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 The intensities are normalized with respect to the frame accumulation time 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 The intensities are NOT normalized with respect to the frame accumulation time More...
 
virtual quint64 cumulateSingleScanIntensities (std::size_t scanNum) const
 
virtual quint64 cumulateScansIntensities (std::size_t scanNumBegin, std::size_t scanNumEnd) const
 
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 39 of file timsframebase.cpp.

40 {
41  qDebug() << timsId;
42  m_timsId = timsId;
43 
44  m_scanNumber = scanNum;
45 }
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 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
scanNumscan 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.

104 {
105  if(scanNum >= m_scanNumber)
106  {
108  QObject::tr("Invalid scan number : scanNum %1 > m_scanNumber %2")
109  .arg(scanNum)
110  .arg(m_scanNumber));
111  }
112 
113  return true;
114 }

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 The intensities are NOT normalized with respect to the frame accumulation time

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 151 of file timsframebase.cpp.

155 {
156  throw PappsoException(
157  QObject::tr(
158  "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
159  "number begin %1 end %2")
160  .arg(scanNumBegin)
161  .arg(scanNumEnd));
162 }

◆ cumulateScansIntensities()

quint64 pappso::TimsFrameBase::cumulateScansIntensities ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 178 of file timsframebase.cpp.

180 {
181  throw PappsoException(
182  QObject::tr(
183  "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
184  "number begin %1 end %2")
185  .arg(scanNumBegin)
186  .arg(scanNumEnd));
187 
188  return 0;
189 }

◆ 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 The intensities are normalized with respect to the frame accumulation time

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 140 of file timsframebase.cpp.

142 {
143  throw PappsoException(
144  QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
145  "number begin %1 end %2")
146  .arg(scanNumBegin)
147  .arg(scanNumEnd));
148 }

◆ cumulateSingleScanIntensities()

quint64 pappso::TimsFrameBase::cumulateSingleScanIntensities ( std::size_t  scanNum) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 166 of file timsframebase.cpp.

167 {
168  throw PappsoException(
169  QObject::tr(
170  "ERROR unable to cumulateSingleScanIntensities in TimsFrameBase for scan "
171  "number %1.").arg(scanNum));
172 
173  return 0;
174 }

◆ 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 278 of file timsframebase.cpp.

279 {
280  return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
281 }
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 527 of file timsframebase.cpp.

531 {
532  Trace im_trace;
533  DataPoint data_point;
534  for(quint32 i = 0; i < m_scanNumber; i++)
535  {
536  data_point.x = i;
537  data_point.y = 0;
538  qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
539  std::vector<quint32> index_list = getScanIndexList(i);
540  auto it_lower = std::find_if(index_list.begin(),
541  index_list.end(),
542  [mz_index_lower_bound](quint32 to_compare) {
543  if(to_compare < mz_index_lower_bound)
544  {
545  return false;
546  }
547  return true;
548  });
549 
550 
551  if(it_lower == index_list.end())
552  {
553  }
554  else
555  {
556 
557 
558  auto it_upper =
559  std::find_if(index_list.begin(),
560  index_list.end(),
561  [mz_index_upper_bound](quint32 to_compare) {
562  if(mz_index_upper_bound >= to_compare)
563  {
564  return false;
565  }
566  return true;
567  });
568  std::vector<quint32> intensity_list = getScanIntensities(i);
569  for(int j = std::distance(index_list.begin(), it_lower);
570  j < std::distance(index_list.begin(), it_upper);
571  j++)
572  {
573  if(method == XicExtractMethod::sum)
574  {
575  data_point.y += intensity_list[j];
576  }
577  else
578  {
579  data_point.y =
580  std::max((double)intensity_list[j], data_point.y);
581  }
582  }
583  }
584  im_trace.push_back(data_point);
585  }
586  qDebug();
587  return im_trace;
588 }
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 132 of file timsframebase.cpp.

133 {
134  throw PappsoException(
135  QObject::tr(
136  "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
137  .arg(scanNum));
138 }

◆ getMaximumRawMassIndex()

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

get the maximum raw mass index contained in this frame

Definition at line 491 of file timsframebase.cpp.

492 {
493  quint32 max_value = 0;
494  for(quint32 i = 0; i < m_scanNumber; i++)
495  {
496  qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
497  std::vector<quint32> index_list = getScanIndexList(i);
498  auto it = std::max_element(index_list.begin(), index_list.end());
499  if(it != index_list.end())
500  {
501  max_value = std::max(max_value, *it);
502  }
503  }
504  return max_value;
505 }

References getScanIndexList(), and m_scanNumber.

◆ getMsLevel()

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

Definition at line 206 of file timsframebase.cpp.

207 {
208  if(m_msMsType == 0)
209  return 1;
210  return 2;
211 }

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 458 of file timsframebase.cpp.

459 {
460  if(msp_mzCalibration == nullptr)
461  {
462 
464  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
465  .arg(__FILE__)
466  .arg(__FUNCTION__)
467  .arg(__LINE__));
468  }
469  return msp_mzCalibration;
470 }
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 117 of file timsframebase.cpp.

118 {
119  throw PappsoException(
120  QObject::tr(
121  "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
122  .arg(scanNum));
123 }

◆ 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 284 of file timsframebase.cpp.

285 {
286  return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
287 }
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 508 of file timsframebase.cpp.

509 {
510  throw PappsoException(
511  QObject::tr(
512  "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
513  .arg(scanNum));
514 }

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 518 of file timsframebase.cpp.

519 {
520  throw PappsoException(
521  QObject::tr(
522  "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
523  .arg(scanNum));
524 }

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 291 of file timsframebase.cpp.

292 {
293  double temp = 1 / one_over_k0;
294  temp = temp - m_timsC6;
295  temp = temp / m_timsC7;
296  temp = 1 / temp;
297  temp = temp - m_timsDvStart;
298  temp = temp / m_timsSlope + m_timsTtrans + m_timsNdelay;
299  return (std::size_t)std::round(temp);
300 }

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

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 214 of file timsframebase.cpp.

215 {
216  return m_time;
217 }
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 126 of file timsframebase.cpp.

127 {
128  return m_scanNumber;
129 }

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 318 of file timsframebase.cpp.

320 {
321  qDebug();
322  // qDebug();
323  // add flanking peaks
324  pappso::Trace local_trace;
325 
326  MzCalibrationInterface *mz_calibration_p =
328 
329 
330  DataPoint element;
331  for(auto &scan_element : accumulated_scans)
332  {
333  // intensity normalization
334  element.y = ((double)scan_element.second) * 100.0 / m_accumulationTime;
335 
336  // mz calibration
337  element.x = mz_calibration_p->getMzFromTofIndex(scan_element.first);
338 
339  local_trace.push_back(element);
340  }
341  local_trace.sortX();
342 
343  qDebug();
344  // qDebug();
345  return local_trace;
346 }
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:148
void sortX()
Definition: trace.cpp:956

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 349 of file timsframebase.cpp.

351 {
352  qDebug();
353  // qDebug();
354  // add flanking peaks
355  std::vector<quint32> keys;
356  transform(begin(accumulated_scans),
357  end(accumulated_scans),
358  back_inserter(keys),
359  [](std::map<quint32, quint32>::value_type const &pair) {
360  return pair.first;
361  });
362  std::sort(keys.begin(), keys.end());
363  pappso::DataPoint data_point_cumul;
364  data_point_cumul.x = 0;
365  data_point_cumul.y = 0;
366 
367  pappso::Trace local_trace;
368 
369  MzCalibrationInterface *mz_calibration_p =
371 
372 
373  quint32 last_key = 0;
374 
375  for(quint32 key : keys)
376  {
377  if(key == last_key + 1)
378  {
379  // cumulate
380  if(accumulated_scans[key] > accumulated_scans[last_key])
381  {
382  if(data_point_cumul.x == last_key)
383  {
384  // growing peak
385  data_point_cumul.x = key;
386  data_point_cumul.y += accumulated_scans[key];
387  }
388  else
389  {
390  // new peak
391  // flush
392  if(data_point_cumul.y > 0)
393  {
394  // intensity normalization
395  data_point_cumul.y *= 100.0 / m_accumulationTime;
396 
397 
398  // mz calibration
399  data_point_cumul.x =
400  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
401  local_trace.push_back(data_point_cumul);
402  }
403 
404  // new point
405  data_point_cumul.x = key;
406  data_point_cumul.y = accumulated_scans[key];
407  }
408  }
409  else
410  {
411  data_point_cumul.y += accumulated_scans[key];
412  }
413  }
414  else
415  {
416  // flush
417  if(data_point_cumul.y > 0)
418  {
419  // intensity normalization
420  data_point_cumul.y *= 100.0 / m_accumulationTime;
421 
422 
423  // qDebug() << "raw data x=" << data_point_cumul.x;
424  // mz calibration
425  data_point_cumul.x =
426  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
427  // qDebug() << "mz=" << data_point_cumul.x;
428  local_trace.push_back(data_point_cumul);
429  }
430 
431  // new point
432  data_point_cumul.x = key;
433  data_point_cumul.y = accumulated_scans[key];
434  }
435 
436  last_key = key;
437  }
438  // flush
439  if(data_point_cumul.y > 0)
440  {
441  // intensity normalization
442  data_point_cumul.y *= 100.0 / m_accumulationTime;
443 
444 
445  // mz calibration
446  data_point_cumul.x =
447  mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
448  local_trace.push_back(data_point_cumul);
449  }
450 
451  local_trace.sortX();
452  qDebug();
453  // qDebug();
454  return local_trace;
455 }
pappso_double x
Definition: datapoint.h:23
pappso_double y
Definition: datapoint.h:24

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 256 of file timsframebase.cpp.

257 {
258  double v = m_timsDvStart +
259  m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
260 
261  if(v < m_timsVmin)
262  {
264  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
265  "calibration, v < m_timsVmin"));
266  }
267 
268 
269  if(v > m_timsVmax)
270  {
272  QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
273  "calibration, v > m_timsVmax"));
274  }
275  return v;
276 }

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 303 of file timsframebase.cpp.

304 {
305  if((m_timsDvStart == other.m_timsDvStart) &&
306  (m_timsTtrans == other.m_timsTtrans) &&
307  (m_timsNdelay == other.m_timsNdelay) && (m_timsVmin == other.m_timsVmin) &&
308  (m_timsVmax == other.m_timsVmax) && (m_timsC6 == other.m_timsC6) &&
309  (m_timsC7 == other.m_timsC7) && (m_timsSlope == other.m_timsSlope))
310  {
311  return true;
312  }
313  return false;
314 }

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 56 of file timsframebase.cpp.

57 {
58  m_accumulationTime = accumulation_time_ms;
59 }

References m_accumulationTime.

◆ setMsMsType()

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

Definition at line 198 of file timsframebase.cpp.

199 {
200 
201  qDebug() << " m_msMsType=" << type;
202  m_msMsType = type;
203 }

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.

76 {
77 
78  /* MzCalibrationModel1 mzCalibration(temperature_correction,
79  digitizerTimebase,
80  digitizerDelay,
81  C0,
82  C1,
83  C2,
84  C3,
85  C4);
86  */
87  msp_mzCalibration = std::make_shared<MzCalibrationModel1>(T1_frame,
88  T2_frame,
89  digitizerTimebase,
90  digitizerDelay,
91  C0,
92  C1,
93  C2,
94  C3,
95  C4,
96  T1_ref,
97  T2_ref,
98  dC1,
99  dC2);
100 }

References msp_mzCalibration.

◆ setMzCalibrationInterfaceSPtr()

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

Definition at line 473 of file timsframebase.cpp.

475 {
476 
477  if(mzCalibration == nullptr)
478  {
479 
481  QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
482  .arg(__FILE__)
483  .arg(__FUNCTION__)
484  .arg(__LINE__));
485  }
486  msp_mzCalibration = mzCalibration;
487 }

References msp_mzCalibration.

◆ setTime()

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

Definition at line 192 of file timsframebase.cpp.

193 {
194  m_time = time;
195 }

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 225 of file timsframebase.cpp.

236 {
237  if(tims_model_type != 2)
238  {
239  throw pappso::PappsoException(QObject::tr(
240  "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
241  }
242  m_timsDvStart = C2; // C2 from TimsCalibration
243  m_timsTtrans = C4; // C4 from TimsCalibration
244  m_timsNdelay = C0; // C0 from TimsCalibration
245  m_timsVmin = C8; // C8 from TimsCalibration
246  m_timsVmax = C9; // C9 from TimsCalibration
247  m_timsC6 = C6;
248  m_timsC7 = C7;
249 
250 
251  m_timsSlope =
252  (C3 - m_timsDvStart) / C1; // //C3 from TimsCalibration // C2 from
253  // TimsCalibration // C1 from TimsCalibration
254 }

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 253 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 257 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 247 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: