#include <msrunxicextractordisk.h>

Inheritance diagram for pappso::MsRunXicExtractorDisk:

Public Member Functions
	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
	MsRunXicExtractorDisk (MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)

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 More...

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...

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 More...

	MsRunXicExtractorInterface (const MsRunXicExtractorInterface &other)

virtual	~MsRunXicExtractorInterface ()

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

XicExtractMethod	m_xicExtractMethod = XicExtractMethod::max

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 )

◆ 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 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 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 319 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 getXicCstSPtr().

◆ 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 244 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 352 of file msrunxicextractordisk.cpp.

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

References pappso::MsRunXicExtractorInterface::msp_msrun_reader.

Referenced by serializeMsRun().

◆ getXicCstSPtr()

XicCstSPtr pappso::MsRunXicExtractorDisk::getXicCstSPtr	(	const MzRange &	mz_range,
		pappso::pappso_double	rt_begin,
		pappso::pappso_double	rt_end
	)

overridevirtual

get a XIC on this MsRun at the given mass range

Parameters

mz_range	mz range to extract
rt_begin	begining of the XIC in seconds
rt_end	end of the XIC in seconds

Reimplemented from pappso::MsRunXicExtractor.

Definition at line 94 of file msrunxicextractordisk.cpp.

 {
   std::shared_ptr<Xic> msrunxic_sp = std::make_shared<Xic>(Xic());
  
   std::vector<MsRunSliceSPtr> slice_list;
   slice_list = acquireSlices(mz_range);
  
   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(mz_range.contains(peak.x))
                 {
                   if(m_xicExtractMethod == 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);
     }
  
   return (msrunxic_sp);
 }

References acquireSlices(), pappso::MzRange::contains(), m_retentionTimeList, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by getXicCstSPtrList().

◆ getXicCstSPtrList()

std::vector< XicCstSPtr > pappso::MsRunXicExtractorDisk::getXicCstSPtrList ( const std::vector< MzRange > & mz_range_list )

overridevirtual

extract a list of XIC given a list of mass to extract

Reimplemented from pappso::MsRunXicExtractor.

Definition at line 146 of file msrunxicextractordisk.cpp.

 {
  
   std::vector<XicCstSPtr> xic_list_return;
   for(auto &range : mz_range_list)
     {
       xic_list_return.push_back(getXicCstSPtr(range, 0, 40000000));
     }
   return xic_list_return;
 }

References getXicCstSPtr().

◆ 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().

◆ serializeMsRun()

void pappso::MsRunXicExtractorDisk::serializeMsRun ( )

protected

Definition at line 159 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 230 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 278 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 102 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_minMz

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

protected

Definition at line 103 of file msrunxicextractordisk.h.

Referenced by serializeMsRun().

◆ m_msRunSliceListCache

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

protected

Definition at line 107 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_mutex

QMutex pappso::MsRunXicExtractorDisk::m_mutex

protected

Definition at line 109 of file msrunxicextractordisk.h.

Referenced by acquireSlices().

◆ m_retentionTimeList

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

protected

Definition at line 100 of file msrunxicextractordisk.h.

Referenced by getXicCstSPtr(), and serializeMsRun().

◆ m_rtSize

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

protected

Definition at line 105 of file msrunxicextractordisk.h.

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

◆ m_temporaryDirectory

QString pappso::MsRunXicExtractorDisk::m_temporaryDirectory

protected

Definition at line 98 of file msrunxicextractordisk.h.

Referenced by MsRunXicExtractorDisk().

◆ mpa_temporaryDirectory

QTemporaryDir* pappso::MsRunXicExtractorDisk::mpa_temporaryDirectory = nullptr

protected

Definition at line 99 of file msrunxicextractordisk.h.

Referenced by 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/xicextractor/private/msrunxicextractordisk.h
pappsomspp/xicextractor/private/msrunxicextractordisk.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsRunXicExtractorDisk() [1/3]

◆ MsRunXicExtractorDisk() [2/3]

◆ ~MsRunXicExtractorDisk()

◆ MsRunXicExtractorDisk() [3/3]

Member Function Documentation

◆ acquireSlices()

◆ appendSliceOnDisk()

◆ endPwizRead()

◆ getXicCstSPtr()

◆ getXicCstSPtrList()

◆ prepareExtractor()

◆ serializeMsRun()

◆ storeSlices()

◆ unserializeSlice()

Member Data Documentation

◆ m_maxMz

◆ m_minMz

◆ m_msRunSliceListCache

◆ m_mutex

◆ m_retentionTimeList

◆ m_rtSize

◆ m_temporaryDirectory

◆ mpa_temporaryDirectory

◆ MsRunXicExtractorFactory