#include <msrunxicextractorinterface.h>

Inheritance diagram for pappso::MsRunXicExtractorInterface:

Public Member Functions
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
	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
virtual void	protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end)=0

Protected Attributes
MsRunReaderSPtr	msp_msrun_reader
Enums::XicExtractMethod	m_xicExtractMethod = Enums::XicExtractMethod::max
double	m_retentionTimeAroundTarget = std::numeric_limits<double>::max()
pappso::FilterInterfaceCstSPtr	mcsp_postExtractionTraceFilter = nullptr

Detailed Description

Definition at line 44 of file msrunxicextractorinterface.h.

Constructor & Destructor Documentation

◆ MsRunXicExtractorInterface() [1/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( MsRunReaderSPtr & msrun_reader )

protected

constructor is private, use the MsRunXicExtractorFactory

Definition at line 40 of file msrunxicextractorinterface.cpp.

  : msp_msrun_reader(msrun_reader)
{
}

References msp_msrun_reader.

Referenced by pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunXicExtractor::MsRunXicExtractor(), MsRunXicExtractorInterface(), and pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

◆ MsRunXicExtractorInterface() [2/2]

pappso::MsRunXicExtractorInterface::MsRunXicExtractorInterface ( const MsRunXicExtractorInterface & other )

protected

Definition at line 46 of file msrunxicextractorinterface.cpp.

  : msp_msrun_reader(other.msp_msrun_reader)
{
  m_xicExtractMethod = other.m_xicExtractMethod;
}

References MsRunXicExtractorInterface(), m_xicExtractMethod, and msp_msrun_reader.

◆ ~MsRunXicExtractorInterface()

pappso::MsRunXicExtractorInterface::~MsRunXicExtractorInterface ( )

protectedvirtual

Definition at line 52 of file msrunxicextractorinterface.cpp.

53{

54}

Member Function Documentation

◆ extractXicCoordSPtrList()

void pappso::MsRunXicExtractorInterface::extractXicCoordSPtrList	(	UiMonitorInterface &	monitor,
		std::vector< XicCoordSPtr > &	xic_coord_list )

finalvirtual

extract a list of XIC given a list of xic coordinates to extract

XicCoord is a vessel containing the xic to fill and coordinates of this XIC in the MS run

Parameters

monitor	process monitoring
xic_coord_list	list of xic coordinates to extract. The order of xic coordinates may change.

Definition at line 172 of file msrunxicextractorinterface.cpp.

{
  qDebug() << xic_coord_list.size();
  monitor.setStatus(QObject::tr("extracting %1 XICs").arg(xic_coord_list.size()));
  monitor.setTotalSteps(xic_coord_list.size());
  protectedExtractXicCoordSPtrList(monitor, xic_coord_list.begin(), xic_coord_list.end());
  monitor.setTotalSteps(0);
  postExtractionProcess(monitor, xic_coord_list.begin(), xic_coord_list.end());
}

References postExtractionProcess(), protectedExtractXicCoordSPtrList(), pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().

Referenced by extractXicCoordSPtrListParallelized().

◆ extractXicCoordSPtrListParallelized()

void pappso::MsRunXicExtractorInterface::extractXicCoordSPtrListParallelized	(	UiMonitorInterface &	monitor,
		std::vector< XicCoordSPtr > &	xic_coord_list )

finalvirtual

multithreaded XIC extraction

divide xic_coord_list and run extractXicCoordSPtrList separated threads

Parameters

monitor	process monitoring
xic_coord_list	list of xic coordinates to extract. The order of xic coordinates may change.

Definition at line 89 of file msrunxicextractorinterface.cpp.

{
  qDebug();
  // get the number of available threads :
  int number_of_threads = QThreadPool::globalInstance()->maxThreadCount();
 
  if(number_of_threads == 1)
    {
      extractXicCoordSPtrList(monitor, xic_coord_list);
    }
  else
    {
      monitor.setStatus(
        QObject::tr("parallelized extraction of %1 XICs").arg(xic_coord_list.size()));
 
      std::size_t chunck_size = xic_coord_list.size() / number_of_threads;
      chunck_size += 1;
      if(chunck_size < 1000)
        chunck_size = 1000;
 
      struct parallelExtractChunck
      {
        std::vector<XicCoordSPtr>::iterator it_xic_coord_begin;
        std::vector<XicCoordSPtr>::iterator it_xic_coord_end;
      };
 
      std::vector<parallelExtractChunck> chunck_list;
      qDebug();
      for(auto it = xic_coord_list.begin(); it != xic_coord_list.end();)
        {
          qDebug() << "chunck_size=" << chunck_size;
          parallelExtractChunck chunck;
          chunck.it_xic_coord_begin = it;
          for(std::size_t i = 0; i < chunck_size && it != xic_coord_list.end(); i++)
            {
              it++;
            }
          chunck.it_xic_coord_end = it;
          chunck_list.push_back(chunck);
        }
      qDebug();
      auto self = this;
 
      qDebug();
      std::function<std::size_t(const parallelExtractChunck &)> extractChunck =
        [self](const parallelExtractChunck &extract_chunck) {
          qDebug();
          UiMonitorVoid monitor;
          self->protectedExtractXicCoordSPtrList(
            monitor, extract_chunck.it_xic_coord_begin, extract_chunck.it_xic_coord_end);
          self->postExtractionProcess(
            monitor, extract_chunck.it_xic_coord_begin, extract_chunck.it_xic_coord_end);
          qDebug();
          return 1;
        };
      qDebug();
      monitor.setTotalSteps(chunck_list.size());
      UiMonitorInterface *monitorRef = &monitor;
      std::function<void(std::size_t &result, const std::size_t &value)> monitorExtract2 =
        [monitorRef](std::size_t &result [[maybe_unused]],
                     const std::size_t &value [[maybe_unused]]) { monitorRef->count(); };
      qDebug();
 
      QFuture<std::size_t> res =
        QtConcurrent::mappedReduced<std::size_t>(chunck_list.begin(),
                                                 chunck_list.end(),
                                                 extractChunck,
                                                 monitorExtract2,
                                                 QtConcurrent::UnorderedReduce);
      qDebug();
 
      /*
        QFuture<std::size_t> res =
          QtConcurrent::mapped(chunck_list.begin(), chunck_list.end(),
        extractChunck);
      */
      res.waitForFinished();
      monitor.setTotalSteps(0);
    }
}

References pappso::UiMonitorInterface::count(), extractXicCoordSPtrList(), pappso::UiMonitorInterface::setStatus(), and pappso::UiMonitorInterface::setTotalSteps().

◆ getMsRunId()

const MsRunIdCstSPtr & pappso::MsRunXicExtractorInterface::getMsRunId ( ) const

Definition at line 69 of file msrunxicextractorinterface.cpp.

{
  return msp_msrun_reader.get()->getMsRunId();
}

References msp_msrun_reader.

◆ getMsRunReaderSPtr()

const MsRunReaderSPtr & pappso::MsRunXicExtractorInterface::getMsRunReaderSPtr ( ) const

get the msrunreader currently used for XIC extraction

Definition at line 75 of file msrunxicextractorinterface.cpp.

{
  return msp_msrun_reader;
}

References msp_msrun_reader.

◆ postExtractionProcess()

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

protectedvirtual

possible post extraction process, eventually trace filters

Definition at line 184 of file msrunxicextractorinterface.cpp.

{
 
  if(mcsp_postExtractionTraceFilter != nullptr)
    {
      monitor.setStatus(QObject::tr("filtering %1 XICs")
                          .arg(std::distance(it_xic_coord_list_begin, it_xic_coord_list_end)));
      for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
        {
          mcsp_postExtractionTraceFilter.get()->filter(*(it->get()->xicSptr.get()));
        }
    }
}

References mcsp_postExtractionTraceFilter, and pappso::UiMonitorInterface::setStatus().

Referenced by extractXicCoordSPtrList().

◆ protectedExtractXicCoordSPtrList()

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

protectedpure virtual

Implemented in pappso::MsRunXicExtractor, pappso::MsRunXicExtractorDisk, and pappso::TimsDirectXicExtractor.

Referenced by extractXicCoordSPtrList().

◆ setPostExtractionTraceFilterCstSPtr()

void pappso::MsRunXicExtractorInterface::setPostExtractionTraceFilterCstSPtr ( pappso::FilterInterfaceCstSPtr & filter )

filter interface to apply just after XIC extration on each trace

Definition at line 81 of file msrunxicextractorinterface.cpp.

{
  mcsp_postExtractionTraceFilter = filter;
}

References pappso::filter, and mcsp_postExtractionTraceFilter.

◆ setRetentionTimeAroundTarget()

void pappso::MsRunXicExtractorInterface::setRetentionTimeAroundTarget ( double range_in_seconds )

set the retention time range in seconds around the target rt

only the interesting part of the xic will be extracted, form the rt target

range_in_seconds to rt target + range in seconds by default, all the LC run time is extracted

Parameters

range_in_seconds range in seconds

Definition at line 63 of file msrunxicextractorinterface.cpp.

{
  m_retentionTimeAroundTarget = range_in_seconds;
}

References m_retentionTimeAroundTarget.

◆ setXicExtractMethod()

void pappso::MsRunXicExtractorInterface::setXicExtractMethod ( Enums::XicExtractMethod method )

set the XIC extraction method

Definition at line 57 of file msrunxicextractorinterface.cpp.

{
  m_xicExtractMethod = method;
}

References m_xicExtractMethod.

Member Data Documentation

◆ m_retentionTimeAroundTarget

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

protected

Definition at line 120 of file msrunxicextractorinterface.h.

Referenced by pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList(), and setRetentionTimeAroundTarget().

◆ m_xicExtractMethod

Enums::XicExtractMethod pappso::MsRunXicExtractorInterface::m_xicExtractMethod = Enums::XicExtractMethod::max

protected

Definition at line 119 of file msrunxicextractorinterface.h.

Referenced by MsRunXicExtractorInterface(), pappso::MsRunXicExtractor::extractOneXicCoord(), pappso::MsRunXicExtractorDisk::extractOneXicCoord(), pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList(), and setXicExtractMethod().

◆ mcsp_postExtractionTraceFilter

pappso::FilterInterfaceCstSPtr pappso::MsRunXicExtractorInterface::mcsp_postExtractionTraceFilter = nullptr

protected

Definition at line 121 of file msrunxicextractorinterface.h.

Referenced by postExtractionProcess(), and setPostExtractionTraceFilterCstSPtr().

◆ msp_msrun_reader

MsRunReaderSPtr pappso::MsRunXicExtractorInterface::msp_msrun_reader

protected

Definition at line 118 of file msrunxicextractorinterface.h.

Referenced by pappso::MsRunXicExtractor::MsRunXicExtractor(), pappso::MsRunXicExtractorDisk::MsRunXicExtractorDisk(), MsRunXicExtractorInterface(), MsRunXicExtractorInterface(), pappso::MsRunXicExtractorDisk::endPwizRead(), pappso::MsRunXicExtractorDiskBuffer::endPwizRead(), pappso::MsRunXicExtractor::extractOneXicCoord(), getMsRunId(), getMsRunReaderSPtr(), pappso::MsRunXicExtractorDisk::prepareExtractor(), and pappso::MsRunXicExtractorDisk::serializeMsRun().

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

pappsomspp/core/xicextractor/msrunxicextractorinterface.h
pappsomspp/core/xicextractor/msrunxicextractorinterface.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MsRunXicExtractorInterface() [1/2]

◆ MsRunXicExtractorInterface() [2/2]

◆ ~MsRunXicExtractorInterface()

Member Function Documentation

◆ extractXicCoordSPtrList()

◆ extractXicCoordSPtrListParallelized()

◆ getMsRunId()

◆ getMsRunReaderSPtr()

◆ postExtractionProcess()

◆ protectedExtractXicCoordSPtrList()

◆ setPostExtractionTraceFilterCstSPtr()

◆ setRetentionTimeAroundTarget()

◆ setXicExtractMethod()

Member Data Documentation

◆ m_retentionTimeAroundTarget

◆ m_xicExtractMethod

◆ mcsp_postExtractionTraceFilter

◆ msp_msrun_reader