pappso::TimsDirectXicExtractor Class Reference

#include <timsdirectxicextractor.h>

Inheritance diagram for pappso::TimsDirectXicExtractor:

Public Member Functions
	TimsDirectXicExtractor (MsRunReaderSPtr &msrun_reader)
virtual	~TimsDirectXicExtractor ()
void	extractXicCoordSPtrList (UiMonitorInterface &monitor, std::vector< XicCoordSPtr > &xic_coord_list) override
	extract a list of XIC given a list of xic coordinates to extract More...
Public Member Functions inherited from pappso::TimsXicExtractorInterface
	TimsXicExtractorInterface (MsRunReaderSPtr &msrun_reader)
virtual	~TimsXicExtractorInterface ()
Public Member Functions inherited from pappso::MsRunXicExtractorInterface
void	setXicExtractMethod (XicExtractMethod method)
	set the XIC extraction method More...
void	setRetentionTimeAroundTarget (double range_in_seconds)
	set the retention time range in seconds around the target rt More...
const MsRunIdCstSPtr &	getMsRunId () const
const MsRunReaderSPtr &	getMsRunReaderSPtr () const
	get the msrunreader currently used for XIC extraction More...

Additional Inherited Members
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 inherited from pappso::TimsXicExtractorInterface
const TimsData *	mp_timsData
Protected Attributes inherited from pappso::MsRunXicExtractorInterface
MsRunReaderSPtr	msp_msrun_reader
XicExtractMethod	m_xicExtractMethod = XicExtractMethod::max
double	m_retentionTimeAroundTarget = std::numeric_limits<double>::max()

Detailed Description

Todo:

write docs

Definition at line 37 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)
{
}

~TimsDirectXicExtractor()

TimsDirectXicExtractor::~TimsDirectXicExtractor ( )

virtual

Destructor

Definition at line 40 of file timsdirectxicextractor.cpp.

{
}

Member Function Documentation

extractXicCoordSPtrList()

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

overridevirtual

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.

Implements pappso::MsRunXicExtractorInterface.

Definition at line 46 of file timsdirectxicextractor.cpp.

{
  qDebug();
  if(xic_coord_list.size() == 0)
    return;
 
  std::vector<XicCoordTims *> xic_coord_tims_list;
  xic_coord_tims_list.reserve(xic_coord_list.size());
 
  for(XicCoordSPtr &xic_coord_sp : xic_coord_list)
    {
      XicCoordTims *p_xic_coord_tims =
        dynamic_cast<XicCoordTims *>(xic_coord_sp.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 =
    mp_timsData->getTimsMS1FrameIdRange(
      xic_coord_tims_list[0]->rtTarget - m_retentionTimeAroundTarget,
      xic_coord_tims_list.back()->rtTarget + m_retentionTimeAroundTarget);
 
  monitor.setStatus(QObject::tr("extracting %1 XICs on %2 Tims frames")
                      .arg(xic_coord_list.size())
                      .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->getTimsFrameCstSPtr(frame_id);
      qDebug();
      double rtframe = frame_sptr.get()->getTime();
      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::UiMonitorInterface::setStatus(), pappso::UiMonitorInterface::setTotalSteps(), and pappso::UiMonitorInterface::shouldIstop().

---

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

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