libpappsomspp
Library for mass spectrometry
pappso::TimsFrameBase Class Reference

#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:
pappso::TimsFrame

Public Member Functions

 TimsFrameBase (std::size_t timsId, quint32 scanNum)
 constructor for binary independant tims frame More...
 
 TimsFrameBase (const TimsFrameBase &other)
 
 ~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 More...
 
virtual std::size_t getNbrPeaks (std::size_t scanNum) const
 
virtual MassSpectrumSPtr getMassSpectrumSPtr (std::size_t scanNum) const
 
virtual Trace cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const
 
virtual void cumulateScansInRawMap (std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const
 cumulate scan list into a trace into a raw spectrum map More...
 
bool checkScanNum (std::size_t scanNum) const
 
void setAccumulationTime (double accumulation_time_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 setTime (double time)
 
void setMsMsType (quint8 type)
 
unsigned int getMsLevel () const
 
double getTime () const
 
std::size_t getId () const
 
double getDriftTime (std::size_t scanNum) const
 get drift time of a scan number in milliseconds More...
 
double getOneOverK0Transformation (std::size_t scanNum) const
 get 1/K0 value of a given scan (mobility value) More...
 
std::size_t getScanNumFromOneOverK0 (double one_over_k0) const
 get the scan number from a given 1/Ko mobility value More...
 
double getVoltageTransformation (std::size_t scanNum) const
 
pappso::Trace getTraceFromCumulatedScans (std::map< quint32, quint32 > &accumulated_scans) const
 transform accumulation of raw scans into a real mass spectrum More...
 
pappso::Trace getTraceFromCumulatedScansBuiltinCentroid (std::map< quint32, quint32 > &accumulated_scans) const
 transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers More...
 
virtual const MzCalibrationInterfaceSPtrgetMzCalibrationInterfaceSPtr () const final
 get the MzCalibration model to compute mz and TOF for this frame More...
 
void setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)
 

Protected Attributes

quint32 m_scanNumber
 total number of scans contained in this frame More...
 
std::size_t m_timsId
 Tims frame database id (the SQL identifier of this frame) More...
 
double m_accumulationTime = 0
 accumulation time in milliseconds More...
 
quint8 m_msMsType = 0
 
double m_time = 0
 retention time More...
 
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 47 of file timsframebase.h.

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

pappso::TimsFrameBase::TimsFrameBase ( std::size_t  timsId,
quint32  scanNum 
)

constructor for binary independant tims frame

Parameters
timsIdtims frame identifier in the database
scanNumthe total number of scans contained in this frame

Definition at line 37 of file timsframebase.cpp.

38 {
39  qDebug() << timsId;
40  m_timsId = timsId;
41 
42  m_scanNumber = scanNum;
43 }

References m_scanNumber, and m_timsId.

◆ TimsFrameBase() [2/2]

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

Copy constructor

Parameters
otherTODO

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )

Destructor

Definition at line 49 of file timsframebase.cpp.

50 {
51 }

Member Function Documentation

◆ checkScanNum()

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

Definition at line 101 of file timsframebase.cpp.

102 {
103  if(scanNum >= m_scanNumber)
104  {
106  QObject::tr("Invalid scan number : scanNum%1 > m_scanNumber")
107  .arg(scanNum));
108  }
109 
110  return true;
111 }

References m_scanNumber.

Referenced by pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrame::getNbrPeaks(), pappso::TimsFrame::getScanIndexList(), and pappso::TimsFrame::getScanIntensities().

◆ cumulateScansInRawMap()

void pappso::TimsFrameBase::cumulateScansInRawMap ( std::map< quint32, quint32 > &  rawSpectrum,
std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

cumulate scan list into a trace into a raw spectrum map

Parameters
rawSpectrumsimple map of integers to cumulate raw counts
scanNumBeginfirst scan to cumulate
scanNumEndlast scan to cumulate

Reimplemented in pappso::TimsFrame.

Definition at line 141 of file timsframebase.cpp.

145 {
146  throw PappsoException(
147  QObject::tr(
148  "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
149  "number begin %1 end %2")
150  .arg(scanNumBegin)
151  .arg(scanNumEnd));
152 }

◆ cumulateScanToTrace()

Trace pappso::TimsFrameBase::cumulateScanToTrace ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 131 of file timsframebase.cpp.

133 {
134  throw PappsoException(
135  QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
136  "number begin %1 end %2")
137  .arg(scanNumBegin)
138  .arg(scanNumEnd));
139 }

◆ getDriftTime()

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

get drift time of a scan number in milliseconds

Parameters
scanNumthe scan number
Returns
time in milliseconds of mobility delay (drift time)

Definition at line 240 of file timsframebase.cpp.

241 {
242  return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
243 }

References m_accumulationTime, and m_scanNumber.

◆ getId()

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

Definition at line 182 of file timsframebase.cpp.

183 {
184  return m_timsId;
185 }

References m_timsId.

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::TimsFrameBase::getMassSpectrumSPtr ( std::size_t  scanNum) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 123 of file timsframebase.cpp.

124 {
125  throw PappsoException(
126  QObject::tr(
127  "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
128  .arg(scanNum));
129 }

◆ getMsLevel()

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

Definition at line 168 of file timsframebase.cpp.

169 {
170  if(m_msMsType == 0)
171  return 1;
172  return 2;
173 }

References m_msMsType.

◆ getMzCalibrationInterfaceSPtr()

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

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

Definition at line 420 of file timsframebase.cpp.

421 {
422  if(msp_mzCalibration == nullptr)
423  {
424 
426  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
427  .arg(__FILE__)
428  .arg(__FUNCTION__)
429  .arg(__LINE__));
430  }
431  return msp_mzCalibration;
432 }

References msp_mzCalibration.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), pappso::TimsFrame::cumulateScanToTrace(), pappso::TimsFrame::getMassSpectrumSPtr(), getTraceFromCumulatedScans(), and getTraceFromCumulatedScansBuiltinCentroid().

◆ getNbrPeaks()

std::size_t pappso::TimsFrameBase::getNbrPeaks ( std::size_t  scanNum) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 114 of file timsframebase.cpp.

115 {
116  throw PappsoException(
117  QObject::tr(
118  "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
119  .arg(scanNum));
120 }

◆ getOneOverK0Transformation()

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

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

Parameters
scanNumthe scan number

Definition at line 246 of file timsframebase.cpp.

247 {
248  return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
249 }

References getVoltageTransformation(), m_timsC6, and m_timsC7.

◆ getScanNumFromOneOverK0()

std::size_t pappso::TimsFrameBase::getScanNumFromOneOverK0 ( double  one_over_k0) const

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

Parameters
one_over_k0the mobility value to tranform
Returns
integer the scan number

Definition at line 253 of file timsframebase.cpp.

254 {
255  double temp = 1 / one_over_k0;
256  temp = temp - m_timsC6;
257  temp = temp / m_timsC7;
258  temp = 1 / temp;
259  temp = temp - m_timsDvStart;
260  temp = temp / m_timsSlope + m_timsTtrans + m_timsNdelay;
261  return (std::size_t)std::round(temp);
262 }

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

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 176 of file timsframebase.cpp.

177 {
178  return m_time;
179 }

References m_time.

◆ getTraceFromCumulatedScans()

pappso::Trace pappso::TimsFrameBase::getTraceFromCumulatedScans ( std::map< quint32, quint32 > &  accumulated_scans) const

transform accumulation of raw scans into a real mass spectrum

Definition at line 280 of file timsframebase.cpp.

282 {
283  qDebug();
284  // qDebug();
285  // add flanking peaks
286  pappso::Trace local_trace;
287 
288  MzCalibrationInterface *mz_calibration_p =
290 
291 
292  DataPoint element;
293  for(auto &scan_element : accumulated_scans)
294  {
295  // intensity normalization
296  element.y = ((double)scan_element.second) * 100.0 / m_accumulationTime;
297 
298  // mz calibration
299  element.x = mz_calibration_p->getMzFromTofIndex(scan_element.first);
300 
301  local_trace.push_back(element);
302  }
303  local_trace.sortX();
304 
305  qDebug();
306  // qDebug();
307  return local_trace;
308 }

References getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), m_accumulationTime, pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getTraceFromCumulatedScansBuiltinCentroid()

pappso::Trace pappso::TimsFrameBase::getTraceFromCumulatedScansBuiltinCentroid ( std::map< quint32, quint32 > &  accumulated_scans) const

transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers

Definition at line 311 of file timsframebase.cpp.

313 {
314  qDebug();
315  // qDebug();
316  // add flanking peaks
317  std::vector<quint32> keys;
318  transform(begin(accumulated_scans),
319  end(accumulated_scans),
320  back_inserter(keys),
321  [](std::map<quint32, quint32>::value_type const &pair) {
322  return pair.first;
323  });
324  std::sort(keys.begin(), keys.end());
325  pappso::DataPoint data_point_cumul;
326  data_point_cumul.x = 0;
327  data_point_cumul.y = 0;
328 
329  pappso::Trace local_trace;
330 
331  MzCalibrationInterface *mz_calibration_p =
333 
334 
335  quint32 last_key = 0;
336 
337  for(quint32 key : keys)
338  {
339  if(key == last_key + 1)
340  {
341  // cumulate
342  if(accumulated_scans[key] > accumulated_scans[last_key])
343  {
344  if(data_point_cumul.x == last_key)
345  {
346  // growing peak
347  data_point_cumul.x = key;
348  data_point_cumul.y += accumulated_scans[key];
349  }
350  else
351  {
352  // new peak
353  // flush
354  if(data_point_cumul.y > 0)
355  {
356  // intensity normalization
357  data_point_cumul.y *= 100.0 / m_accumulationTime;
358 
359 
360  // mz calibration
361  data_point_cumul.x =
362  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
363  local_trace.push_back(data_point_cumul);
364  }
365 
366  // new point
367  data_point_cumul.x = key;
368  data_point_cumul.y = accumulated_scans[key];
369  }
370  }
371  else
372  {
373  data_point_cumul.y += accumulated_scans[key];
374  }
375  }
376  else
377  {
378  // flush
379  if(data_point_cumul.y > 0)
380  {
381  // intensity normalization
382  data_point_cumul.y *= 100.0 / m_accumulationTime;
383 
384 
385  qDebug() << "raw data x=" << data_point_cumul.x;
386  // mz calibration
387  data_point_cumul.x =
388  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
389  qDebug() << "mz=" << data_point_cumul.x;
390  local_trace.push_back(data_point_cumul);
391  }
392 
393  // new point
394  data_point_cumul.x = key;
395  data_point_cumul.y = accumulated_scans[key];
396  }
397 
398  last_key = key;
399  }
400  // flush
401  if(data_point_cumul.y > 0)
402  {
403  // intensity normalization
404  data_point_cumul.y *= 100.0 / m_accumulationTime;
405 
406 
407  // mz calibration
408  data_point_cumul.x =
409  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
410  local_trace.push_back(data_point_cumul);
411  }
412 
413  local_trace.sortX();
414  qDebug();
415  // qDebug();
416  return local_trace;
417 }

References getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), m_accumulationTime, pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getVoltageTransformation()

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

Definition at line 218 of file timsframebase.cpp.

219 {
220  double v = m_timsDvStart +
221  m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
222 
223  if(v < m_timsVmin)
224  {
226  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
227  "calibration, v < m_timsVmin"));
228  }
229 
230 
231  if(v > m_timsVmax)
232  {
234  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
235  "calibration, v > m_timsVmax"));
236  }
237  return v;
238 }

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 265 of file timsframebase.cpp.

266 {
267  if((m_timsDvStart == other.m_timsDvStart) &&
268  (m_timsTtrans == other.m_timsTtrans) &&
269  (m_timsNdelay == other.m_timsNdelay) && (m_timsVmin == other.m_timsVmin) &&
270  (m_timsVmax == other.m_timsVmax) && (m_timsC6 == other.m_timsC6) &&
271  (m_timsC7 == other.m_timsC7) && (m_timsSlope == other.m_timsSlope))
272  {
273  return true;
274  }
275  return false;
276 }

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

◆ setAccumulationTime()

void pappso::TimsFrameBase::setAccumulationTime ( double  accumulation_time_ms)

Definition at line 54 of file timsframebase.cpp.

55 {
56  m_accumulationTime = accumulation_time_ms;
57 }

References m_accumulationTime.

◆ setMsMsType()

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

Definition at line 160 of file timsframebase.cpp.

161 {
162 
163  qDebug() << " m_msMsType=" << type;
164  m_msMsType = type;
165 }

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 61 of file timsframebase.cpp.

74 {
75 
76  /* MzCalibrationModel1 mzCalibration(temperature_correction,
77  digitizerTimebase,
78  digitizerDelay,
79  C0,
80  C1,
81  C2,
82  C3,
83  C4);
84  */
85  msp_mzCalibration = std::make_shared<MzCalibrationModel1>(T1_frame,
86  T2_frame,
87  digitizerTimebase,
88  digitizerDelay,
89  C0,
90  C1,
91  C2,
92  C3,
93  C4,
94  T1_ref,
95  T2_ref,
96  dC1,
97  dC2);
98 }

References msp_mzCalibration.

◆ setMzCalibrationInterfaceSPtr()

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

Definition at line 435 of file timsframebase.cpp.

437 {
438 
439  if(mzCalibration == nullptr)
440  {
441 
443  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
444  .arg(__FILE__)
445  .arg(__FUNCTION__)
446  .arg(__LINE__));
447  }
448  msp_mzCalibration = mzCalibration;
449 }

References msp_mzCalibration.

◆ setTime()

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

Definition at line 154 of file timsframebase.cpp.

155 {
156  m_time = time;
157 }

References m_time.

◆ 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 187 of file timsframebase.cpp.

198 {
199  if(tims_model_type != 2)
200  {
201  throw pappso::PappsoException(QObject::tr(
202  "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
203  }
204  m_timsDvStart = C2; // C2 from TimsCalibration
205  m_timsTtrans = C4; // C4 from TimsCalibration
206  m_timsNdelay = C0; // C0 from TimsCalibration
207  m_timsVmin = C8; // C8 from TimsCalibration
208  m_timsVmax = C9; // C9 from TimsCalibration
209  m_timsC6 = C6;
210  m_timsC7 = C7;
211 
212 
213  m_timsSlope =
214  (C3 - m_timsDvStart) / C1; // //C3 from TimsCalibration // C2 from
215  // TimsCalibration // C1 from TimsCalibration
216 }

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

Member Data Documentation

◆ m_accumulationTime

double pappso::TimsFrameBase::m_accumulationTime = 0
protected

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0
protected

Definition at line 177 of file timsframebase.h.

Referenced by getMsLevel(), and setMsMsType().

◆ m_scanNumber

quint32 pappso::TimsFrameBase::m_scanNumber
protected

total number of scans contained in this frame

Definition at line 165 of file timsframebase.h.

Referenced by pappso::TimsFrame::TimsFrame(), TimsFrameBase(), checkScanNum(), getDriftTime(), and pappso::TimsFrame::getNbrPeaks().

◆ m_time

double pappso::TimsFrameBase::m_time = 0
protected

retention time

Definition at line 181 of file timsframebase.h.

Referenced by pappso::TimsFrame::extractTimsXicListInRtRange(), getTime(), and setTime().

◆ m_timsC6

double pappso::TimsFrameBase::m_timsC6 = 0
protected

◆ m_timsC7

double pappso::TimsFrameBase::m_timsC7 = 0
protected

◆ m_timsDvStart

double pappso::TimsFrameBase::m_timsDvStart = 0
protected

◆ m_timsId

std::size_t pappso::TimsFrameBase::m_timsId
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 171 of file timsframebase.h.

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

◆ m_timsNdelay

double pappso::TimsFrameBase::m_timsNdelay = 0
protected

◆ m_timsSlope

double pappso::TimsFrameBase::m_timsSlope
protected

◆ m_timsTtrans

double pappso::TimsFrameBase::m_timsTtrans = 0
protected

◆ m_timsVmax

double pappso::TimsFrameBase::m_timsVmax = 0
protected

◆ m_timsVmin

double pappso::TimsFrameBase::m_timsVmin = 0
protected

◆ msp_mzCalibration

MzCalibrationInterfaceSPtr pappso::TimsFrameBase::msp_mzCalibration = nullptr
protected

The documentation for this class was generated from the following files:
pappso::TimsFrameBase::m_timsId
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
Definition: timsframebase.h:171
pappso::TimsFrameBase::msp_mzCalibration
MzCalibrationInterfaceSPtr msp_mzCalibration
Definition: timsframebase.h:194
pappso::DataPoint::y
pappso_double y
Definition: datapoint.h:23
pappso::TimsFrameBase::m_timsSlope
double m_timsSlope
Definition: timsframebase.h:184
pappso::TimsFrameBase::m_timsC7
double m_timsC7
Definition: timsframebase.h:192
pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
Definition: timsframebase.cpp:420
pappso::DataPoint
Definition: datapoint.h:21
pappso::TimsFrameBase::m_accumulationTime
double m_accumulationTime
accumulation time in milliseconds
Definition: timsframebase.h:175
pappso::TimsFrameBase::m_time
double m_time
retention time
Definition: timsframebase.h:181
pappso::ExceptionOutOfRange
Definition: exceptionoutofrange.h:32
pappso::Trace
A simple container of DataPoint instances.
Definition: trace.h:132
pappso::TimsFrameBase::getVoltageTransformation
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Definition: timsframebase.cpp:218
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Definition: timsframebase.h:183
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Definition: datapoint.h:22
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Definition: trace.cpp:792
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Definition: timsframebase.h:188
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Definition: timsframebase.h:189
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total number of scans contained in this frame
Definition: timsframebase.h:165
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Definition: timsframebase.h:191
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Definition: timsframebase.h:177
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Definition: timsframebase.h:190
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Definition: pappsoexception.h:42