libpappsomspp
Library for mass spectrometry
pappso::TimsFrame Class Reference

#include <timsframe.h>

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

Classes

struct  XicComputeStructure
 

Public Member Functions

 TimsFrame (std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
 
 TimsFrame (const TimsFrame &other)
 
 ~TimsFrame ()
 
virtual std::size_t getNbrPeaks (std::size_t scanNum) const override
 
virtual Trace cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const override
 cumulate scan list into a trace More...
 
virtual void cumulateScansInRawMap (std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
 cumulate scan list into a trace into a raw spectrum map More...
 
void cumulateScans (std::size_t scanNumBegin, std::size_t scanNumEnd, std::map< quint32, quint32 > &accumulate_into) const
 cumulate a scan list into a map of integers More...
 
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...
 
std::vector< quint32 > getScanIntensities (std::size_t scanNum) const
 get raw intensities without transformation from one scan it needs intensity normalization More...
 
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr (std::size_t scanNum) const
 get the mass spectrum corresponding to a scan number More...
 
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr (std::size_t scanNum) const override
 
- Public Member Functions inherited from pappso::TimsFrameBase
 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...
 
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 Member Functions

void extractTimsXicListInRtRange (std::vector< TimsXicStructure >::iterator &itXicListbegin, std::vector< TimsXicStructure >::iterator &itXicListend, XicExtractMethod method) const
 

Private Member Functions

void unshufflePacket (const char *src)
 
std::size_t getScanOffset (std::size_t scanNum) const
 
void cumulateScan (std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
 cumulate a scan into a map More...
 
pappso::TraceSPtr getRawTraceSPtr (std::size_t scanNum) const
 

Private Attributes

friend TimsDirectXicExtractor
 
QByteArray m_timsDataFrame
 

Additional Inherited Members

- Protected Attributes inherited from pappso::TimsFrameBase
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 52 of file timsframe.h.

Constructor & Destructor Documentation

◆ TimsFrame() [1/2]

pappso::TimsFrame::TimsFrame ( std::size_t  timsId,
quint32  scanNum,
char *  p_bytes,
std::size_t  len 
)

Default constructor

Definition at line 57 of file timsframe.cpp.

61  : TimsFrameBase(timsId, scanNum)
62 {
63  // langella@themis:~/developpement/git/bruker/cbuild$
64  // ./src/sample/timsdataSamplePappso
65  // /gorgone/pappso/fichiers_fabricants/Bruker/Demo_TimsTOF_juin2019/Samples/1922001/1922001-1_S-415_Pep_Pur-1ul_Slot1-10_1_2088.d/
66  qDebug() << timsId;
67 
68  m_timsDataFrame.resize(len);
69 
70  if(p_bytes != nullptr)
71  {
72  unshufflePacket(p_bytes);
73  }
74  else
75  {
76  if(m_scanNumber == 0)
77  {
78 
80  QObject::tr("TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
81  .arg(m_timsId)
82  .arg(m_scanNumber)
83  .arg(len));
84  }
85  }
86 }

References pappso::TimsFrameBase::m_scanNumber, m_timsDataFrame, pappso::TimsFrameBase::m_timsId, and unshufflePacket().

◆ TimsFrame() [2/2]

pappso::TimsFrame::TimsFrame ( const TimsFrame other)

Copy constructor

Parameters
otherTODO

Definition at line 88 of file timsframe.cpp.

88  : TimsFrameBase(other)
89 {
90 }

◆ ~TimsFrame()

pappso::TimsFrame::~TimsFrame ( )

Destructor

Definition at line 92 of file timsframe.cpp.

93 {
94 }

Member Function Documentation

◆ cumulateScan()

void pappso::TimsFrame::cumulateScan ( std::size_t  scanNum,
std::map< quint32, quint32 > &  accumulate_into 
) const
private

cumulate a scan into a map

Definition at line 216 of file timsframe.cpp.

218 {
219  qDebug();
220 
221  if(m_timsDataFrame.size() == 0)
222  return;
223  // checkScanNum(scanNum);
224 
225 
226  std::size_t size = getNbrPeaks(scanNum);
227 
228  std::size_t offset = getScanOffset(scanNum);
229 
230  qint32 previous = -1;
231  for(std::size_t i = 0; i < size; i++)
232  {
233  quint32 x =
234  (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
235  previous);
236  quint32 y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
237  (i * 8) + 4));
238 
239  previous = x;
240 
241  auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
242 
243  if(ret.second == false)
244  {
245  // already existed : cumulate
246  ret.first->second += y;
247  }
248  }
249  qDebug();
250 }

References getNbrPeaks(), getScanOffset(), m_timsDataFrame, and pappso::y.

Referenced by cumulateScansInRawMap(), and cumulateScanToTrace().

◆ cumulateScans()

void pappso::TimsFrame::cumulateScans ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd,
std::map< quint32, quint32 > &  accumulate_into 
) const

cumulate a scan list into a map of integers

Parameters
scanNumBeginfirst scan to cumulate
scanNumEndlast scan to cumulate
accumulate_intomap of x and y integer values

◆ cumulateScansInRawMap()

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

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 from pappso::TimsFrameBase.

Definition at line 310 of file timsframe.cpp.

313 {
314  qDebug();
315 
316  if(m_timsDataFrame.size() == 0)
317  return;
318  try
319  {
320 
321  std::size_t imax = scanNumEnd + 1;
322  qDebug();
323  for(std::size_t i = scanNumBegin; i < imax; i++)
324  {
325  qDebug() << i;
326  cumulateScan(i, rawSpectrum);
327  qDebug() << i;
328  // local_accumulationTime += m_accumulationTime;
329  }
330  }
331 
332  catch(std::exception &error)
333  {
334  qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
335  .arg(__FUNCTION__)
336  .arg(scanNumBegin)
337  .arg(scanNumEnd)
338  .arg(error.what());
339  }
340 }

References cumulateScan(), and m_timsDataFrame.

◆ cumulateScanToTrace()

Trace pappso::TimsFrame::cumulateScanToTrace ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
overridevirtual

cumulate scan list into a trace

Parameters
scanNumBeginfirst scan to cumulate
scanNumEndlast scan to cumulate
Returns
Trace mz and intensity values

Reimplemented from pappso::TimsFrameBase.

Definition at line 254 of file timsframe.cpp.

256 {
257  qDebug();
258 
259  Trace new_trace;
260 
261  try
262  {
263  if(m_timsDataFrame.size() == 0)
264  return new_trace;
265  std::map<quint32, quint32> raw_spectrum;
266  // double local_accumulationTime = 0;
267 
268  std::size_t imax = scanNumEnd + 1;
269  qDebug();
270  for(std::size_t i = scanNumBegin; i < imax; i++)
271  {
272  qDebug() << i;
273  cumulateScan(i, raw_spectrum);
274  qDebug() << i;
275  // local_accumulationTime += m_accumulationTime;
276  }
277  qDebug();
278  pappso::DataPoint data_point_cumul;
279 
280 
281  MzCalibrationInterface *mz_calibration_p =
283 
284 
285  for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
286  {
287  data_point_cumul.x =
288  mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
289  // normalization
290  data_point_cumul.y =
291  pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
292  new_trace.push_back(data_point_cumul);
293  }
294  new_trace.sortX();
295  qDebug();
296  }
297 
298  catch(std::exception &error)
299  {
300  qDebug() << QString(
301  "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
302  .arg(scanNumBegin, scanNumEnd)
303  .arg(error.what());
304  }
305  return new_trace;
306 }

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

◆ extractTimsXicListInRtRange()

void pappso::TimsFrame::extractTimsXicListInRtRange ( std::vector< TimsXicStructure >::iterator &  itXicListbegin,
std::vector< TimsXicStructure >::iterator &  itXicListend,
XicExtractMethod  method 
) const
protected

Definition at line 404 of file timsframe.cpp.

408 {
409  std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
410 
411  for(auto it = itXicListbegin; it != itXicListend; it++)
412  {
413  tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, *it));
414  }
415  if(tmp_xic_list.size() == 0)
416  return;
417  /*
418  std::sort(tmp_xic_list.begin(), tmp_xic_list.end(), [](const TimsXicStructure
419  &a, const TimsXicStructure &b) { return a.mobilityIndexBegin <
420  b.mobilityIndexBegin;
421  });
422  */
423  std::vector<std::size_t> unique_scan_num_list;
424  for(auto &&struct_xic : tmp_xic_list)
425  {
426  for(std::size_t scan = struct_xic.mobilityIndexBegin;
427  scan <= struct_xic.mobilityIndexEnd;
428  scan++)
429  {
430  unique_scan_num_list.push_back(scan);
431  }
432  }
433  std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
434  auto it_scan_num_end =
435  std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
436  auto it_scan_num = unique_scan_num_list.begin();
437 
438  while(it_scan_num != it_scan_num_end)
439  {
440  TraceSPtr ms_spectrum = getRawTraceSPtr(*it_scan_num);
441  for(auto &&tmp_xic_struct : tmp_xic_list)
442  {
443  if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
444  ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
445  {
446  if(method == XicExtractMethod::max)
447  {
448  tmp_xic_struct.tmpIntensity +=
449  ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
450  tmp_xic_struct.mzIndexUpperBound);
451  }
452  else
453  {
454  // sum
455  tmp_xic_struct.tmpIntensity +=
456  ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
457  tmp_xic_struct.mzIndexUpperBound);
458  }
459  }
460  }
461  it_scan_num++;
462  }
463 
464  for(auto &&tmp_xic_struct : tmp_xic_list)
465  {
466  if(tmp_xic_struct.tmpIntensity != 0)
467  {
468  tmp_xic_struct.xic_ptr->push_back(
469  {m_time, tmp_xic_struct.tmpIntensity});
470  }
471  }
472 }

References getRawTraceSPtr(), pappso::TimsFrameBase::m_time, and pappso::sum.

◆ getMassSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr pappso::TimsFrame::getMassSpectrumCstSPtr ( std::size_t  scanNum) const

get the mass spectrum corresponding to a scan number

Parameters
scanNumthe scan number to retrieve

Definition at line 344 of file timsframe.cpp.

345 {
346  qDebug();
347  return getMassSpectrumSPtr(scanNum);
348 }

References getMassSpectrumSPtr().

◆ getMassSpectrumSPtr()

pappso::MassSpectrumSPtr pappso::TimsFrame::getMassSpectrumSPtr ( std::size_t  scanNum) const
overridevirtual

Reimplemented from pappso::TimsFrameBase.

Definition at line 351 of file timsframe.cpp.

352 {
353 
354  qDebug() << " scanNum=" << scanNum;
355 
356  checkScanNum(scanNum);
357 
358  qDebug();
359 
360  pappso::MassSpectrumSPtr mass_spectrum_sptr =
361  std::make_shared<pappso::MassSpectrum>();
362  // std::vector<DataPoint>
363 
364  if(m_timsDataFrame.size() == 0)
365  return mass_spectrum_sptr;
366  qDebug();
367 
368  std::size_t size = getNbrPeaks(scanNum);
369 
370  std::size_t offset = getScanOffset(scanNum);
371 
372  MzCalibrationInterface *mz_calibration_p =
374 
375 
376  qint32 previous = -1;
377  qint32 tof_index;
378  std::vector<quint32> index_list;
379  DataPoint data_point;
380  for(std::size_t i = 0; i < size; i++)
381  {
382  tof_index =
383  (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
384  previous);
385  data_point.y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
386  (i * 8) + 4));
387 
388  // intensity normalization
389  data_point.y *= 100.0 / m_accumulationTime;
390 
391  previous = tof_index;
392 
393 
394  // mz calibration
395  data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index);
396  mass_spectrum_sptr.get()->push_back(data_point);
397  }
398  qDebug();
399  return mass_spectrum_sptr;
400 }

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by getMassSpectrumCstSPtr().

◆ getNbrPeaks()

std::size_t pappso::TimsFrame::getNbrPeaks ( std::size_t  scanNum) const
overridevirtual

Reimplemented from pappso::TimsFrameBase.

Definition at line 125 of file timsframe.cpp.

126 {
127  if(m_timsDataFrame.size() == 0)
128  return 0;
129  /*
130  if(scanNum == 0)
131  {
132  quint32 res = (*(quint32 *)(m_timsDataFrame.constData() + 4)) -
133  (*(quint32 *)(m_timsDataFrame.constData()-4));
134  return res / 2;
135  }*/
136  if(scanNum == (m_scanNumber - 1))
137  {
138  auto nb_uint4 = m_timsDataFrame.size() / 4;
139 
140  std::size_t cumul = 0;
141  for(quint32 i = 0; i < m_scanNumber; i++)
142  {
143  cumul += (*(quint32 *)(m_timsDataFrame.constData() + (i * 4)));
144  }
145  return (nb_uint4 - cumul) / 2;
146  }
147  checkScanNum(scanNum);
148 
149  // quint32 *res = (quint32 *)(m_timsDataFrame.constData() + (scanNum * 4));
150  // qDebug() << " res=" << *res;
151  return (*(quint32 *)(m_timsDataFrame.constData() + ((scanNum + 1) * 4))) / 2;
152 }

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::m_scanNumber, and m_timsDataFrame.

Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().

◆ getRawTraceSPtr()

pappso::TraceSPtr pappso::TimsFrame::getRawTraceSPtr ( std::size_t  scanNum) const
private

Definition at line 476 of file timsframe.cpp.

477 {
478 
479  qDebug();
480 
481  pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
482  // std::vector<DataPoint>
483 
484  if(m_timsDataFrame.size() == 0)
485  return trace_sptr;
486  qDebug();
487 
488  std::size_t size = getNbrPeaks(scanNum);
489 
490  std::size_t offset = getScanOffset(scanNum);
491 
492  qint32 previous = -1;
493  std::vector<quint32> index_list;
494  for(std::size_t i = 0; i < size; i++)
495  {
496  DataPoint data_point(
497  (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
498  previous),
499  (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8) +
500  4)));
501 
502  // intensity normalization
503  data_point.y *= 100.0 / m_accumulationTime;
504 
505  previous = data_point.x;
506  }
507  qDebug();
508  return trace_sptr;
509 }

References getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by extractTimsXicListInRtRange().

◆ getScanIndexList()

std::vector< quint32 > pappso::TimsFrame::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

Definition at line 167 of file timsframe.cpp.

168 {
169  qDebug();
170  checkScanNum(scanNum);
171  std::vector<quint32> scan_tof;
172 
173  if(m_timsDataFrame.size() == 0)
174  return scan_tof;
175  scan_tof.resize(getNbrPeaks(scanNum));
176 
177  std::size_t offset = getScanOffset(scanNum);
178 
179  qint32 previous = -1;
180  for(std::size_t i = 0; i < scan_tof.size(); i++)
181  {
182  scan_tof[i] =
183  (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
184  previous;
185  previous = scan_tof[i];
186  }
187  qDebug();
188  return scan_tof;
189 }

References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.

◆ getScanIntensities()

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

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

Definition at line 192 of file timsframe.cpp.

193 {
194  qDebug();
195  checkScanNum(scanNum);
196  std::vector<quint32> scan_intensities;
197 
198  if(m_timsDataFrame.size() == 0)
199  return scan_intensities;
200 
201  scan_intensities.resize(getNbrPeaks(scanNum));
202 
203  std::size_t offset = getScanOffset(scanNum);
204 
205  for(std::size_t i = 0; i < scan_intensities.size(); i++)
206  {
207  scan_intensities[i] = (*(quint32 *)(m_timsDataFrame.constData() +
208  (offset * 4) + (i * 8) + 4));
209  }
210  qDebug();
211  return scan_intensities;
212 }

References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.

◆ getScanOffset()

std::size_t pappso::TimsFrame::getScanOffset ( std::size_t  scanNum) const
private

Definition at line 155 of file timsframe.cpp.

156 {
157  std::size_t offset = 0;
158  for(std::size_t i = 0; i < (scanNum + 1); i++)
159  {
160  offset += (*(quint32 *)(m_timsDataFrame.constData() + (i * 4)));
161  }
162  return offset;
163 }

References m_timsDataFrame.

Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().

◆ unshufflePacket()

void pappso::TimsFrame::unshufflePacket ( const char *  src)
private

Definition at line 98 of file timsframe.cpp.

99 {
100  qDebug();
101  quint64 len = m_timsDataFrame.size();
102  if(len % 4 != 0)
103  {
105  QObject::tr("TimsFrame::unshufflePacket error: len%4 != 0"));
106  }
107 
108  quint64 nb_uint4 = len / 4;
109 
110  char *dest = m_timsDataFrame.data();
111  quint64 src_offset = 0;
112 
113  for(quint64 j = 0; j < 4; j++)
114  {
115  for(quint64 i = 0; i < nb_uint4; i++)
116  {
117  dest[(i * 4) + j] = src[src_offset];
118  src_offset++;
119  }
120  }
121  qDebug();
122 }

References m_timsDataFrame.

Referenced by TimsFrame().

Member Data Documentation

◆ m_timsDataFrame

◆ TimsDirectXicExtractor

friend pappso::TimsFrame::TimsDirectXicExtractor
private

Definition at line 54 of file timsframe.h.


The documentation for this class was generated from the following files:
pappso::TimsFrameBase::checkScanNum
bool checkScanNum(std::size_t scanNum) const
Definition: timsframebase.cpp:101
pappso::TimsFrameBase::m_timsId
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
Definition: timsframebase.h:171
pappso::DataPoint::y
pappso_double y
Definition: datapoint.h:23
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::TimsFrame::getMassSpectrumSPtr
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
Definition: timsframe.cpp:351
pappso::DataPoint
Definition: datapoint.h:21
pappso::TimsFrame::getRawTraceSPtr
pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
Definition: timsframe.cpp:476
pappso::PeptideIonCter::y
@ y
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::TimsFrame::m_timsDataFrame
QByteArray m_timsDataFrame
Definition: timsframe.h:158
pappso::TimsFrame::unshufflePacket
void unshufflePacket(const char *src)
Definition: timsframe.cpp:98
pappso::TraceSPtr
std::shared_ptr< Trace > TraceSPtr
Definition: trace.h:119
pappso::TimsFrame::getNbrPeaks
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
Definition: timsframe.cpp:125
pappso::DataPoint::x
pappso_double x
Definition: datapoint.h:22
pappso::TimsFrameBase::TimsFrameBase
TimsFrameBase(std::size_t timsId, quint32 scanNum)
constructor for binary independant tims frame
Definition: timsframebase.cpp:37
pappso::XicExtractMethod::sum
@ sum
sum of intensities
pappso::TimsFrame::getScanOffset
std::size_t getScanOffset(std::size_t scanNum) const
Definition: timsframe.cpp:155
pappso::TimsFrameBase::m_scanNumber
quint32 m_scanNumber
total number of scans contained in this frame
Definition: timsframebase.h:165
pappso::TimsFrame::cumulateScan
void cumulateScan(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan into a map
Definition: timsframe.cpp:216
pappso::MassSpectrumSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
Definition: massspectrum.h:54
pappso::PappsoException
Definition: pappsoexception.h:42