libpappsomspp
Library for mass spectrometry
pappso::TimsFrameBase Class Reference

#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:
pappso::TimsFrame pappso::TimsFrameType1

Public Member Functions

 TimsFrameBase (std::size_t timsId, quint32 scanNum)
 constructor for binary independant tims frame More...
 
 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 More...
 
virtual std::size_t getNbrPeaks (std::size_t scanNum) const
 get the number of peaks in this spectrum need the binary file More...
 
virtual std::size_t getTotalNumberOfScans () const
 get the number of scans contained in this frame each scan represents an ion mobility slice More...
 
virtual quint32 getMaximumRawMassIndex () const
 get the maximum raw mass index contained in this frame More...
 
virtual MassSpectrumSPtr getMassSpectrumSPtr (std::size_t scanNum) const
 get Mass spectrum with peaks for this scan number need the binary file More...
 
virtual Trace cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const
 cumulate spectrum given a scan number range need the binary file More...
 
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
 check that this scan number exists More...
 
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
 get voltage for a given scan number More...
 
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)
 
virtual std::vector< quint32 > getScanIndexList (std::size_t scanNum) const
 get raw index list for one given scan index are not TOF nor m/z, just index on digitizer More...
 
virtual std::vector< quint32 > getScanIntensities (std::size_t scanNum) const
 get raw intensities without transformation from one scan it needs intensity normalization More...
 
virtual Trace getIonMobilityTraceByMzIndexRange (std::size_t mz_index_lower_bound, std::size_t mz_index_upper_bound, XicExtractMethod method) const
 get a mobility trace cumulating intensities inside the given mass index range More...
 

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 38 of file timsframebase.cpp.

39 {
40  qDebug() << timsId;
41  m_timsId = timsId;
42 
43  m_scanNumber = scanNum;
44 }
quint32 m_scanNumber
total number of scans contained in this frame
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)

References m_scanNumber, and m_timsId.

◆ TimsFrameBase() [2/2]

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

Copy constructor

Parameters
otherTODO

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )
virtual

Destructor

Definition at line 50 of file timsframebase.cpp.

51 {
52 }

Member Function Documentation

◆ checkScanNum()

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

check that this scan number exists

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

Definition at line 102 of file timsframebase.cpp.

103 {
104  if(scanNum >= m_scanNumber)
105  {
107  QObject::tr("Invalid scan number : scanNum %1 > m_scanNumber %2")
108  .arg(scanNum)
109  .arg(m_scanNumber));
110  }
111 
112  return true;
113 }

References m_scanNumber.

Referenced by pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), pappso::TimsFrame::getNbrPeaks(), pappso::TimsFrame::getScanIndexList(), pappso::TimsFrameType1::getScanIndexList(), pappso::TimsFrame::getScanIntensities(), and pappso::TimsFrameType1::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
scanNumBeginscan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEndscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 149 of file timsframebase.cpp.

153 {
154  throw PappsoException(
155  QObject::tr(
156  "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
157  "number begin %1 end %2")
158  .arg(scanNumBegin)
159  .arg(scanNumEnd));
160 }

◆ cumulateScanToTrace()

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

cumulate spectrum given a scan number range need the binary file

Parameters
scanNumBeginscan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEndscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 139 of file timsframebase.cpp.

141 {
142  throw PappsoException(
143  QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
144  "number begin %1 end %2")
145  .arg(scanNumBegin)
146  .arg(scanNumEnd));
147 }

◆ getDriftTime()

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

get drift time of a scan number in milliseconds

Parameters
scanNumscan 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 248 of file timsframebase.cpp.

249 {
250  return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
251 }
double m_accumulationTime
accumulation time in milliseconds

References m_accumulationTime, and m_scanNumber.

◆ getId()

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

◆ getIonMobilityTraceByMzIndexRange()

Trace pappso::TimsFrameBase::getIonMobilityTraceByMzIndexRange ( std::size_t  mz_index_lower_bound,
std::size_t  mz_index_upper_bound,
XicExtractMethod  method 
) const
virtual

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

Parameters
mz_index_lower_boundraw mass index lower bound
mz_index_upper_boundraw mass index upper bound
methodmax or sum intensities

Definition at line 497 of file timsframebase.cpp.

501 {
502  Trace im_trace;
503  DataPoint data_point;
504  for(quint32 i = 0; i < m_scanNumber; i++)
505  {
506  data_point.x = i;
507  data_point.y = 0;
508  qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
509  std::vector<quint32> index_list = getScanIndexList(i);
510  auto it_lower = std::find_if(index_list.begin(),
511  index_list.end(),
512  [mz_index_lower_bound](quint32 to_compare) {
513  if(to_compare < mz_index_lower_bound)
514  {
515  return false;
516  }
517  return true;
518  });
519 
520 
521  if(it_lower == index_list.end())
522  {
523  }
524  else
525  {
526 
527 
528  auto it_upper =
529  std::find_if(index_list.begin(),
530  index_list.end(),
531  [mz_index_upper_bound](quint32 to_compare) {
532  if(mz_index_upper_bound >= to_compare)
533  {
534  return false;
535  }
536  return true;
537  });
538  std::vector<quint32> intensity_list = getScanIntensities(i);
539  for(int j = std::distance(index_list.begin(), it_lower);
540  j < std::distance(index_list.begin(), it_upper);
541  j++)
542  {
543  if(method == XicExtractMethod::sum)
544  {
545  data_point.y += intensity_list[j];
546  }
547  else
548  {
549  data_point.y =
550  std::max((double)intensity_list[j], data_point.y);
551  }
552  }
553  }
554  im_trace.push_back(data_point);
555  }
556  qDebug();
557  return im_trace;
558 }
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
@ sum
sum of intensities

References getScanIndexList(), getScanIntensities(), m_scanNumber, pappso::sum, pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getMassSpectrumSPtr()

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

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

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

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

Definition at line 131 of file timsframebase.cpp.

132 {
133  throw PappsoException(
134  QObject::tr(
135  "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
136  .arg(scanNum));
137 }

◆ getMaximumRawMassIndex()

quint32 pappso::TimsFrameBase::getMaximumRawMassIndex ( ) const
virtual

get the maximum raw mass index contained in this frame

Definition at line 461 of file timsframebase.cpp.

462 {
463  quint32 max_value = 0;
464  for(quint32 i = 0; i < m_scanNumber; i++)
465  {
466  qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
467  std::vector<quint32> index_list = getScanIndexList(i);
468  auto it = std::max_element(index_list.begin(), index_list.end());
469  if(it != index_list.end())
470  {
471  max_value = std::max(max_value, *it);
472  }
473  }
474  return max_value;
475 }

References getScanIndexList(), and m_scanNumber.

◆ getMsLevel()

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

Definition at line 176 of file timsframebase.cpp.

177 {
178  if(m_msMsType == 0)
179  return 1;
180  return 2;
181 }

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 428 of file timsframebase.cpp.

429 {
430  if(msp_mzCalibration == nullptr)
431  {
432 
434  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
435  .arg(__FILE__)
436  .arg(__FUNCTION__)
437  .arg(__LINE__));
438  }
439  return msp_mzCalibration;
440 }
MzCalibrationInterfaceSPtr msp_mzCalibration

References msp_mzCalibration.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), pappso::TimsFrame::cumulateScanToTrace(), pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), getTraceFromCumulatedScans(), and getTraceFromCumulatedScansBuiltinCentroid().

◆ getNbrPeaks()

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

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

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

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

Definition at line 116 of file timsframebase.cpp.

117 {
118  throw PappsoException(
119  QObject::tr(
120  "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
121  .arg(scanNum));
122 }

◆ getOneOverK0Transformation()

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

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

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

Definition at line 254 of file timsframebase.cpp.

255 {
256  return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
257 }
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number

References getVoltageTransformation(), m_timsC6, and m_timsC7.

◆ getScanIndexList()

std::vector< quint32 > pappso::TimsFrameBase::getScanIndexList ( std::size_t  scanNum) const
virtual

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

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

Definition at line 478 of file timsframebase.cpp.

479 {
480  throw PappsoException(
481  QObject::tr(
482  "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
483  .arg(scanNum));
484 }

Referenced by getIonMobilityTraceByMzIndexRange(), and getMaximumRawMassIndex().

◆ getScanIntensities()

std::vector< quint32 > pappso::TimsFrameBase::getScanIntensities ( std::size_t  scanNum) const
virtual

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

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

Definition at line 488 of file timsframebase.cpp.

489 {
490  throw PappsoException(
491  QObject::tr(
492  "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
493  .arg(scanNum));
494 }

Referenced by getIonMobilityTraceByMzIndexRange().

◆ 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 in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 261 of file timsframebase.cpp.

262 {
263  double temp = 1 / one_over_k0;
264  temp = temp - m_timsC6;
265  temp = temp / m_timsC7;
266  temp = 1 / temp;
267  temp = temp - m_timsDvStart;
268  temp = temp / m_timsSlope + m_timsTtrans + m_timsNdelay;
269  return (std::size_t)std::round(temp);
270 }

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

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 184 of file timsframebase.cpp.

185 {
186  return m_time;
187 }
double m_time
retention time

References m_time.

◆ 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 125 of file timsframebase.cpp.

126 {
127  return m_scanNumber;
128 }

References m_scanNumber.

Referenced by pappso::BaseColorMapPlotWidget::addColorMap().

◆ 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 288 of file timsframebase.cpp.

290 {
291  qDebug();
292  // qDebug();
293  // add flanking peaks
294  pappso::Trace local_trace;
295 
296  MzCalibrationInterface *mz_calibration_p =
298 
299 
300  DataPoint element;
301  for(auto &scan_element : accumulated_scans)
302  {
303  // intensity normalization
304  element.y = ((double)scan_element.second) * 100.0 / m_accumulationTime;
305 
306  // mz calibration
307  element.x = mz_calibration_p->getMzFromTofIndex(scan_element.first);
308 
309  local_trace.push_back(element);
310  }
311  local_trace.sortX();
312 
313  qDebug();
314  // qDebug();
315  return local_trace;
316 }
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
A simple container of DataPoint instances.
Definition: trace.h:147
void sortX()
Definition: trace.cpp:936

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 319 of file timsframebase.cpp.

321 {
322  qDebug();
323  // qDebug();
324  // add flanking peaks
325  std::vector<quint32> keys;
326  transform(begin(accumulated_scans),
327  end(accumulated_scans),
328  back_inserter(keys),
329  [](std::map<quint32, quint32>::value_type const &pair) {
330  return pair.first;
331  });
332  std::sort(keys.begin(), keys.end());
333  pappso::DataPoint data_point_cumul;
334  data_point_cumul.x = 0;
335  data_point_cumul.y = 0;
336 
337  pappso::Trace local_trace;
338 
339  MzCalibrationInterface *mz_calibration_p =
341 
342 
343  quint32 last_key = 0;
344 
345  for(quint32 key : keys)
346  {
347  if(key == last_key + 1)
348  {
349  // cumulate
350  if(accumulated_scans[key] > accumulated_scans[last_key])
351  {
352  if(data_point_cumul.x == last_key)
353  {
354  // growing peak
355  data_point_cumul.x = key;
356  data_point_cumul.y += accumulated_scans[key];
357  }
358  else
359  {
360  // new peak
361  // flush
362  if(data_point_cumul.y > 0)
363  {
364  // intensity normalization
365  data_point_cumul.y *= 100.0 / m_accumulationTime;
366 
367 
368  // mz calibration
369  data_point_cumul.x =
370  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
371  local_trace.push_back(data_point_cumul);
372  }
373 
374  // new point
375  data_point_cumul.x = key;
376  data_point_cumul.y = accumulated_scans[key];
377  }
378  }
379  else
380  {
381  data_point_cumul.y += accumulated_scans[key];
382  }
383  }
384  else
385  {
386  // flush
387  if(data_point_cumul.y > 0)
388  {
389  // intensity normalization
390  data_point_cumul.y *= 100.0 / m_accumulationTime;
391 
392 
393  // qDebug() << "raw data x=" << data_point_cumul.x;
394  // mz calibration
395  data_point_cumul.x =
396  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
397  // qDebug() << "mz=" << data_point_cumul.x;
398  local_trace.push_back(data_point_cumul);
399  }
400 
401  // new point
402  data_point_cumul.x = key;
403  data_point_cumul.y = accumulated_scans[key];
404  }
405 
406  last_key = key;
407  }
408  // flush
409  if(data_point_cumul.y > 0)
410  {
411  // intensity normalization
412  data_point_cumul.y *= 100.0 / m_accumulationTime;
413 
414 
415  // mz calibration
416  data_point_cumul.x =
417  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
418  local_trace.push_back(data_point_cumul);
419  }
420 
421  local_trace.sortX();
422  qDebug();
423  // qDebug();
424  return local_trace;
425 }
pappso_double x
Definition: datapoint.h:22
pappso_double y
Definition: datapoint.h:23

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

get voltage for a given scan number

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1
Returns
double volt measure

Definition at line 226 of file timsframebase.cpp.

227 {
228  double v = m_timsDvStart +
229  m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
230 
231  if(v < m_timsVmin)
232  {
234  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
235  "calibration, v < m_timsVmin"));
236  }
237 
238 
239  if(v > m_timsVmax)
240  {
242  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
243  "calibration, v > m_timsVmax"));
244  }
245  return v;
246 }

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 273 of file timsframebase.cpp.

274 {
275  if((m_timsDvStart == other.m_timsDvStart) &&
276  (m_timsTtrans == other.m_timsTtrans) &&
277  (m_timsNdelay == other.m_timsNdelay) && (m_timsVmin == other.m_timsVmin) &&
278  (m_timsVmax == other.m_timsVmax) && (m_timsC6 == other.m_timsC6) &&
279  (m_timsC7 == other.m_timsC7) && (m_timsSlope == other.m_timsSlope))
280  {
281  return true;
282  }
283  return false;
284 }

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 55 of file timsframebase.cpp.

56 {
57  m_accumulationTime = accumulation_time_ms;
58 }

References m_accumulationTime.

◆ setMsMsType()

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

Definition at line 168 of file timsframebase.cpp.

169 {
170 
171  qDebug() << " m_msMsType=" << type;
172  m_msMsType = type;
173 }

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 62 of file timsframebase.cpp.

75 {
76 
77  /* MzCalibrationModel1 mzCalibration(temperature_correction,
78  digitizerTimebase,
79  digitizerDelay,
80  C0,
81  C1,
82  C2,
83  C3,
84  C4);
85  */
86  msp_mzCalibration = std::make_shared<MzCalibrationModel1>(T1_frame,
87  T2_frame,
88  digitizerTimebase,
89  digitizerDelay,
90  C0,
91  C1,
92  C2,
93  C3,
94  C4,
95  T1_ref,
96  T2_ref,
97  dC1,
98  dC2);
99 }

References msp_mzCalibration.

◆ setMzCalibrationInterfaceSPtr()

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

Definition at line 443 of file timsframebase.cpp.

445 {
446 
447  if(mzCalibration == nullptr)
448  {
449 
451  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
452  .arg(__FILE__)
453  .arg(__FUNCTION__)
454  .arg(__LINE__));
455  }
456  msp_mzCalibration = mzCalibration;
457 }

References msp_mzCalibration.

◆ setTime()

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

Definition at line 162 of file timsframebase.cpp.

163 {
164  m_time = time;
165 }

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 195 of file timsframebase.cpp.

206 {
207  if(tims_model_type != 2)
208  {
209  throw pappso::PappsoException(QObject::tr(
210  "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
211  }
212  m_timsDvStart = C2; // C2 from TimsCalibration
213  m_timsTtrans = C4; // C4 from TimsCalibration
214  m_timsNdelay = C0; // C0 from TimsCalibration
215  m_timsVmin = C8; // C8 from TimsCalibration
216  m_timsVmax = C9; // C9 from TimsCalibration
217  m_timsC6 = C6;
218  m_timsC7 = C7;
219 
220 
221  m_timsSlope =
222  (C3 - m_timsDvStart) / C1; // //C3 from TimsCalibration // C2 from
223  // TimsCalibration // C1 from TimsCalibration
224 }

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

Member Data Documentation

◆ m_accumulationTime

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0
protected

Definition at line 243 of file timsframebase.h.

Referenced by getMsLevel(), and setMsMsType().

◆ m_scanNumber

◆ m_time

double pappso::TimsFrameBase::m_time = 0
protected

retention time

Definition at line 247 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 237 of file timsframebase.h.

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

◆ 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: