#include <timsdiaslices.h>

Classes
struct	MsMsWindow
struct	MsMsWindowGroup
struct	MsMsWindowGroupList
struct	FrameSliceRange

Public Member Functions
	TimsDiaSlices (QSqlQuery &query, TimsData *tims_data_origin)
	~TimsDiaSlices ()
const MsMsWindowGroupList &	getMsMsWindowGroupList () const
const std::map< std::size_t, MsMsWindowGroup * > &	getMapFrame2WindowGroupPtr () const
std::size_t	getGlobalSliceIndexBeginByFrameId (std::size_t frame_id) const
std::size_t	getFrameIdByGlobalSliceIndex (std::size_t global_slice_id) const
std::size_t	getTotalSlicesCount () const
	get the number of DIA MS2 slices analyzed by PASEF
const MsMsWindow &	getMsMsWindowByGlobalSliceIndex (std::size_t global_slice_index) const
TimsDataFastMap &	getCombinedMs2ScansByGlobalSliceIndex (std::size_t global_slice_index) const
void	getMs2QualifiedSpectrumByGlobalSliceIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data) const
void	getMs1QualifiedSpectrumByGlobalSliceIndex (const MsRunIdCstSPtr &msrun_id, QualifiedMassSpectrum &mass_spectrum, std::size_t global_slice_index, bool want_binary_data, int rt_position=0) const
	get MS1 spectrum corresponding to the given slice extract MS1 mz range and mobility range corresponding to a global slice
std::size_t	getLastMs1FrameIdByMs2FrameId (std::size_t frame_id) const

Private Member Functions
const FrameSliceRange &	getFrameSliceRangeByGlobalSliceIndex (std::size_t global_slice_index) const

Private Attributes
TimsData *	mp_timsDataOrigin
MsMsWindowGroupList	m_msMsWindowGroupList
std::map< std::size_t, MsMsWindowGroup * >	m_mapFrame2WindowGroupPtr
std::vector< std::size_t >	m_frameId2GlobalSliceIndexBegin
std::vector< std::size_t >	m_ms2frameId2Ms1FrameId
std::vector< std::size_t >	m_ms1frameIdList
std::vector< FrameSliceRange >	m_frameSliceRangeList
bool	m_builtinMs2Centroid = true
	enable builtin centroid on raw tims integers by default
std::size_t	m_totalSlicesCount

Detailed Description

Todo: write docs

Definition at line 37 of file timsdiaslices.h.

Constructor & Destructor Documentation

◆ TimsDiaSlices()

pappso::TimsDiaSlices::TimsDiaSlices	(	QSqlQuery &	query,
		TimsData *	tims_data_origin )

Default constructor

Definition at line 110 of file timsdiaslices.cpp.

  : mp_timsDataOrigin(tims_data_origin)
{
 
  /*
CREATE TABLE IF NOT EXISTS "DiaFrameMsMsWindows" (
"WindowGroup"   INTEGER NOT NULL,
"ScanNumBegin"  INTEGER NOT NULL,
"ScanNumEnd"    INTEGER NOT NULL,
"IsolationMz"   REAL NOT NULL,
"IsolationWidth"    REAL NOT NULL,
"CollisionEnergy"   REAL NOT NULL,
FOREIGN KEY("WindowGroup") REFERENCES "FrameMsMsWindowGroups"("Id"),
PRIMARY KEY("WindowGroup","ScanNumBegin")
) WITHOUT ROWID;
*/
 
  if(!query.exec("SELECT WindowGroup, ScanNumBegin, ScanNumEnd, IsolationMz, "
                 "IsolationWidth, CollisionEnergy FROM DiaFrameMsMsWindows;"))
    {
      qDebug();
      throw ExceptionNotFound(QObject::tr("ERROR : executing %1 :\n%2")
                                .arg(query.lastQuery())
                                .arg(query.lastError().text()));
    }
  else
    {
 
      qDebug() << query.size();
      if(query.size() == 0)
        {
          qDebug();
          // FIXME: this exception is thrown, but my file is DDA.
          // That's not a nice info...
          throw ExceptionNotFound(
            QObject::tr("ERROR : DiaFrameMsMsWindows table is empty in SqlLite database"));
        }
      MsMsWindow msms_window;
      while(query.next())
        {
          qDebug();
          msms_window.WindowGroup     = query.value(0).toLongLong();
          msms_window.ScanNumBegin    = query.value(1).toLongLong();
          msms_window.ScanNumEnd      = query.value(2).toLongLong();
          msms_window.IsolationMz     = query.value(3).toDouble();
          msms_window.IsolationWidth  = query.value(4).toDouble();
          msms_window.CollisionEnergy = query.value(5).toDouble();
 
          qDebug();
          m_msMsWindowGroupList.addInGroup(msms_window);
        }
 
      if(m_msMsWindowGroupList.size() == 0)
        {
          qDebug();
          // FIXME: this exception is thrown, but my file is DDA.
          // That's not a nice info...
          throw ExceptionNotFound(
            QObject::tr("ERROR : no DiaFrameMsMsWindows in SqlLite database"));
        }
    }
 
  qDebug();
  std::size_t max_frame_id = 0;
  if(!query.exec("SELECT Frame, WindowGroup FROM DiaFrameMsMsInfo;"))
    {
      qDebug();
      throw pappso::ExceptionNotFound(
        QObject::tr("ERROR : no DiaFrameMsMsInfo in SqlLite database"));
    }
  else
    {
      qDebug() << query.size();
      if(query.size() == 0)
        {
          qDebug();
          throw pappso::ExceptionNotFound(
            QObject::tr("ERROR : no DiaFrameMsMsInfo in SqlLite database"));
        }
      while(query.next())
        {
          qDebug();
          max_frame_id = query.value(0).toLongLong();
          m_mapFrame2WindowGroupPtr[query.value(0).toLongLong()] =
            m_msMsWindowGroupList.getWindowGroupPtrByGroupId(query.value(1).toLongLong());
        }
 
      if(m_mapFrame2WindowGroupPtr.size() == 0)
        {
          qDebug();
          throw ExceptionNotFound(QObject::tr("ERROR : no DiaFrameMsMsInfo in SqlLite database"));
        }
    }
  qDebug();
 
  m_frameId2GlobalSliceIndexBegin.resize(max_frame_id + 1);
 
  m_ms2frameId2Ms1FrameId.resize(max_frame_id + 1);
  std::size_t last_ms1       = 0;
  std::size_t previous_frame = 0;
 
  std::size_t cumul_global_slice = 0;
  m_ms1frameIdList.clear();
  for(const std::pair<std::size_t, MsMsWindowGroup *> pair_frame_pgroup : m_mapFrame2WindowGroupPtr)
    {
      if(previous_frame != pair_frame_pgroup.first - 1)
        {
          last_ms1 = previous_frame + 1;
          m_ms1frameIdList.push_back(last_ms1);
        }
      previous_frame = pair_frame_pgroup.first;
      qDebug() << pair_frame_pgroup.first << " " << m_frameId2GlobalSliceIndexBegin.size();
      FrameSliceRange slice_range;
      qDebug() << pair_frame_pgroup.first;
      slice_range.frame_id                                     = pair_frame_pgroup.first;
      slice_range.begin_global_slice_index                     = cumul_global_slice;
      m_frameId2GlobalSliceIndexBegin[pair_frame_pgroup.first] = cumul_global_slice;
      m_ms2frameId2Ms1FrameId[pair_frame_pgroup.first]         = last_ms1;
 
      cumul_global_slice += pair_frame_pgroup.second->size();
 
      if(cumul_global_slice > 0)
        slice_range.end_global_slice_index = cumul_global_slice - 1;
      m_frameSliceRangeList.push_back(slice_range);
    }
 
  qDebug();
  m_totalSlicesCount = cumul_global_slice;
}

References m_msMsWindowGroupList, and mp_timsDataOrigin.

◆ ~TimsDiaSlices()

pappso::TimsDiaSlices::~TimsDiaSlices ( )

Destructor

Definition at line 240 of file timsdiaslices.cpp.

241{

242}

References ~TimsDiaSlices().

Referenced by ~TimsDiaSlices().

Member Function Documentation

◆ getCombinedMs2ScansByGlobalSliceIndex()

TimsDataFastMap & pappso::TimsDiaSlices::getCombinedMs2ScansByGlobalSliceIndex ( std::size_t global_slice_index ) const

Definition at line 318 of file timsdiaslices.cpp.

{
 
  qDebug();
  TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
  raw_spectrum.clear();
  try
    {
      FrameSliceRange range = getFrameSliceRangeByGlobalSliceIndex(global_slice_index);
 
      MsMsWindow window = m_mapFrame2WindowGroupPtr.at(range.frame_id)
                            ->at(global_slice_index - range.begin_global_slice_index);
      qDebug();
      TimsFrameCstSPtr tims_frame;
      tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(range.frame_id);
      qDebug();
      /*combiner.combine(combiner_result,
        tims_frame.get()->cumulateScanToTrace(
        scan_mobility_start, scan_mobility_end));*/
      tims_frame.get()->combineScansInTofIndexIntensityMap(
        raw_spectrum, window.ScanNumBegin, window.ScanNumEnd);
      qDebug();
    }
 
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("ERROR in %1 (global_slice_index=%2):\n%3")
                              .arg(__FUNCTION__)
                              .arg(global_slice_index)
                              .arg(error.qwhat()));
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure %1 ").arg(error.what());
    }
  return raw_spectrum;
  qDebug();
}

References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::clear(), pappso::TimsDiaSlices::FrameSliceRange::frame_id, getCombinedMs2ScansByGlobalSliceIndex(), getFrameSliceRangeByGlobalSliceIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), m_mapFrame2WindowGroupPtr, mp_timsDataOrigin, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, and pappso::PappsoException::what().

Referenced by getCombinedMs2ScansByGlobalSliceIndex().

◆ getFrameIdByGlobalSliceIndex()

std::size_t pappso::TimsDiaSlices::getFrameIdByGlobalSliceIndex ( std::size_t global_slice_id ) const

Definition at line 261 of file timsdiaslices.cpp.

{
  return (getFrameSliceRangeByGlobalSliceIndex(global_slice_id).frame_id);
}

References getFrameIdByGlobalSliceIndex(), and getFrameSliceRangeByGlobalSliceIndex().

Referenced by getFrameIdByGlobalSliceIndex().

◆ getFrameSliceRangeByGlobalSliceIndex()

const TimsDiaSlices::FrameSliceRange & pappso::TimsDiaSlices::getFrameSliceRangeByGlobalSliceIndex ( std::size_t global_slice_index ) const

private

Definition at line 267 of file timsdiaslices.cpp.

{
 
  qDebug();
  auto it = std::find_if(m_frameSliceRangeList.cbegin(),
                         m_frameSliceRangeList.cend(),
                         [global_slice_index](const FrameSliceRange &x) {
                           if(global_slice_index < x.begin_global_slice_index)
                             return false;
                           if(global_slice_index > x.end_global_slice_index)
                             return false;
                           return true;
                         });
 
  if(it != m_frameSliceRangeList.cend())
    {
      return *it;
    }
  qDebug();
  throw ExceptionNotFound(
    QObject::tr("ERROR : GlobalSliceIndex %1 not found").arg(global_slice_index));
}

References getFrameSliceRangeByGlobalSliceIndex(), m_frameSliceRangeList, and pappso::x.

Referenced by getCombinedMs2ScansByGlobalSliceIndex(), getFrameIdByGlobalSliceIndex(), getFrameSliceRangeByGlobalSliceIndex(), getMs1QualifiedSpectrumByGlobalSliceIndex(), getMs2QualifiedSpectrumByGlobalSliceIndex(), and getMsMsWindowByGlobalSliceIndex().

◆ getGlobalSliceIndexBeginByFrameId()

std::size_t pappso::TimsDiaSlices::getGlobalSliceIndexBeginByFrameId ( std::size_t frame_id ) const

Definition at line 256 of file timsdiaslices.cpp.

{
  return (m_frameId2GlobalSliceIndexBegin[frame_id]);
}

References getGlobalSliceIndexBeginByFrameId(), and m_frameId2GlobalSliceIndexBegin.

Referenced by getGlobalSliceIndexBeginByFrameId().

◆ getLastMs1FrameIdByMs2FrameId()

std::size_t pappso::TimsDiaSlices::getLastMs1FrameIdByMs2FrameId ( std::size_t frame_id ) const

Definition at line 310 of file timsdiaslices.cpp.

{
 
  return m_ms2frameId2Ms1FrameId.at(frame_id);
}

References getLastMs1FrameIdByMs2FrameId(), and m_ms2frameId2Ms1FrameId.

Referenced by getLastMs1FrameIdByMs2FrameId(), and getMs1QualifiedSpectrumByGlobalSliceIndex().

◆ getMapFrame2WindowGroupPtr()

const std::map< std::size_t, TimsDiaSlices::MsMsWindowGroup * > & pappso::TimsDiaSlices::getMapFrame2WindowGroupPtr ( ) const

Definition at line 245 of file timsdiaslices.cpp.

{
  return m_mapFrame2WindowGroupPtr;
}

References getMapFrame2WindowGroupPtr(), and m_mapFrame2WindowGroupPtr.

Referenced by getMapFrame2WindowGroupPtr().

◆ getMs1QualifiedSpectrumByGlobalSliceIndex()

void pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex	(	const MsRunIdCstSPtr &	msrun_id,
		QualifiedMassSpectrum &	mass_spectrum,
		std::size_t	global_slice_index,
		bool	want_binary_data,
		int	rt_position = 0 ) const

get MS1 spectrum corresponding to the given slice extract MS1 mz range and mobility range corresponding to a global slice

Parameters

msrun_id
mass_spectrum
global_slice_index
want_binary_data
rt_position	relative MS1 frame retention time : 0 latest MS1 frame, +1 next MS1 frame, -1 previous MS1 frame

Definition at line 500 of file timsdiaslices.cpp.

{
 
  qDebug();
  try
    {
      FrameSliceRange range = getFrameSliceRangeByGlobalSliceIndex(global_slice_index);
 
      MsMsWindow window = m_mapFrame2WindowGroupPtr.at(range.frame_id)
                            ->at(global_slice_index - range.begin_global_slice_index);
 
      std::size_t ms1_frame_id = getLastMs1FrameIdByMs2FrameId(range.frame_id);
      if(rt_position != 0)
        {
          std::size_t i = 0;
          for(i = 0; i < m_ms1frameIdList.size(); i++)
            {
              if(m_ms1frameIdList.at(i) == ms1_frame_id)
                break;
            }
          long index = (long)i + rt_position;
          if((index > -1) && (index < (long)m_ms1frameIdList.size()))
            ms1_frame_id = m_ms1frameIdList.at(index);
        }
 
      MassSpectrumId spectrum_id;
 
      spectrum_id.setSpectrumIndex(global_slice_index);
      spectrum_id.setNativeId(
        QString("global_slice_index=%1 frame=%2 begin=%3 end=%4 group=%5 slice=%6")
          .arg(global_slice_index)
          .arg(ms1_frame_id)
          .arg(window.ScanNumBegin)
          .arg(window.ScanNumEnd)
          .arg(window.WindowGroup)
          .arg(window.SliceIndex));
 
      spectrum_id.setMsRunId(msrun_id);
 
      mass_spectrum.setMassSpectrumId(spectrum_id);
 
      mass_spectrum.setMsLevel(1);
      // mass_spectrum.setPrecursorSpectrumIndex(spectrum_descr.ms1_index);
 
      mass_spectrum.setEmptyMassSpectrum(true);
 
      qDebug();
 
      // get precursor ion data
 
      // mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
 
 
      qDebug() << window.ScanNumBegin;
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexBegin,
                                      (qulonglong)window.ScanNumBegin);
 
 
      qDebug() << window.ScanNumEnd;
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexEnd,
                                      (qulonglong)window.ScanNumEnd);
      qDebug();
      TimsFrameBaseCstSPtr tims_frame;
 
 
      if(want_binary_data)
        {
          qDebug() << "bindec";
          tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(ms1_frame_id);
        }
      else
        {
          tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(ms1_frame_id);
        }
      mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
 
 
      mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
        tims_frame.get()->getOneOverK0Transformation(window.ScanNumBegin));
 
      mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0End,
        tims_frame.get()->getOneOverK0Transformation(window.ScanNumEnd));
 
      qDebug();
      /*combiner.combine(combiner_result,
        tims_frame.get()->cumulateScanToTrace(
        scan_mobility_start, scan_mobility_end));*/
      if(want_binary_data)
        {
 
          double mz = (window.IsolationMz - (window.IsolationWidth / 2));
          qDebug() << mz;
 
          quint32 tof_index_begin =
            tims_frame.get()->getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(mz);
 
          mz = (window.IsolationMz + (window.IsolationWidth / 2));
          qDebug() << mz;
          quint32 tof_index_end =
            tims_frame.get()->getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(mz);
 
          qDebug() << "tof_index_begin=" << tof_index_begin << " tof_index_end=" << tof_index_end;
 
          TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
          raw_spectrum.clear();
          tims_frame.get()->combineScansInTofIndexIntensityMap(
            raw_spectrum, window.ScanNumBegin, window.ScanNumEnd, tof_index_begin, tof_index_end);
 
 
          Trace trace;
          if(m_builtinMs2Centroid)
            {
              // raw_spectrum.removeArtefactualSpike();
              raw_spectrum.builtInCentroid();
            }
 
          trace = tims_frame.get()->getTraceFromTofIndexIntensityMap(raw_spectrum);
 
          if(trace.size() > 0)
            {
              mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
              mass_spectrum.setEmptyMassSpectrum(false);
            }
          else
            {
              mass_spectrum.setMassSpectrumSPtr(nullptr);
              mass_spectrum.setEmptyMassSpectrum(true);
            }
        }
      qDebug();
    }
 
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("ERROR in %1 (global_slice_index=%2):\n%3")
                              .arg(__FUNCTION__)
                              .arg(global_slice_index)
                              .arg(error.qwhat()));
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure %1 ").arg(error.what());
    }
  qDebug();
}

References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), getLastMs1FrameIdByMs2FrameId(), getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::TimsDiaSlices::MsMsWindow::IsolationMz, pappso::TimsDiaSlices::MsMsWindow::IsolationWidth, m_builtinMs2Centroid, m_mapFrame2WindowGroupPtr, m_ms1frameIdList, mp_timsDataOrigin, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDiaSlices::MsMsWindow::SliceIndex, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::PappsoException::what(), and pappso::TimsDiaSlices::MsMsWindow::WindowGroup.

Referenced by getMs1QualifiedSpectrumByGlobalSliceIndex().

◆ getMs2QualifiedSpectrumByGlobalSliceIndex()

void pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex	(	const MsRunIdCstSPtr &	msrun_id,
		QualifiedMassSpectrum &	mass_spectrum,
		std::size_t	global_slice_index,
		bool	want_binary_data ) const

Definition at line 357 of file timsdiaslices.cpp.

{
 
  qDebug();
  try
    {
      FrameSliceRange range = getFrameSliceRangeByGlobalSliceIndex(global_slice_index);
 
      MsMsWindow window = m_mapFrame2WindowGroupPtr.at(range.frame_id)
                            ->at(global_slice_index - range.begin_global_slice_index);
 
      MassSpectrumId spectrum_id;
 
      spectrum_id.setSpectrumIndex(global_slice_index);
      spectrum_id.setNativeId(
        QString("global_slice_index=%1 frame=%2 begin=%3 end=%4 group=%5 slice=%6")
          .arg(global_slice_index)
          .arg(range.frame_id)
          .arg(window.ScanNumBegin)
          .arg(window.ScanNumEnd)
          .arg(window.WindowGroup)
          .arg(window.SliceIndex));
 
      spectrum_id.setMsRunId(msrun_id);
 
      mass_spectrum.setMassSpectrumId(spectrum_id);
 
      mass_spectrum.setMsLevel(2);
      // mass_spectrum.setPrecursorSpectrumIndex(spectrum_descr.ms1_index);
 
      mass_spectrum.setEmptyMassSpectrum(true);
 
      qDebug();
 
      // get precursor ion data
 
      // mass_spectrum.appendPrecursorIonData(spectrum_descr.precursor_ion_data);
 
      mass_spectrum.setPrecursorNativeId(QString("frame_id=%1 begin=%2 end=%3 group=%4 slice=%5")
                                           .arg(m_ms2frameId2Ms1FrameId.at(range.frame_id))
                                           .arg(window.ScanNumBegin)
                                           .arg(window.ScanNumEnd)
                                           .arg(window.WindowGroup)
                                           .arg(window.SliceIndex));
 
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationWindowTargetMz,
                                      window.IsolationMz);
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationWindowLowerOffset,
                                      window.IsolationWidth);
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::IsolationWindowUpperOffset,
                                      window.IsolationWidth);
 
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::CollisionEnergy,
                                      window.CollisionEnergy);
 
 
      qDebug() << window.ScanNumBegin;
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexBegin,
                                      (qulonglong)window.ScanNumBegin);
 
 
      qDebug() << window.ScanNumEnd;
      mass_spectrum.setParameterValue(QualifiedMassSpectrumParameter::TimsFrameIonMobScanIndexEnd,
                                      (qulonglong)window.ScanNumEnd);
      qDebug();
      TimsFrameBaseCstSPtr tims_frame;
 
 
      if(want_binary_data)
        {
          qDebug() << "bindec";
          tims_frame = mp_timsDataOrigin->getTimsFrameCstSPtrCached(range.frame_id);
        }
      else
        {
          tims_frame = mp_timsDataOrigin->getTimsFrameBaseCstSPtrCached(range.frame_id);
        }
 
      mass_spectrum.setRtInSeconds(tims_frame.get()->getRtInSeconds());
 
 
      mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0Begin,
        tims_frame.get()->getOneOverK0Transformation(window.ScanNumBegin));
 
      mass_spectrum.setParameterValue(
        QualifiedMassSpectrumParameter::IonMobOneOverK0End,
        tims_frame.get()->getOneOverK0Transformation(window.ScanNumEnd));
 
      qDebug();
      /*combiner.combine(combiner_result,
        tims_frame.get()->cumulateScanToTrace(
        scan_mobility_start, scan_mobility_end));*/
      if(want_binary_data)
        {
 
          TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
          raw_spectrum.clear();
          tims_frame.get()->combineScansInTofIndexIntensityMap(
            raw_spectrum, window.ScanNumBegin, window.ScanNumEnd);
 
 
          Trace trace;
          if(m_builtinMs2Centroid)
            {
              // raw_spectrum.removeArtefactualSpike();
              raw_spectrum.builtInCentroid();
            }
 
          trace = tims_frame.get()->getTraceFromTofIndexIntensityMap(raw_spectrum);
 
          if(trace.size() > 0)
            {
              mass_spectrum.setMassSpectrumSPtr(MassSpectrum(trace).makeMassSpectrumSPtr());
              mass_spectrum.setEmptyMassSpectrum(false);
            }
          else
            {
              mass_spectrum.setMassSpectrumSPtr(nullptr);
              mass_spectrum.setEmptyMassSpectrum(true);
            }
        }
      qDebug();
    }
 
  catch(PappsoException &error)
    {
      throw PappsoException(QObject::tr("ERROR in %1 (global_slice_index=%2):\n%3")
                              .arg(__FUNCTION__)
                              .arg(global_slice_index)
                              .arg(error.qwhat()));
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure %1 ").arg(error.what());
    }
  qDebug();
}

References pappso::TimsDiaSlices::FrameSliceRange::begin_global_slice_index, pappso::TimsDataFastMap::builtInCentroid(), pappso::TimsDataFastMap::clear(), pappso::CollisionEnergy, pappso::TimsDiaSlices::MsMsWindow::CollisionEnergy, pappso::TimsDiaSlices::FrameSliceRange::frame_id, getFrameSliceRangeByGlobalSliceIndex(), getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::IonMobOneOverK0Begin, pappso::IonMobOneOverK0End, pappso::TimsDiaSlices::MsMsWindow::IsolationMz, pappso::TimsDiaSlices::MsMsWindow::IsolationWidth, pappso::IsolationWindowLowerOffset, pappso::IsolationWindowTargetMz, pappso::IsolationWindowUpperOffset, m_builtinMs2Centroid, m_mapFrame2WindowGroupPtr, m_ms2frameId2Ms1FrameId, mp_timsDataOrigin, pappso::PappsoException::qwhat(), pappso::TimsDiaSlices::MsMsWindow::ScanNumBegin, pappso::TimsDiaSlices::MsMsWindow::ScanNumEnd, pappso::QualifiedMassSpectrum::setEmptyMassSpectrum(), pappso::QualifiedMassSpectrum::setMassSpectrumId(), pappso::QualifiedMassSpectrum::setMassSpectrumSPtr(), pappso::QualifiedMassSpectrum::setMsLevel(), pappso::MassSpectrumId::setMsRunId(), pappso::MassSpectrumId::setNativeId(), pappso::QualifiedMassSpectrum::setParameterValue(), pappso::QualifiedMassSpectrum::setPrecursorNativeId(), pappso::QualifiedMassSpectrum::setRtInSeconds(), pappso::MassSpectrumId::setSpectrumIndex(), pappso::TimsDiaSlices::MsMsWindow::SliceIndex, pappso::TimsFrameIonMobScanIndexBegin, pappso::TimsFrameIonMobScanIndexEnd, pappso::PappsoException::what(), and pappso::TimsDiaSlices::MsMsWindow::WindowGroup.

Referenced by getMs2QualifiedSpectrumByGlobalSliceIndex().

◆ getMsMsWindowByGlobalSliceIndex()

const TimsDiaSlices::MsMsWindow & pappso::TimsDiaSlices::getMsMsWindowByGlobalSliceIndex ( std::size_t global_slice_index ) const

Definition at line 297 of file timsdiaslices.cpp.

{
  qDebug() << global_slice_index;
  const TimsDiaSlices::FrameSliceRange &range =
    getFrameSliceRangeByGlobalSliceIndex(global_slice_index);
 
  qDebug() << "range.frame_id=" << range.frame_id
           << " range.begin_global_slice_index=" << range.begin_global_slice_index;
  return m_mapFrame2WindowGroupPtr.at(range.frame_id)
    ->at(global_slice_index - range.begin_global_slice_index);
}