#include <timsframemobilitytraces.h>

Public Member Functions
	TimsFrameMobilityTraces ()
	TimsFrameMobilityTraces (const TimsFrameMobilityTraces &other)
	~TimsFrameMobilityTraces ()
void	extractMobilityTraces (pappso::TimsFrameCstSPtr timsframe_sptr, std::size_t ion_mob_begin, std::size_t ion_mob_end, std::size_t max_traces)
const std::vector< pappso::TraceCstSPtr > &	getIonMobTraceList () const
const std::vector< std::size_t > &	getTofIndexList () const
const std::vector< std::size_t > &	getScanIndexList () const
const std::vector< double >	getMzList () const

Private Attributes
pappso::TimsFrameCstSPtr	mcsp_timsFrameCstSPtr
std::vector< pappso::TraceCstSPtr >	m_ionMobTraceList
std::vector< std::size_t >	m_tofIndexList
std::vector< std::size_t >	m_scanIndexList

Detailed Description

Todo: write docs

Definition at line 38 of file timsframemobilitytraces.h.

Constructor & Destructor Documentation

◆ TimsFrameMobilityTraces() [1/2]

pappso::TimsFrameMobilityTraces::TimsFrameMobilityTraces ( )

Default constructor

Definition at line 34 of file timsframemobilitytraces.cpp.

35{

36}

Referenced by TimsFrameMobilityTraces().

◆ TimsFrameMobilityTraces() [2/2]

pappso::TimsFrameMobilityTraces::TimsFrameMobilityTraces ( const TimsFrameMobilityTraces & other )

Copy constructor

Parameters

other TODO

Definition at line 38 of file timsframemobilitytraces.cpp.

40{

41}

References TimsFrameMobilityTraces().

◆ ~TimsFrameMobilityTraces()

pappso::TimsFrameMobilityTraces::~TimsFrameMobilityTraces ( )

Destructor

Definition at line 43 of file timsframemobilitytraces.cpp.

44{

45}

Member Function Documentation

◆ extractMobilityTraces()

void pappso::TimsFrameMobilityTraces::extractMobilityTraces	(	pappso::TimsFrameCstSPtr	timsframe_sptr,
		std::size_t	ion_mob_begin,
		std::size_t	ion_mob_end,
		std::size_t	max_traces )

Definition at line 47 of file timsframemobilitytraces.cpp.

{
  m_tofIndexList.clear();
  m_ionMobTraceList.clear();
  m_scanIndexList.clear();
  mcsp_timsFrameCstSPtr = timsframe_sptr;
 
  pappso::TimsDataFastMap raw_spectrum = pappso::TimsDataFastMap::getTimsDataFastMapInstance();
  timsframe_sptr.get()->combineScansInTofIndexIntensityMap(
    raw_spectrum, scan_index_begin, scan_index_end);
 
  pappso::Trace total_spectrum;
 
  for(auto index : raw_spectrum.getTofIndexList())
    {
 
      total_spectrum.push_back({(double)index, (double)raw_spectrum.readIntensity(index)});
    }
  total_spectrum.sortY(Enums::SortOrder::descending);
 
  qDebug() << total_spectrum.size();
 
  total_spectrum.sortY(Enums::SortOrder::descending);
 
  for(std::size_t i = scan_index_begin; i < (scan_index_end + 1); i++)
    {
      m_scanIndexList.push_back(i);
    }
 
  for(auto &datapoint : total_spectrum)
    {
      pappso::Trace trace(
        timsframe_sptr.get()->getIonMobilityTraceByTofIndexRange(datapoint.x - 1,
                                                                 datapoint.x + 1,
                                                                 Enums::XicExtractMethod::sum,
                                                                 scan_index_begin,
                                                                 scan_index_end));
 
      m_ionMobTraceList.push_back(trace.makeTraceSPtr());
      m_tofIndexList.push_back(datapoint.x);
      if(m_ionMobTraceList.size() >= max_traces)
        break;
    }
  qDebug();
}

References pappso::Enums::descending, pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsDataFastMap::getTofIndexList(), m_ionMobTraceList, m_scanIndexList, m_tofIndexList, pappso::Trace::makeTraceSPtr(), mcsp_timsFrameCstSPtr, pappso::TimsDataFastMap::readIntensity(), pappso::Trace::sortY(), and pappso::Enums::sum.

◆ getIonMobTraceList()

const std::vector< pappso::TraceCstSPtr > & pappso::TimsFrameMobilityTraces::getIonMobTraceList ( ) const

Definition at line 97 of file timsframemobilitytraces.cpp.

{
  return m_ionMobTraceList;
}

References m_ionMobTraceList.

◆ getMzList()

const std::vector< double > pappso::TimsFrameMobilityTraces::getMzList ( ) const

Definition at line 107 of file timsframemobilitytraces.cpp.

{
  MzCalibrationInterface *mz_calibration_p =
    mcsp_timsFrameCstSPtr.get()->getMzCalibrationInterfaceSPtr().get();
  if(mz_calibration_p == nullptr)
    {
      throw pappso::ExceptionNotFound(QObject::tr("mz calibration pointer not found"));
    }
  std::vector<double> mz_list;
  for(std::size_t tof : m_tofIndexList)
    {
      mz_list.push_back(mz_calibration_p->getMzFromTofIndex((quint32)tof));
    }
  return mz_list;
}