer::MsRunXicExtractorDiskBuffer().

◆ MsRunXicExtractorDisk() [2/3]

pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk ( const MsRunXicExtractorDisk & other )

Definition at line 47 of file msrunxicextractordisk.cpp.

  : pappso::MsRunXicExtractor(other)
{
 
  m_temporaryDirectory   = other.m_temporaryDirectory;
  mpa_temporaryDirectory = new QTemporaryDir(
    QString("%1/msrun_%2_")
      .arg(m_temporaryDirectory)
      .arg(msp_msrun_reader.get()->getMsRunId().get()->getXmlId()));
}

References pappso::MsRunXicExtractor::MsRunXicExtractor(), MsRunXicExtractorDisk(), m_temporaryDirectory, mpa_temporaryDirectory, and pappso::MsRunXicExtractorInterface::msp_msrun_reader.

◆ ~MsRunXicExtractorDisk()

pappso::MsRunXicExtractorDisk::~MsRunXicExtractorDisk ( )

virtual

Definition at line 58 of file msrunxicextractordisk.cpp.

{
  if(mpa_temporaryDirectory != nullptr)
    {
      delete mpa_temporaryDirectory;
    }
}

References mpa_temporaryDirectory.

◆ MsRunXicExtractorDisk() [3/3]

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

protected

Definition at line 39 of file msrunxicextractordisk.cpp.

  : pappso::MsRunXicExtractor(msrun_reader)
{
  mpa_temporaryDirectory = nullptr;
  m_temporaryDirectory   = temporary_dir.absolutePath();
}

References pappso::MsRunXicExtractor::MsRunXicExtractor(), m_temporaryDirectory, and mpa_temporaryDirectory.

Member Function Documentation

◆ acquireSlices()

std::vector< MsRunSliceSPtr > pappso::MsRunXicExtractorDisk::acquireSlices ( const MzRange & mz_range )

protected

retrieve all the slices corresponding to a given mz_range

Parameters

mz_range desired mz range

Definition at line 327 of file msrunxicextractordisk.cpp.

{
  QMutexLocker lock(&m_mutex);
  std::vector<MsRunSliceSPtr> slice_list;
  for(unsigned int i = mz_range.lower(); i <= mz_range.upper(); i++)
    {
      auto it = std::find_if(m_msRunSliceListCache.begin(),
                             m_msRunSliceListCache.end(),
                             [i](const MsRunSliceSPtr &slice_sp) {
                               return slice_sp.get()->getSliceNumber() == i;
                             });
      if(it != m_msRunSliceListCache.end())
        {
          slice_list.push_back(*it);
          m_msRunSliceListCache.push_back(*it);
        }
      else
        {
          MsRunSliceSPtr slice_sp = unserializeSlice(i);
          slice_list.push_back(slice_sp);
          m_msRunSliceListCache.push_back(slice_sp);
        }
    }
 
  if(m_msRunSliceListCache.size() > 20)
    {
      m_msRunSliceListCache.pop_front();
    }
  return slice_list;
}

References pappso::MzRange::lower(), m_msRunSliceListCache, m_mutex, unserializeSlice(), and pappso::MzRange::upper().

Referenced by extractOneXicCoord().

◆ appendSliceOnDisk()

void pappso::MsRunXicExtractorDisk::appendSliceOnDisk	(	unsigned int	slice_number,
		MassSpectrum &	spectrum,
		std::size_t	ipos )

protected

append a slice on disk (in a file)

Parameters

slice_number	the slice number == dalton integer
spectrum	the part of the mass spectrum (mz/intensity) in the range of the slice number
ipos	the position in the retention time vector

Definition at line 252 of file msrunxicextractordisk.cpp.

{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
  QFile slice_file(
    QString("%1/%2").arg(mpa_temporaryDirectory->path()).arg(slice_number));
  bool new_file = false;
  if(!slice_file.exists())
    {
      new_file = true;
    }
  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)slice_number;
      stream << (quint32)m_rtSize;
    }
 
  stream << (quint32)ipos;
  stream << spectrum;
 
  slice_file.flush();
  slice_file.close();
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References m_rtSize, and mpa_temporaryDirectory.

Referenced by storeSlices().

◆ endPwizRead()

void pappso::MsRunXicExtractorDisk::endPwizRead ( )

protectedvirtual

Reimplemented in pappso::MsRunXicExtractorDiskBuffer.

Definition at line 360 of file msrunxicextractordisk.cpp.

{
  msp_msrun_reader.get()->releaseDevice();
}

References pappso::MsRunXicExtractorInterface::msp_msrun_reader.

Referenced by serializeMsRun().

◆ extractOneXicCoord()

void pappso::MsRunXicExtractorDisk::extractOneXicCoord ( XicCoord & xic_coord )

private

Definition at line 115 of file msrunxicextractordisk.cpp.

{
  std::shared_ptr<Xic> msrunxic_sp = xic_coord.xicSptr;
 
  double rt_begin = xic_coord.rtTarget - m_retentionTimeAroundTarget;
  double rt_end   = xic_coord.rtTarget + m_retentionTimeAroundTarget;
 
 
  std::vector<MsRunSliceSPtr> slice_list;
  slice_list = acquireSlices(xic_coord.mzRange);
 
  if(slice_list.size() == 0)
    {
      throw pappso::PappsoException(
        QObject::tr("Error getMsRunXicSp slice_list.size() == 0"));
    }
 
  for(std::size_t i = 0; i < m_retentionTimeList.size(); i++)
    {
 
      DataPoint xic_element;
      xic_element.x = m_retentionTimeList[i];
      xic_element.y = 0;
      if((xic_element.x < rt_begin) || (xic_element.x > rt_end))
        continue;
 
      for(auto &&msrun_slice : slice_list)
        {
          const MassSpectrum &spectrum = msrun_slice.get()->getSpectrum(i);
          for(auto &&peak : spectrum)
            {
              if(xic_coord.mzRange.contains(peak.x))
                {
                  if(m_xicExtractMethod == Enums::XicExtractMethod::sum)
                    {
                      xic_element.y += peak.y;
                    }
                  else
                    {
                      if(xic_element.y < peak.y)
                        {
                          xic_element.y = peak.y;
                        }
                    }
                }
            }
        }
      msrunxic_sp.get()->push_back(xic_element);
    }
}

References acquireSlices(), pappso::MzRange::contains(), pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, m_retentionTimeList, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::XicCoord::mzRange, pappso::XicCoord::rtTarget, pappso::Enums::sum, pappso::DataPoint::x, pappso::XicCoord::xicSptr, and pappso::DataPoint::y.

Referenced by protectedExtractXicCoordSPtrList().

◆ prepareExtractor()

void pappso::MsRunXicExtractorDisk::prepareExtractor ( )

protected

Definition at line 67 of file msrunxicextractordisk.cpp.

{
  qDebug();
  try
    {
      serializeMsRun();
      // msp_msrun_reader = nullptr;
    }
  catch(pappso::PappsoException &errora)
    {
      qDebug();
      throw pappso::PappsoException(
        QObject::tr("Error reading file (%1) : %2")
          .arg(msp_msrun_reader.get()->getMsRunId().get()->toString())
          .arg(errora.qwhat()));
    }
  catch(std::exception &error)
    {
      qDebug();
      throw pappso::PappsoException(
        QObject::tr("Error reading file (%1) using : %2")
          .arg(msp_msrun_reader.get()->getMsRunId().get()->toString())
          .arg(error.what()));
    }
}

References pappso::MsRunXicExtractorInterface::msp_msrun_reader, pappso::PappsoException::qwhat(), and serializeMsRun().

◆ protectedExtractXicCoordSPtrList()

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

overrideprotectedvirtual

Reimplemented from pappso::MsRunXicExtractor.

Definition at line 95 of file msrunxicextractordisk.cpp.

{
  // sort xic by mz:
  std::sort(it_xic_coord_list_begin,
            it_xic_coord_list_end,
            [](XicCoordSPtr &a, XicCoordSPtr &b) {
              return a.get()->mzRange.getMz() < b.get()->mzRange.getMz();
            });
 
  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
    {
      extractOneXicCoord(*(it->get()));
      monitor.count();
    }
}

References pappso::a, pappso::b, pappso::UiMonitorInterface::count(), and extractOneXicCoord().

◆ serializeMsRun()

void pappso::MsRunXicExtractorDisk::serializeMsRun ( )

protected

Definition at line 167 of file msrunxicextractordisk.cpp.

{
  qDebug();
  m_minMz = 5000;
  m_maxMz = 0;
 
  unsigned int slice_number;
  std::map<unsigned int, MassSpectrum> spectrum_map;
 
  /*
    const pwiz::msdata::SpectrumList *p_spectrum_list =
      p_msdatafile->run.spectrumListPtr.get();
 
    std::size_t spectrum_list_size = p_spectrum_list->size();
    pwiz::msdata::SpectrumPtr pwiz_spectrum;
    */
 
  m_rtSize = m_msrun_points.size();
 
 
  MassSpectrumCstSPtr spectrum;
  for(auto &&msrun_point : m_msrun_points)
    {
 
      spectrum_map.clear();
 
      m_retentionTimeList.push_back(msrun_point.rt);
 
      spectrum =
        msp_msrun_reader.get()->massSpectrumCstSPtr(msrun_point.spectrum_index);
 
      const MassSpectrum *p_spectrum = spectrum.get();
      if(p_spectrum->size() > 0)
        {
          if(p_spectrum->begin()->x < m_minMz)
            {
              m_minMz = p_spectrum->begin()->x;
            }
          // iterate through the m/z-intensity pairs
 
          if(p_spectrum->back().x > m_maxMz)
            {
              m_maxMz = p_spectrum->back().x;
            }
 
          for(auto &peak : *p_spectrum)
            {
 
              slice_number = peak.x;
 
              std::pair<std::map<unsigned int, MassSpectrum>::iterator, bool>
                ret = spectrum_map.insert(std::pair<unsigned int, MassSpectrum>(
                  slice_number, MassSpectrum()));
 
              ret.first->second.push_back(peak);
              // auto ret = spectrum_map.insert(std::pair<unsigned int,
              // MassSpectrum>(slice_number,MassSpectrum()));
              // ret.first->second.push_back(peak);
            }
 
          // slices are ready for this retention time
          storeSlices(spectrum_map, m_retentionTimeList.size() - 1);
        }
    }
 
  endPwizRead();
  qDebug();
}

References endPwizRead(), m_maxMz, m_minMz, pappso::MsRunXicExtractor::m_msrun_points, m_retentionTimeList, m_rtSize, pappso::MsRunXicExtractorInterface::msp_msrun_reader, and storeSlices().

Referenced by prepareExtractor().

◆ storeSlices()

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

protectedvirtual

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 in pappso::MsRunXicExtractorDiskBuffer.

Definition at line 238 of file msrunxicextractordisk.cpp.

{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
 
  for(auto &&spectrum_pair : spectrum_map)
    {
      appendSliceOnDisk(spectrum_pair.first, spectrum_pair.second, ipos);
    }
 
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
}

References appendSliceOnDisk().

Referenced by serializeMsRun().

◆ unserializeSlice()

MsRunSliceSPtr pappso::MsRunXicExtractorDisk::unserializeSlice ( unsigned int slice_number )

protected

get one slice from disk by her slice number (dalton)

Parameters

slice_number the slice number == dalton integer

Definition at line 286 of file msrunxicextractordisk.cpp.

{
  qDebug();
  try
    {
      std::shared_ptr<MsRunSlice> msrun_slice_sp =
        std::make_shared<MsRunSlice>(MsRunSlice());
 
      QFile slice_file(
        QString("%1/%2").arg(mpa_temporaryDirectory->path()).arg(slice_number));
      if(!slice_file.exists())
        {
          msrun_slice_sp.get()->setSize(m_rtSize);
          msrun_slice_sp.get()->setSliceNumber(slice_number);
          return msrun_slice_sp;
        }
      if(!slice_file.open(QIODevice::ReadOnly))
        {
          throw pappso::PappsoException(
            QObject::tr("unable to open file %1 in readonly")
              .arg(slice_file.fileName()));
        }
      QDataStream stream(&slice_file);
 
      stream >> *(msrun_slice_sp.get());
 
      slice_file.close();
 
      return msrun_slice_sp;
    }
  catch(pappso::PappsoException &error)
    {
      throw pappso::PappsoException(
        QObject::tr("error unserializing slice %1:\n%2")
          .arg(slice_number)
          .arg(error.qwhat()));
    }
  qDebug();
}

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

Referenced by acquireSlices().

Member Data Documentation

◆ m_maxMz

pappso::pappso_double pappso::MsRunXicExtractorDisk::m_maxMz = 0

protected

Definition at line 103 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_minMz

pappso::pappso_double pappso::MsRunXicExtractorDisk::m_minMz = 5000

protected

Definition at line 104 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_msRunSliceListCache

std::deque<MsRunSliceSPtr> pappso::MsRunXicExtractorDisk::m_msRunSliceListCache

protected

Definition at line 108 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_mutex

QMutex pappso::MsRunXicExtractorDisk::m_mutex

protected

Definition at line 110 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_retentionTimeList

std::vector<pappso::pappso_double> pappso::MsRunXicExtractorDisk::m_retentionTimeList

protected

Definition at line 101 of file msrunxicextractordisk.h.

Referenced by extractOneXicCoord(), and serializeMsRun().

◆ m_rtSize

std::size_t pappso::MsRunXicExtractorDisk::m_rtSize = 0

protected

Definition at line 106 of file msrunxicextractordisk.h.

Referenced by appendSliceOnDisk(), pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk(), serializeMsRun(), and unserializeSlice().

◆ m_temporaryDirectory

QString pappso::MsRunXicExtractorDisk::m_temporaryDirectory

protected

Definition at line 99 of file msrunxicextractordisk.h.

Referenced by MsRunXicExtractorDisk(), and MsRunXicExtractorDisk().

◆ mpa_temporaryDirectory

QTemporaryDir* pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory = nullptr

protected

Definition at line 100 of file msrunxicextractordisk.h.

Referenced by MsRunXicExtractorDisk(), MsRunXicExtractorDisk(), ~MsRunXicExtractorDisk(), appendSliceOnDisk(), pappso::MsRunXicExtractorDiskBuffer::flushBufferOnDisk(), and unserializeSlice().

◆ MsRunXicExtractorFactory

friend pappso::MsRunXicExtractorDisk::MsRunXicExtractorFactory

private

Definition at line 46 of file msrunxicextractordisk.h.

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

pappsomspp/core/xicextractor/private/msrunxicextractordisk.h
pappsomspp/core/xicextractor/private/msrunxicextractordisk.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsRunXicExtractorDisk() [1/3]

◆ MsRunXicExtractorDisk() [2/3]

◆ ~MsRunXicExtractorDisk()

◆ MsRunXicExtractorDisk() [3/3]

Member Function Documentation

◆ acquireSlices()

◆ appendSliceOnDisk()

◆ endPwizRead()

◆ extractOneXicCoord()

◆ prepareExtractor()

◆ protectedExtractXicCoordSPtrList()

◆ serializeMsRun()

◆ storeSlices()

◆ unserializeSlice()

Member Data Documentation

◆ m_maxMz

◆ m_minMz

◆ m_msRunSliceListCache

◆ m_mutex

◆ m_retentionTimeList

◆ m_rtSize

◆ m_temporaryDirectory

◆ mpa_temporaryDirectory

◆ MsRunXicExtractorFactory