#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:

Classes
struct	TofIndexIntensityPair

Public Member Functions
	TimsFrameBase (std::size_t frameId, quint32 scanCount)
	constructor for binary independant tims frame

	TimsFrameBase (const TimsFrameBase &other)

virtual	~TimsFrameBase ()

virtual bool	hasSameCalibrationData (const TimsFrameBase &other) const
	tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled between frames

virtual std::size_t	getScanPeakCount (std::size_t scanIndex) const
	get the number of peaks in this spectrum need the binary file

virtual std::size_t	getTotalNumberOfScans () const
	get the number of scans contained in this frame each scan represents an ion mobility slice

virtual quint32	getMaximumRawMassIndex () const
	get the maximum raw mass index contained in this frame

virtual MassSpectrumSPtr	getMassSpectrumSPtr (std::size_t scan_index) const
	get Mass spectrum with peaks for this scan index need the binary file

virtual pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtr (std::size_t scan_index) const final
	get the mass spectrum corresponding to a scan index

virtual Trace	cumulateScansToTrace (std::size_t scanIndexBegin, std::size_t scanIndexEnd) const
	cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time

virtual Trace	combineScansToTraceWithDowngradedMzResolution (std::size_t tof_index_merge_window, std::size_t scanIndexBegin, std::size_t scanIndexEnd, quint32 &minimum_tof_index_out, quint32 &maximum_tof_index_out) const
	cumulate spectrum given a scan index range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution

virtual Trace	combineScansToTraceWithDowngradedMzResolution2 (std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, std::size_t mobility_scan_begin, std::size_t mobility_scan_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const
	cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution

virtual Trace	getMobilityScan (std::size_t scan_index, std::size_t tof_index_merge_window, double mz_range_begin, double mz_range_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const
	get a single mobility scan m/z + intensities

virtual void	combineScansInTofIndexIntensityMap (TimsDataFastMap &tof_index_intensity_map, std::size_t scan_index_begin, std::size_t scan_index_end) const
	cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time

virtual void	combineScansInTofIndexIntensityMap (TimsDataFastMap &tof_index_intensity_map, std::size_t scan_index_begin, std::size_t scan_index_end, quint32 tof_index_begin, quint32 tof_index_end) const
	cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time

virtual quint64	cumulateScanIntensities (std::size_t scan_index) const

virtual quint64	cumulateScanRangeIntensities (std::size_t scan_index_begin, std::size_t scan_index_end) const

bool	checkScanNum (std::size_t scanNum) const
	check that this scan number exists

void	setAcqDurationInMilliseconds (double acquisition_duration_ms)

void	setMzCalibration (double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)

void	setTimsCalibration (int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)

void	setRtInSeconds (double time)

void	setMsMsType (quint8 type)

unsigned int	getMsLevel () const

double	getRtInSeconds () const

std::size_t	getId () const

double	getDriftTimeInMilliseconds (std::size_t scan_index) const
	get drift time of a scan number in milliseconds

double	getOneOverK0Transformation (std::size_t scan_index) const
	get 1/K0 value of a given scan (mobility value)

std::size_t	getScanIndexFromOneOverK0 (double one_over_k0) const
	get the scan number from a given 1/Ko mobility value

double	getVoltageTransformation (std::size_t scanNum) const
	get voltage for a given scan number

pappso::Trace	getTraceFromTofIndexIntensityMap (TimsDataFastMap &accumulated_scans) const
	transform accumulation of raw scans into a real mass spectrum

virtual const MzCalibrationInterfaceSPtr &	getMzCalibrationInterfaceSPtr () const final
	get the MzCalibration model to compute mz and TOF for this frame

void	setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)

virtual std::vector< quint32 >	getScanTofIndexList (std::size_t scan_index) const
	get raw index list for one given scan index are not TOF nor m/z, just index on digitizer

virtual std::vector< quint32 >	getScanIntensityList (std::size_t scan_index) const
	get raw intensities without transformation from one scan it needs intensity normalization

virtual Trace	getIonMobilityTraceByTofIndexRange (std::size_t tof_index_begin, std::size_t tof_index_end, Enums::XicExtractMethod method, std::size_t scan_index_begin, std::size_t scan_index_end) const
	get a mobility trace cumulating intensities inside the given mass index range

Protected Member Functions
virtual std::vector< TofIndexIntensityPair > &	downgradeResolutionOfTofIndexIntensityPairList (std::size_t tof_index_merge_window, std::vector< TofIndexIntensityPair > &spectrum) const
	Downgrade the TOF index resolution to lower the number of real m/z computations.

Protected Attributes
quint32	m_scanCount
	total number of scans contained in this frame

std::size_t	m_frameId
	Tims frame database id (the SQL identifier of this frame)

double	m_acqDurationInMilliseconds = 0
	acquisition duration in milliseconds

quint8	m_msMsType = 0

double	m_rtInSeconds = 0
	retention time

double	m_timsDvStart = 0

double	m_timsSlope

double	m_timsTtrans = 0

double	m_timsNdelay = 0

double	m_timsVmin = 0

double	m_timsVmax = 0

double	m_timsC6 = 0

double	m_timsC7 = 0

MzCalibrationInterfaceSPtr	msp_mzCalibration = nullptr

Detailed Description

Todo: write docs

Definition at line 49 of file timsframebase.h.

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

pappso::TimsFrameBase::TimsFrameBase	(	std::size_t	frameId,
		quint32	scanCount )

constructor for binary independant tims frame

Parameters

timsId	tims frame identifier in the database
scanCount	the number of scans in this frame

Definition at line 39 of file timsframebase.cpp.

{
  qDebug() << frame_id;
  m_frameId = frame_id;
 
  m_scanCount = scanCount;
}

References m_frameId, and m_scanCount.

Referenced by pappso::TimsFrame::TimsFrame(), pappso::TimsFrame::TimsFrame(), pappso::TimsFrame::TimsFrame(), TimsFrameBase(), and hasSameCalibrationData().

◆ TimsFrameBase() [2/2]

pappso::TimsFrameBase::TimsFrameBase ( const TimsFrameBase & other )

Copy constructor

Parameters

other TODO

Definition at line 47 of file timsframebase.cpp.

48{

49}

References TimsFrameBase().

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )

virtual

Destructor

Definition at line 51 of file timsframebase.cpp.

52{

53}

Member Function Documentation

◆ checkScanNum()

bool pappso::TimsFrameBase::checkScanNum ( std::size_t scanNum ) const

check that this scan number exists

Parameters

scanNum scan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 103 of file timsframebase.cpp.

{
  if(scanNum >= m_scanCount)
    {
      throw pappso::ExceptionOutOfRange(
        QObject::tr("Invalid scan number : scanNum %1  > m_scanNumber %2")
          .arg(scanNum)
          .arg(m_scanCount));
    }
 
  return true;
}

References m_scanCount.

Referenced by pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), pappso::TimsFrame::getScanIntensityList(), pappso::TimsFrameType1::getScanIntensityList(), pappso::TimsFrame::getScanPeakCount(), pappso::TimsFrame::getScanTofIndexList(), and pappso::TimsFrameType1::getScanTofIndexList().

◆ combineScansInTofIndexIntensityMap() [1/2]

void pappso::TimsFrameBase::combineScansInTofIndexIntensityMap	(	TimsDataFastMap &	tof_index_intensity_map,
		std::size_t	scan_index_begin,
		std::size_t	scan_index_end ) const

virtual

cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time

Parameters

tof_index_intensity_map	simple map of integers to cumulate raw counts
scan_index_begin	scan index in the frame in the order it lies in binary file, from 0 to N-1
scan_index_end	scan index in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 206 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
      "number begin %1 end %2")
      .arg(scanNumBegin)
      .arg(scanNumEnd));
}

◆ combineScansInTofIndexIntensityMap() [2/2]

void pappso::TimsFrameBase::combineScansInTofIndexIntensityMap	(	TimsDataFastMap &	tof_index_intensity_map,
		std::size_t	scan_index_begin,
		std::size_t	scan_index_end,
		quint32	tof_index_begin,
		quint32	tof_index_end ) const

virtual

cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time

Parameters

tof_index_intensity_map	simple map of integers to cumulate raw counts
scan_index_begin	scan index in the frame in the order it lies in binary file, from 0 to N-1
scan_index_end	scan index in the frame in the order it lies in binary file, from 0 to N-1
tof_index_begin
tof_index_end

Reimplemented in pappso::TimsFrame.

Definition at line 221 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
      "number begin %1 end %2, tof index begin %3, tof index end %4")
      .arg(scanNumBegin)
      .arg(scanNumEnd)
      .arg(tof_index_begin)
      .arg(tof_index_end));
}

◆ combineScansToTraceWithDowngradedMzResolution()

Trace pappso::TimsFrameBase::combineScansToTraceWithDowngradedMzResolution	(	std::size_t	tof_index_merge_window,
		std::size_t	scanIndexBegin,
		std::size_t	scanIndexEnd,
		quint32 &	minimum_tof_index_out,
		quint32 &	maximum_tof_index_out ) const

virtual

cumulate spectrum given a scan index range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution

Parameters

tof_index_merge_window	width of the TOF index window used to merge all intensities into a single point. This results in faster computing.
scanIndexBegin	scan index in the frame in the order it lies in binary file, from 0 to N-1
scanIndexEnd	scan index in the frame in the order it lies in binary file, from 0 to N-1
minimum_tof_index_out	report the minimum mz index contained in the resulting trace
maximum_tof_index_out	report the maximum mz index contained in the resulting trace

Reimplemented in pappso::TimsFrame.

Definition at line 160 of file timsframebase.cpp.

{
  throw PappsoException(QObject::tr("Non implemented function %1 %2 %3")
                          .arg(__FILE__)
                          .arg(__FUNCTION__)
                          .arg(__LINE__));
}

◆ combineScansToTraceWithDowngradedMzResolution2()

Trace pappso::TimsFrameBase::combineScansToTraceWithDowngradedMzResolution2	(	std::size_t	mz_index_merge_window,
		double	mz_range_begin,
		double	mz_range_end,
		std::size_t	mobility_scan_begin,
		std::size_t	mobility_scan_end,
		quint32 &	mz_minimum_index_out,
		quint32 &	mz_maximum_index_out ) const

virtual

cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution

Parameters

mzindex_merge_window	width of the mzindex window used to merge all intensities into a single point. This results in faster computing.
mz_range_begin
mz_range_end
scanNumBegin	scan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEnd	scan number in the frame in the order it lies in binary file, from 0 to N-1
mz_minimum_index	report the minimum mz index contained in the resulting trace (constrained by the mz_range_begin)
mz_maximum_index	report the maximum mz index contained in the resulting trace (constrained by the mz_range_end)

Reimplemented in pappso::TimsFrame.

Definition at line 174 of file timsframebase.cpp.

{
  throw PappsoException(QObject::tr("Non implemented function %1 %2 %3")
                          .arg(__FILE__)
                          .arg(__FUNCTION__)
                          .arg(__LINE__));
}

◆ cumulateScanIntensities()

quint64 pappso::TimsFrameBase::cumulateScanIntensities ( std::size_t scan_index ) const

virtual

Reimplemented in pappso::TimsFrame.

Definition at line 239 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to cumulateSingleScanIntensities in TimsFrameBase for scan "
      "number %1.")
      .arg(scanNum));
 
  return 0;
}

◆ cumulateScanRangeIntensities()

quint64 pappso::TimsFrameBase::cumulateScanRangeIntensities	(	std::size_t	scan_index_begin,
		std::size_t	scan_index_end ) const

virtual

Reimplemented in pappso::TimsFrame.

Definition at line 252 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
      "number begin %1 end %2")
      .arg(scanNumBegin)
      .arg(scanNumEnd));
 
  return 0;
}

◆ cumulateScansToTrace()

Trace pappso::TimsFrameBase::cumulateScansToTrace	(	std::size_t	scanIndexBegin,
		std::size_t	scanIndexEnd ) const

virtual

cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time

Parameters

scanIndexBegin	scan index in the frame in the order it lies in the frame in the binary file, from 0 to N-1
scanIndexEnd	scan number in the frame in the order it lies in the frame in the binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 149 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
                "number begin %1 end %2")
      .arg(scanNumBegin)
      .arg(scanNumEnd));
}

◆ downgradeResolutionOfTofIndexIntensityPairList()

std::vector< TimsFrameBase::TofIndexIntensityPair > & pappso::TimsFrameBase::downgradeResolutionOfTofIndexIntensityPairList	(	std::size_t	tof_index_merge_window,
		std::vector< TofIndexIntensityPair > &	spectrum ) const

protectedvirtual

Downgrade the TOF index resolution to lower the number of real m/z computations.

This function merges together into a single TOF index bin all the TOF

indices contained in the tof_index_merge_window. Then the window is shifted and the operation is performed again. When all the list of \l{TofIndexIntensityPair}s has been gone through, the resolution of the data has effectively been downgrade by a factor corresponding to tof_index_merge_window.

 @param tof_index_merge_window width of the TOF index window used to merge

all intensities into a single point. This results in faster computing.

Parameters

rawSpectrum the spectrum to shrink

Definition at line 566 of file timsframebase.cpp.

{
 
  qDebug() << rawSpectrum.size();
  std::vector<TimsFrameBase::TofIndexIntensityPair> new_spectrum;
 
  TimsFrameBase::TofIndexIntensityPair current_point;
  current_point.intensity_index = 0;
  current_point.tof_index       = 0;
  for(auto &pair_mz_intensity : rawSpectrum)
    {
      quint32 mzkey = (pair_mz_intensity.tof_index / mzindex_merge_window);
      mzkey = (mzkey * mzindex_merge_window) + (mzindex_merge_window / 2);
 
      if(current_point.tof_index != mzkey)
        {
          if(current_point.tof_index > 0)
            {
              new_spectrum.push_back(current_point);
            }
 
          current_point.intensity_index = pair_mz_intensity.intensity_index;
          current_point.tof_index       = mzkey;
        }
      else
        {
          current_point.intensity_index += pair_mz_intensity.intensity_index;
        }
    }
 
  if(current_point.tof_index > 0)
    {
      new_spectrum.push_back(current_point);
    }
  rawSpectrum = new_spectrum;
  qDebug() << rawSpectrum.size();
  return rawSpectrum;
}

References downgradeResolutionOfTofIndexIntensityPairList(), pappso::TimsFrameBase::TofIndexIntensityPair::intensity_index, and pappso::TimsFrameBase::TofIndexIntensityPair::tof_index.

Referenced by downgradeResolutionOfTofIndexIntensityPairList(), and pappso::TimsFrame::getMobilityScan().

◆ getDriftTimeInMilliseconds()

double pappso::TimsFrameBase::getDriftTimeInMilliseconds ( std::size_t scan_index ) const

get drift time of a scan number in milliseconds

Parameters

scanNum scan number in the frame in the order it lies in binary file, from 0 to N-1

Returns: time in milliseconds of mobility delay (drift time)

Definition at line 356 of file timsframebase.cpp.

{
  return (m_acqDurationInMilliseconds / (double)m_scanCount) *
         ((double)scanNum);
}

References m_acqDurationInMilliseconds, and m_scanCount.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getId()

std::size_t pappso::TimsFrameBase::getId ( ) const

Definition at line 294 of file timsframebase.cpp.

{
  return m_frameId;
}

References m_frameId.

Referenced by pappso::TimsFrameType1::getMassSpectrumSPtr(), pappso::TimsFrameType1::getScanIntensityList(), pappso::TimsFrameType1::getScanTofIndexList(), and pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList().

◆ getIonMobilityTraceByTofIndexRange()

Trace pappso::TimsFrameBase::getIonMobilityTraceByTofIndexRange	(	std::size_t	tof_index_begin,
		std::size_t	tof_index_end,
		Enums::XicExtractMethod	method,
		std::size_t	scan_index_begin,
		std::size_t	scan_index_end ) const

virtual

get a mobility trace cumulating intensities inside the given mass index range

Parameters

tof_index_begin	raw mass index lower bound
tof_index_end	raw mass index upper bound
method	max or sum intensities
scan_index_begin	first mobility scan to integrate
scan_index_end	last mobility scan to integrate

Definition at line 498 of file timsframebase.cpp.

{
  Trace im_trace;
  DataPoint data_point;
  if(scan_index_end > m_scanCount)
    scan_index_end = m_scanCount;
  for(quint32 i = scan_index_begin; i < (scan_index_end + 1); i++)
    {
      data_point.x = i;
      data_point.y = 0;
      qDebug() << "m_scanNumber=" << m_scanCount << " i=" << i;
      std::vector<quint32> index_list = getScanTofIndexList(i);
      auto it_lower                   = std::find_if(index_list.begin(),
                                   index_list.end(),
                                   [tof_index_begin](quint32 to_compare) {
                                     if(to_compare < tof_index_begin)
                                       {
                                         return false;
                                       }
                                     return true;
                                   });
 
 
      if(it_lower == index_list.end())
        {
        }
      else
        {
 
 
          auto it_upper                       = std::find_if(index_list.begin(),
                                       index_list.end(),
                                       [tof_index_end](quint32 to_compare) {
                                         if(tof_index_end >= to_compare)
                                           {
                                             return false;
                                           }
                                         return true;
                                       });
          std::vector<quint32> intensity_list = getScanIntensityList(i);
          for(int j = std::distance(index_list.begin(), it_lower);
              j < std::distance(index_list.begin(), it_upper);
              j++)
            {
              if(method == Enums::XicExtractMethod::sum)
                {
                  data_point.y += intensity_list[j];
                }
              else
                {
                  data_point.y =
                    std::max((double)intensity_list[j], data_point.y);
                }
            }
        }
      im_trace.push_back(data_point);
    }
  qDebug();
  return im_trace;
}

References getScanIntensityList(), getScanTofIndexList(), m_scanCount, pappso::Enums::sum, pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getMassSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr pappso::TimsFrameBase::getMassSpectrumCstSPtr ( std::size_t scan_index ) const

finalvirtual

get the mass spectrum corresponding to a scan index

Parameters

scan_index the scan index of the mass spectrum to retrieve

Definition at line 142 of file timsframebase.cpp.

{
  // qDebug();
 
  return getMassSpectrumSPtr(scanNum);
}

References getMassSpectrumSPtr().

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::TimsFrameBase::getMassSpectrumSPtr ( std::size_t scan_index ) const

virtual

get Mass spectrum with peaks for this scan index need the binary file

Parameters

scan_index scan index in the frame in the order it lies in binary file, from 0 to N-1 (this is the mobility index)

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 132 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
      .arg(scanNum));
}

Referenced by getMassSpectrumCstSPtr().

◆ getMaximumRawMassIndex()

quint32 pappso::TimsFrameBase::getMaximumRawMassIndex ( ) const

virtual

get the maximum raw mass index contained in this frame

Definition at line 462 of file timsframebase.cpp.

{
  quint32 max_value = 0;
  for(quint32 i = 0; i < m_scanCount; i++)
    {
      qDebug() << "m_scanNumber=" << m_scanCount << " i=" << i;
      std::vector<quint32> index_list = getScanTofIndexList(i);
      auto it = std::max_element(index_list.begin(), index_list.end());
      if(it != index_list.end())
        {
          max_value = std::max(max_value, *it);
        }
    }
  return max_value;
}

References getScanTofIndexList(), and m_scanCount.

◆ getMobilityScan()

Trace pappso::TimsFrameBase::getMobilityScan	(	std::size_t	scan_index,
		std::size_t	tof_index_merge_window,
		double	mz_range_begin,
		double	mz_range_end,
		quint32 &	mz_minimum_index_out,
		quint32 &	mz_maximum_index_out ) const

virtual

get a single mobility scan m/z + intensities

Parameters

scanIndex	scan number in the frame in the order it lies in binary file, from 0 to N-1
tof_index_merge_window	width of the TOF index window used to merge all intensities into a single point. This results in faster computing.
mz_range_begin
mz_range_end
mz_minimum_index	report the minimum mz index contained in the resulting trace (constrained by the mz_range_begin)
mz_maximum_index	report the maximum mz index contained in the resulting trace (constrained by the mz_range_end)

Reimplemented in pappso::TimsFrame.

Definition at line 190 of file timsframebase.cpp.

{
  throw PappsoException(QObject::tr("Non implemented function %1 %2 %3")
                          .arg(__FILE__)
                          .arg(__FUNCTION__)
                          .arg(__LINE__));
}

◆ getMsLevel()

unsigned int pappso::TimsFrameBase::getMsLevel ( ) const

Definition at line 280 of file timsframebase.cpp.

{
  if(m_msMsType == 0)
    return 1;
  return 2;
}

References m_msMsType.

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getMzCalibrationInterfaceSPtr()

const MzCalibrationInterfaceSPtr & pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr ( ) const

finalvirtual

get the MzCalibration model to compute mz and TOF for this frame

Definition at line 429 of file timsframebase.cpp.

{
  if(msp_mzCalibration == nullptr)
    {
 
      throw pappso::PappsoException(
        QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
          .arg(__FILE__)
          .arg(__FUNCTION__)
          .arg(__LINE__));
    }
  return msp_mzCalibration;
}

References msp_mzCalibration.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), and getTraceFromTofIndexIntensityMap().

◆ getOneOverK0Transformation()

double pappso::TimsFrameBase::getOneOverK0Transformation ( std::size_t scan_index ) const

get 1/K0 value of a given scan (mobility value)

Parameters

scanNum scan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 363 of file timsframebase.cpp.

{
  return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
}

References getVoltageTransformation(), m_timsC6, and m_timsC7.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getRtInSeconds()

double pappso::TimsFrameBase::getRtInSeconds ( ) const

Definition at line 288 of file timsframebase.cpp.

{
  return m_rtInSeconds;
}

References m_rtInSeconds.

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram(), pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getScanIndexFromOneOverK0()

std::size_t pappso::TimsFrameBase::getScanIndexFromOneOverK0 ( double one_over_k0 ) const

get the scan number from a given 1/Ko mobility value

Parameters

one_over_k0 the mobility value to tranform

Returns: integer the scan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 370 of file timsframebase.cpp.

{
  double temp = 1 / one_over_k0;
  temp        = temp - m_timsC6;
  temp        = temp / m_timsC7;
  temp        = 1 / temp;
  temp        = temp - m_timsDvStart;
  temp        = temp / m_timsSlope + m_timsTtrans + m_timsNdelay;
  return (std::size_t)std::round(temp);
}

References m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, and m_timsTtrans.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getScanIntensityList()

std::vector< quint32 > pappso::TimsFrameBase::getScanIntensityList ( std::size_t scan_index ) const

virtual

get raw intensities without transformation from one scan it needs intensity normalization

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 489 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
      .arg(scanNum));
}

Referenced by getIonMobilityTraceByTofIndexRange().

◆ getScanPeakCount()

std::size_t pappso::TimsFrameBase::getScanPeakCount ( std::size_t scanIndex ) const

virtual

get the number of peaks in this spectrum need the binary file

Parameters

scanIndex scan index in the frame in the order it lies in frame's binary data, from 0 to N-1

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 117 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
      .arg(scanNum));
}

◆ getScanTofIndexList()

std::vector< quint32 > pappso::TimsFrameBase::getScanTofIndexList ( std::size_t scan_index ) const

virtual

get raw index list for one given scan index are not TOF nor m/z, just index on digitizer

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 479 of file timsframebase.cpp.

{
  throw PappsoException(
    QObject::tr(
      "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
      .arg(scanNum));
}

Referenced by getIonMobilityTraceByTofIndexRange(), and getMaximumRawMassIndex().

◆ getTotalNumberOfScans()

std::size_t pappso::TimsFrameBase::getTotalNumberOfScans ( ) const

virtual

get the number of scans contained in this frame each scan represents an ion mobility slice

Definition at line 126 of file timsframebase.cpp.

{
  return m_scanCount;
}

References m_scanCount.

Referenced by pappso::BaseColorMapPlotWidget::addColorMap(), pappso::TimsFramesMsRunReader::computeTicChromatogram(), pappso::TimsFramesMsRunReader::readSpectrumCollection2(), and pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getTraceFromTofIndexIntensityMap()

pappso::Trace pappso::TimsFrameBase::getTraceFromTofIndexIntensityMap ( TimsDataFastMap & accumulated_scans ) const

transform accumulation of raw scans into a real mass spectrum

Definition at line 397 of file timsframebase.cpp.

{
  qDebug();
  // qDebug();
  // add flanking peaks
  pappso::Trace local_trace;
 
  MzCalibrationInterface *mz_calibration_p =
    getMzCalibrationInterfaceSPtr().get();
 
 
  DataPoint element;
  for(quint32 tof_index : accumulated_scans.getTofIndexList())
    {
      // intensity normalization
      element.y = ((double)accumulated_scans.readIntensity(tof_index)) * 100.0 /
                  m_acqDurationInMilliseconds;
 
      // mz calibration
      element.x = mz_calibration_p->getMzFromTofIndex(tof_index);
 
      local_trace.push_back(element);
    }
  local_trace.sortX();
 
  qDebug();
  // qDebug();
  return local_trace;
}

References getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsDataFastMap::getTofIndexList(), m_acqDurationInMilliseconds, pappso::TimsDataFastMap::readIntensity(), pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getVoltageTransformation()

double pappso::TimsFrameBase::getVoltageTransformation ( std::size_t scanNum ) const

get voltage for a given scan number

Parameters

scanNum scan number in the frame in the order it lies in binary file, from 0 to N-1

Returns: double volt measure

Definition at line 330 of file timsframebase.cpp.

{
  double v = m_timsDvStart +
             m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
 
  if(v < m_timsVmin)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
                    "calibration, v < m_timsVmin %1 < %2")
          .arg(v)
          .arg(m_timsVmin));
    }
 
 
  if(v > m_timsVmax)
    {
      throw pappso::PappsoException(
        QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
                    "calibration, v > m_timsVmax  %1 > %2")
          .arg(v)
          .arg(m_timsVmax));
    }
  return v;
}

References m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

Referenced by getOneOverK0Transformation().

◆ hasSameCalibrationData()

bool pappso::TimsFrameBase::hasSameCalibrationData ( const TimsFrameBase & other ) const

virtual

tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled between frames

Definition at line 382 of file timsframebase.cpp.

{
  if((m_timsDvStart == other.m_timsDvStart) &&
     (m_timsTtrans == other.m_timsTtrans) &&
     (m_timsNdelay == other.m_timsNdelay) && (m_timsVmin == other.m_timsVmin) &&
     (m_timsVmax == other.m_timsVmax) && (m_timsC6 == other.m_timsC6) &&
     (m_timsC7 == other.m_timsC7) && (m_timsSlope == other.m_timsSlope))
    {
      return true;
    }
  return false;
}

References TimsFrameBase(), m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

◆ setAcqDurationInMilliseconds()

void pappso::TimsFrameBase::setAcqDurationInMilliseconds ( double acquisition_duration_ms )

Definition at line 56 of file timsframebase.cpp.

{
  m_acqDurationInMilliseconds = acquisition_duration_ms;
}

References m_acqDurationInMilliseconds.

◆ setMsMsType()

void pappso::TimsFrameBase::setMsMsType ( quint8 type )

Definition at line 272 of file timsframebase.cpp.

{
 
  qDebug() << " m_msMsType=" << type;
  m_msMsType = type;
}

References m_msMsType.

◆ setMzCalibration()

void pappso::TimsFrameBase::setMzCalibration	(	double	T1_frame,
		double	T2_frame,
		double	digitizerTimebase,
		double	digitizerDelay,
		double	C0,
		double	C1,
		double	C2,
		double	C3,
		double	C4,
		double	T1_ref,
		double	T2_ref,
		double	dC1,
		double	dC2 )

Definition at line 63 of file timsframebase.cpp.

{
 
  /*  MzCalibrationModel1 mzCalibration(temperature_correction,
                                 digitizerTimebase,
                                 digitizerDelay,
                                 C0,
                                 C1,
                                 C2,
                                 C3,
                                 C4);
                                 */
  msp_mzCalibration = std::make_shared<MzCalibrationModel1>(T1_frame,
                                                            T2_frame,
                                                            digitizerTimebase,
                                                            digitizerDelay,
                                                            C0,
                                                            C1,
                                                            C2,
                                                            C3,
                                                            C4,
                                                            T1_ref,
                                                            T2_ref,
                                                            dC1,
                                                            dC2);
}

References msp_mzCalibration.

◆ setMzCalibrationInterfaceSPtr()

void pappso::TimsFrameBase::setMzCalibrationInterfaceSPtr ( MzCalibrationInterfaceSPtr mzCalibration )

Definition at line 444 of file timsframebase.cpp.

{
 
  if(mzCalibration == nullptr)
    {
 
      throw pappso::PappsoException(
        QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
          .arg(__FILE__)
          .arg(__FUNCTION__)
          .arg(__LINE__));
    }
  msp_mzCalibration = mzCalibration;
}

References msp_mzCalibration.

◆ setRtInSeconds()

void pappso::TimsFrameBase::setRtInSeconds ( double time )

Definition at line 266 of file timsframebase.cpp.

{
  m_rtInSeconds = time;
}

References m_rtInSeconds.

◆ setTimsCalibration()

void pappso::TimsFrameBase::setTimsCalibration	(	int	tims_model_type,
		double	C0,
		double	C1,
		double	C2,
		double	C3,
		double	C4,
		double	C5,
		double	C6,
		double	C7,
		double	C8,
		double	C9 )

Definition at line 299 of file timsframebase.cpp.

{
  if(tims_model_type != 2)
    {
      throw pappso::PappsoException(QObject::tr(
        "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
    }
  m_timsDvStart = C2; // C2 from TimsCalibration
  m_timsTtrans  = C4; // C4 from TimsCalibration
  m_timsNdelay  = C0; // C0 from TimsCalibration
  m_timsVmin    = C8; // C8 from TimsCalibration
  m_timsVmax    = C9; // C9 from TimsCalibration
  m_timsC6      = C6;
  m_timsC7      = C7;
 
 
  m_timsSlope =
    (C3 - m_timsDvStart) / C1; //  //C3 from TimsCalibration // C2 from
                               //  TimsCalibration // C1 from TimsCalibration
}

References m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

Member Data Documentation

◆ m_acqDurationInMilliseconds

double pappso::TimsFrameBase::m_acqDurationInMilliseconds = 0

protected

acquisition duration in milliseconds

Definition at line 394 of file timsframebase.h.

Referenced by pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScanIntensities(), pappso::TimsFrame::cumulateScansToTrace(), getDriftTimeInMilliseconds(), pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), pappso::TimsFrame::getMobilityScan(), pappso::TimsFrame::getRawTraceSPtr(), pappso::TimsFrameType1::getRawTraceSPtr(), pappso::TimsFrameType1::getRawValuePairList(), getTraceFromTofIndexIntensityMap(), and setAcqDurationInMilliseconds().

◆ m_frameId

std::size_t pappso::TimsFrameBase::m_frameId

protected

Tims frame database id (the SQL identifier of this frame)

Warning: in sqlite, there is another field called TimsId : this is not that, because it is in fact an offset in bytes in the binary file.

Definition at line 390 of file timsframebase.h.

Referenced by pappso::TimsFrame::TimsFrame(), TimsFrameBase(), pappso::TimsFrameType1::TimsFrameType1(), getId(), and pappso::TimsFrameType1::lzfDecompressScan().

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0

protected

Definition at line 396 of file timsframebase.h.

Referenced by getMsLevel(), and setMsMsType().

◆ m_rtInSeconds

double pappso::TimsFrameBase::m_rtInSeconds = 0

protected

retention time

Definition at line 400 of file timsframebase.h.

Referenced by pappso::TimsFrame::extractTimsXicListInRtRange(), getRtInSeconds(), and setRtInSeconds().

◆ m_scanCount

quint32 pappso::TimsFrameBase::m_scanCount

protected

total number of scans contained in this frame

Definition at line 384 of file timsframebase.h.

Referenced by pappso::TimsFrame::TimsFrame(), TimsFrameBase(), pappso::TimsFrameType1::TimsFrameType1(), checkScanNum(), pappso::TimsFrameType1::copyAndLzfDecompress(), pappso::TimsFrame::extractTimsXicListInRtRange(), getDriftTimeInMilliseconds(), getIonMobilityTraceByTofIndexRange(), getMaximumRawMassIndex(), pappso::TimsFrame::getScanPeakCount(), and getTotalNumberOfScans().

◆ m_timsC6

double pappso::TimsFrameBase::m_timsC6 = 0

protected

Definition at line 410 of file timsframebase.h.

Referenced by getOneOverK0Transformation(), getScanIndexFromOneOverK0(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsC7

double pappso::TimsFrameBase::m_timsC7 = 0

protected

Definition at line 411 of file timsframebase.h.

Referenced by getOneOverK0Transformation(), getScanIndexFromOneOverK0(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsDvStart

double pappso::TimsFrameBase::m_timsDvStart = 0

protected

Definition at line 402 of file timsframebase.h.

Referenced by getScanIndexFromOneOverK0(), getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsNdelay

double pappso::TimsFrameBase::m_timsNdelay = 0

protected

Definition at line 407 of file timsframebase.h.

Referenced by getScanIndexFromOneOverK0(), getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsSlope

double pappso::TimsFrameBase::m_timsSlope

protected

Initial value:

=

0

Definition at line 403 of file timsframebase.h.

Referenced by getScanIndexFromOneOverK0(), getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsTtrans

double pappso::TimsFrameBase::m_timsTtrans = 0

protected

Definition at line 406 of file timsframebase.h.

Referenced by getScanIndexFromOneOverK0(), getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsVmax

double pappso::TimsFrameBase::m_timsVmax = 0

protected

Definition at line 409 of file timsframebase.h.

Referenced by getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ m_timsVmin

double pappso::TimsFrameBase::m_timsVmin = 0

protected

Definition at line 408 of file timsframebase.h.

Referenced by getVoltageTransformation(), hasSameCalibrationData(), and setTimsCalibration().

◆ msp_mzCalibration

MzCalibrationInterfaceSPtr pappso::TimsFrameBase::msp_mzCalibration = nullptr

protected

Definition at line 413 of file timsframebase.h.

Referenced by pappso::TimsFrame::getMobilityScan(), getMzCalibrationInterfaceSPtr(), setMzCalibration(), and setMzCalibrationInterfaceSPtr().

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

pappsomspp/core/vendors/tims/timsframebase.h
pappsomspp/core/vendors/tims/timsframebase.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

◆ TimsFrameBase() [2/2]

◆ ~TimsFrameBase()

Member Function Documentation

◆ checkScanNum()

◆ combineScansInTofIndexIntensityMap() [1/2]

◆ combineScansInTofIndexIntensityMap() [2/2]

◆ combineScansToTraceWithDowngradedMzResolution()

◆ combineScansToTraceWithDowngradedMzResolution2()

◆ cumulateScanIntensities()

◆ cumulateScanRangeIntensities()

◆ cumulateScansToTrace()

◆ downgradeResolutionOfTofIndexIntensityPairList()

◆ getDriftTimeInMilliseconds()

◆ getId()

◆ getIonMobilityTraceByTofIndexRange()

◆ getMassSpectrumCstSPtr()

◆ getMassSpectrumSPtr()

◆ getMaximumRawMassIndex()

◆ getMobilityScan()

◆ getMsLevel()

◆ getMzCalibrationInterfaceSPtr()

◆ getOneOverK0Transformation()

◆ getRtInSeconds()

◆ getScanIndexFromOneOverK0()

◆ getScanIntensityList()

◆ getScanPeakCount()

◆ getScanTofIndexList()

◆ getTotalNumberOfScans()

◆ getTraceFromTofIndexIntensityMap()

◆ getVoltageTransformation()

◆ hasSameCalibrationData()

◆ setAcqDurationInMilliseconds()

◆ setMsMsType()

◆ setMzCalibration()

◆ setMzCalibrationInterfaceSPtr()

◆ setRtInSeconds()

◆ setTimsCalibration()

Member Data Documentation

◆ m_acqDurationInMilliseconds

◆ m_frameId

◆ m_msMsType

◆ m_rtInSeconds

◆ m_scanCount

◆ m_timsC6

◆ m_timsC7

◆ m_timsDvStart

◆ m_timsNdelay

◆ m_timsSlope

◆ m_timsTtrans

◆ m_timsVmax

◆ m_timsVmin

◆ msp_mzCalibration