pappso::TimsDirectXicExtractor Class Reference

#include <timsdirectxicextractor.h>

Inheritance diagram for pappso::TimsDirectXicExtractor:

Public Member Functions
	TimsDirectXicExtractor (const TimsData *mp_tims_data)
virtual	~TimsDirectXicExtractor ()
Public Member Functions inherited from pappso::TimsXicExtractorInterface
	TimsXicExtractorInterface (const TimsData *mp_tims_data)
virtual	~TimsXicExtractorInterface ()
void	setXicExtractMethod (XicExtractMethod method)
	set the XIC extraction method More...

Protected Member Functions
virtual void	extractTimsXicList (std::vector< TimsXicStructure > &timsXicList, double rtRange) const override
	extract XICs for given coordinates XICs are extracted given their coordinates : retention time target, mobility range, mz range More...

Additional Inherited Members
Protected Attributes inherited from pappso::TimsXicExtractorInterface
const TimsData *	mp_timsData
XicExtractMethod	m_xicExtractMethod = XicExtractMethod::max

Detailed Description

Todo:

write docs

Definition at line 37 of file timsdirectxicextractor.h.

Constructor & Destructor Documentation

TimsDirectXicExtractor()

TimsDirectXicExtractor::TimsDirectXicExtractor

(

const TimsData *

mp_tims_data

)

Default constructor

Definition at line 32 of file timsdirectxicextractor.cpp.

  : pappso::TimsXicExtractorInterface(mp_tims_data)
{
}

~TimsDirectXicExtractor()

TimsDirectXicExtractor::~TimsDirectXicExtractor ( )

virtual

Destructor

Definition at line 37 of file timsdirectxicextractor.cpp.

{
}

Member Function Documentation

extractTimsXicList()

void TimsDirectXicExtractor::extractTimsXicList ( std::vector< TimsXicStructure > &  timsXicList, double  rtRange  ) const

overrideprotectedvirtual

extract XICs for given coordinates XICs are extracted given their coordinates : retention time target, mobility range, mz range

Parameters

timsXicList	list of TIMS XIC structures (XIC coordinates)
rtRange	the range in seconds that will be applied before and after XIC rtTarget to extract signal

Implements pappso::TimsXicExtractorInterface.

Definition at line 43 of file timsdirectxicextractor.cpp.

{
  if(timsXicList.size() == 0)
    return;
  std::sort(timsXicList.begin(),
            timsXicList.end(),
            [](const TimsXicStructure &a, const TimsXicStructure &b) {
              return a.rtTarget < b.rtTarget;
            });
 
  std::vector<std::size_t> tims_frameid_list =
    mp_timsData->getTimsMS1FrameIdRange(timsXicList[0].rtTarget - rtRange,
                                        timsXicList.back().rtTarget + rtRange);
 
  std::vector<TimsXicStructure>::iterator itXicListbegin = timsXicList.begin();
  std::vector<TimsXicStructure>::iterator itXicListend   = timsXicList.begin();
 
  for(std::size_t frame_id : tims_frameid_list)
    {
      TimsFrameCstSPtr frame_sptr = mp_timsData->getTimsFrameCstSPtr(frame_id);
      double rt                   = frame_sptr.get()->getTime();
      while((itXicListbegin != timsXicList.end()) &&
            ((itXicListbegin->rtTarget - rtRange) < rt))
        {
          itXicListbegin++;
        }
      while((itXicListend != timsXicList.end()) &&
            (rt < (itXicListend->rtTarget + rtRange)))
        {
          itXicListend++;
        }
      frame_sptr.get()->extractTimsXicListInRtRange(
        itXicListbegin, itXicListend, m_xicExtractMethod);
    }
}

References pappso::TimsData::getTimsFrameCstSPtr(), pappso::TimsData::getTimsMS1FrameIdRange(), pappso::TimsXicExtractorInterface::m_xicExtractMethod, and pappso::TimsXicExtractorInterface::mp_timsData.

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

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