pappso::TimsDirectXicExtractor Class Reference

#include <timsdirectxicextractor.h>

Inheritance diagram for pappso::TimsDirectXicExtractor:

Public Member Functions
	TimsDirectXicExtractor (MsRunReaderSPtr &msrun_reader)
virtual	~TimsDirectXicExtractor ()
Public Member Functions inherited from pappso::TimsXicExtractorInterface
	TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
virtual	~TimsXicExtractorInterface ()
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
void	protectedExtractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_begin, std::vector< XicCoordSPtr >::iterator it_xic_coord_list_end) override
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

Additional Inherited Members
Protected Attributes inherited from pappso::TimsXicExtractorInterface
TimsData *	mp_timsData
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

Detailed Description

Todo

write docs

Definition at line 36 of file timsdirectxicextractor.h.

Constructor & Destructor Documentation

TimsDirectXicExtractor()

TimsDirectXicExtractor::TimsDirectXicExtractor

(

MsRunReaderSPtr &

msrun_reader

)

Default constructor

Definition at line 35 of file timsdirectxicextractor.cpp.

  : pappso::TimsXicExtractorInterface(msrun_reader)
{
}

References pappso::TimsXicExtractorInterface::TimsXicExtractorInterface().

~TimsDirectXicExtractor()

TimsDirectXicExtractor::~TimsDirectXicExtractor ( )

virtual

Destructor

Definition at line 40 of file timsdirectxicextractor.cpp.

{
}

Member Function Documentation

protectedExtractXicCoordSPtrList()

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

overrideprotectedvirtual

Implements pappso::MsRunXicExtractorInterface.

Definition at line 46 of file timsdirectxicextractor.cpp.

{
  qDebug();
  std::size_t xic_total_number = std::distance(it_xic_coord_list_begin, it_xic_coord_list_end);
  if(xic_total_number == 0)
    return;
 
  std::vector<XicCoordTims *> xic_coord_tims_list;
  xic_coord_tims_list.reserve(xic_total_number);
 
  for(auto it = it_xic_coord_list_begin; it != it_xic_coord_list_end; it++)
    {
      XicCoordTims *p_xic_coord_tims = dynamic_cast<XicCoordTims *>(it->get());
      if(p_xic_coord_tims == nullptr)
        {
        }
      else
        {
          xic_coord_tims_list.push_back(p_xic_coord_tims);
        }
    }
 
  std::sort(
    xic_coord_tims_list.begin(),
    xic_coord_tims_list.end(),
    [](const XicCoordTims *pa, const XicCoordTims *pb) { return pa->rtTarget < pb->rtTarget; });
  std::vector<std::size_t> tims_frameid_list;
  try
    {
      tims_frameid_list = mp_timsData->getTimsMS1FrameIdsInRtRange(
        xic_coord_tims_list[0]->rtTarget - m_retentionTimeAroundTarget,
        xic_coord_tims_list.back()->rtTarget + m_retentionTimeAroundTarget);
    }
  catch(pappso::PappsoException &error)
    {
      throw pappso::PappsoException(QObject::tr("ERROR in %1 %2 %3:\n%4")
                                      .arg(__FUNCTION__)
                                      .arg(xic_coord_tims_list[0]->rtTarget)
                                      .arg(xic_coord_tims_list.back()->rtTarget)
                                      .arg(error.qwhat()));
    }
  monitor.setStatus(QObject::tr("extracting %1 XICs on %2 Tims frames")
                      .arg(xic_total_number)
                      .arg(tims_frameid_list.size()));
  monitor.setTotalSteps(tims_frameid_list.size());
 
  qDebug() << " tims_frameid_list.size()=" << tims_frameid_list.size();
  qDebug() << " rt begin=" << xic_coord_tims_list[0]->rtTarget;
  qDebug() << " rt end=" << xic_coord_tims_list.back()->rtTarget;
  for(std::size_t frame_id : tims_frameid_list)
    {
      std::vector<XicCoordTims *>::iterator itXicListbegin = xic_coord_tims_list.begin();
      std::vector<XicCoordTims *>::iterator itXicListend   = xic_coord_tims_list.end();
      qDebug();
      TimsFrameCstSPtr frame_sptr = mp_timsData->getTimsFrameCstSPtrCached(frame_id);
      qDebug();
      double rtframe = frame_sptr.get()->getRtInSeconds();
      qDebug();
 
      double rtbeginframe = rtframe - m_retentionTimeAroundTarget;
      double rtendframe   = rtframe + m_retentionTimeAroundTarget;
 
      if(rtbeginframe < 0)
        rtbeginframe = 0;
 
      qDebug() << rtbeginframe;
      while((itXicListbegin != itXicListend) && ((*itXicListbegin)->rtTarget < rtbeginframe))
        {
          itXicListbegin++;
        }
      qDebug();
      itXicListend = itXicListbegin;
      while((itXicListend != xic_coord_tims_list.end()) && ((*itXicListend)->rtTarget < rtendframe))
        {
          itXicListend++;
        }
      frame_sptr.get()->extractTimsXicListInRtRange(
        itXicListbegin, itXicListend, m_xicExtractMethod);
 
      qDebug() << "" << frame_sptr.get()->getId();
      monitor.count();
      if(monitor.shouldIstop())
        {
          throw pappso::ExceptionInterrupted(QObject::tr("Xic extraction process interrupted"));
        }
    }
  qDebug();
}

References pappso::UiMonitorInterface::count(), pappso::TimsFrame::extractTimsXicListInRtRange(), pappso::TimsFrameBase::getId(), pappso::TimsFrameBase::getRtInSeconds(), pappso::MsRunXicExtractorInterface::m_retentionTimeAroundTarget, pappso::MsRunXicExtractorInterface::m_xicExtractMethod, pappso::TimsXicExtractorInterface::mp_timsData, pappso::PappsoException::qwhat(), pappso::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::setTotalSteps(), and pappso::UiMonitorInterface::shouldIstop().

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

• pappsomspp/core/vendors/tims/xicextractor/timsdirectxicextractor.h
• pappsomspp/core/vendors/tims/xicextractor/timsdirectxicextractor.cpp