libpappsomspp
Library for mass spectrometry
pappso::MsRunRetentionTime< T > Class Template Reference

#include <msrunretentiontime.h>

Classes

struct  PeptideMs2Point
 

Public Member Functions

 MsRunRetentionTime (MsRunReaderSPtr msrun_reader_sp)
 
 MsRunRetentionTime (const MsRunRetentionTime< T > &other)
 
 ~MsRunRetentionTime ()
 
pappso::MsRunReaderSPtr getMsRunReaderSPtr () const
 
void setMs2MedianFilter (const FilterMorphoMedian &ms2MedianFilter)
 
void setMs2MeanFilter (const FilterMorphoMean &ms2MeanFilter)
 
void setMs1MeanFilter (const FilterMorphoMean &ms1MeanFilter)
 
Trace getCommonDeltaRt (const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
 
void addPeptideAsSeamark (const T &peptide_str, std::size_t ms2_spectrum_index)
 collects all peptide evidences of a given MSrun seamarks has to be converted to peptide retention time using computePeptideRetentionTimes More...
 
void computePeptideRetentionTimes ()
 convert Peptide seamarks into PeptideMs2Point this is required before computing alignment More...
 
std::size_t getNumberOfCorrectedValues () const
 
Trace align (const MsRunRetentionTime< T > &msrun_retention_time_reference)
 
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & getSeamarks () const
 
const std::vector< double > & getAlignedRetentionTimeVector () const
 
const std::vector< RtPoint > & getMs1RetentionTimeVector () const
 
bool isAligned () const
 
double translateOriginal2AlignedRetentionTime (double original_retention_time) const
 

Protected Member Functions

double getFrontRetentionTimeReference () const
 
double getBackRetentionTimeReference () const
 
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > getSeamarksReferences () const
 

Private Types

enum  ComputeRetentionTimeReference { ComputeRetentionTimeReference::maximum_intensity, ComputeRetentionTimeReference::weighted_intensity, ComputeRetentionTimeReference::last }
 

Private Member Functions

void getCommonDeltaRt (Trace &delta_rt, const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
 
void correctNewTimeValues (Trace &ms1_aligned_points, double correction_parameter)
 
void linearRegressionMs2toMs1 (Trace &ms1_aligned_points, const Trace &common_points)
 

Private Attributes

FilterMorphoMedian m_ms2MedianFilter
 
FilterMorphoMean m_ms2MeanFilter
 
FilterMorphoMean m_ms1MeanFilter
 
pappso::MsRunReaderSPtr msp_msrunReader
 
pappso::MsRunIdCstSPtr mcsp_msrunId
 
std::vector< RtPointm_ms1RetentionTimeVector
 
std::vector< double > m_alignedRetentionTimeVector
 
std::vector< MsRunRetentionTimeSeamarkPoint< T > > m_seamarks
 
std::size_t m_valuesCorrected = 0
 
std::vector< PeptideMs2Pointm_allMs2Points
 
ComputeRetentionTimeReference m_retentionTimeReferenceMethod
 

Detailed Description

template<class T>
class pappso::MsRunRetentionTime< T >

Definition at line 49 of file msrunretentiontime.h.

Member Enumeration Documentation

◆ ComputeRetentionTimeReference

template<class T >
enum pappso::MsRunRetentionTime::ComputeRetentionTimeReference
strongprivate
Enumerator
maximum_intensity 
weighted_intensity 
last 

Definition at line 59 of file msrunretentiontime.h.

60  {
61  maximum_intensity,
62  weighted_intensity,
63  last
64  };

Constructor & Destructor Documentation

◆ MsRunRetentionTime() [1/2]

template<class T >
MsRunRetentionTime::MsRunRetentionTime ( MsRunReaderSPtr  msrun_reader_sp)

Definition at line 82 of file msrunretentiontime.cpp.

84 {
85  msp_msrunReader = msrun_reader_sp;
86  mcsp_msrunId = msp_msrunReader.get()->getMsRunId();
88  msrun_reader_sp.get()->readSpectrumCollection(handler);
89 
90 
91  std::sort(m_ms1RetentionTimeVector.begin(),
93  [](const RtPoint &a, const RtPoint &b) {
94  return (a.retentionTime < b.retentionTime);
95  });
96 }

References pappso::MsRunRetentionTime< T >::m_ms1RetentionTimeVector, pappso::MsRunRetentionTime< T >::mcsp_msrunId, and pappso::MsRunRetentionTime< T >::msp_msrunReader.

◆ MsRunRetentionTime() [2/2]

◆ ~MsRunRetentionTime()

template<class T >
MsRunRetentionTime::~MsRunRetentionTime

Definition at line 118 of file msrunretentiontime.cpp.

119 {
120 }

Member Function Documentation

◆ addPeptideAsSeamark()

template<class T >
void MsRunRetentionTime::addPeptideAsSeamark ( const T &  peptide_str,
std::size_t  ms2_spectrum_index 
)

collects all peptide evidences of a given MSrun seamarks has to be converted to peptide retention time using computePeptideRetentionTimes

Definition at line 184 of file msrunretentiontime.cpp.

186 {
187 
188  qDebug();
189  msp_msrunReader.get()->acquireDevice();
190  PeptideMs2Point ms2point;
191  ms2point.entityHash = peptide_id;
192  QualifiedMassSpectrum spectrum =
193  msp_msrunReader.get()->qualifiedMassSpectrum(ms2_spectrum_index, false);
194  ms2point.precursorIntensity = spectrum.getPrecursorIntensity();
195  ms2point.retentionTime = spectrum.getRtInSeconds();
196 
197  // addSeamark(m_hash_fn(peptide_str.toStdString()), retentionTime);
198 
199  m_allMs2Points.push_back(ms2point);
200 
201  qDebug();
202 }

References pappso::MsRunRetentionTime< T >::PeptideMs2Point::entityHash, pappso::QualifiedMassSpectrum::getPrecursorIntensity(), pappso::QualifiedMassSpectrum::getRtInSeconds(), pappso::MsRunRetentionTime< T >::PeptideMs2Point::precursorIntensity, and pappso::MsRunRetentionTime< T >::PeptideMs2Point::retentionTime.

◆ align()

template<class T >
Trace MsRunRetentionTime::align ( const MsRunRetentionTime< T > &  msrun_retention_time_reference)

Definition at line 411 of file msrunretentiontime.cpp.

413 {
414  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks;
415  if(msrun_retention_time_reference.isAligned())
416  {
417  other_seamarks = msrun_retention_time_reference.getSeamarksReferences();
418  }
419  else
420  {
421  other_seamarks = msrun_retention_time_reference.getSeamarks();
422  }
423  qDebug();
424  if((m_ms1MeanFilter.getHalfWindowSize() * 2 + 1) >=
426  {
427  throw ExceptionNotPossible(
428  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
429  "\ntoo few MS1 points (%3)")
430  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
431  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
432  .arg(m_ms1RetentionTimeVector.size()));
433  }
434 
435  qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime
436  << " " << other_seamarks[0].entityHash
437  << other_seamarks[0].retentionTime << " ";
438  // both seamarks has to be ordered
439  Trace common_points;
440  getCommonDeltaRt(common_points, other_seamarks);
441 
442  // writeTrace("lib_ms2_delta_rt.ods", common_points);
443 
444  qDebug() << common_points.front().x << " " << common_points.front().y;
445  m_ms2MedianFilter.filter(common_points);
446  // writeTrace("lib_ms2_delta_rt_median.ods", common_points);
447  m_ms2MeanFilter.filter(common_points);
448  // writeTrace("lib_ms2_delta_rt_mean.ods", common_points);
449  // convert common delta rt to real retention times (for convenience)
450  qDebug() << common_points.front().x << " " << common_points.front().y;
451 
452 
453  // add a first point to ensure coherence:
454  DataPoint first_point;
455  first_point.x = m_ms1RetentionTimeVector.front().retentionTime - (double)1;
456  if(first_point.x < 0)
457  {
458  first_point.x = 0;
459  }
460  first_point.y =
461  m_ms1RetentionTimeVector.front().retentionTime -
462  msrun_retention_time_reference.getFrontRetentionTimeReference();
463 
464  common_points.push_back(first_point);
465  // add a last point to ensure coherence:
466  DataPoint last_point;
467  last_point.x = m_ms1RetentionTimeVector.back().retentionTime + 1;
468  last_point.y = m_ms1RetentionTimeVector.back().retentionTime -
469  msrun_retention_time_reference.getBackRetentionTimeReference();
470  common_points.push_back(last_point);
471  common_points.sortX();
472 
473  // now, it is possible for each time range to give a new MS1 time using a
474  // linear regression on MS2 corrected times
476 
477  qDebug() << common_points.front().x << " " << common_points.front().y;
478 
479  Trace ms1_aligned_points;
480 
481  linearRegressionMs2toMs1(ms1_aligned_points, common_points);
482 
483  // writeTrace("lib_ms1_map_rt.ods", ms1_aligned_points);
484  qDebug();
485  // smoothing on MS1 points
486  m_ms1MeanFilter.filter(ms1_aligned_points);
487 
488  // writeTrace("lib_ms1_map_rt_mean.ods", ms1_aligned_points);
489  // final aligned retentionTime vector
490 
491  for(DataPoint &data_point : ms1_aligned_points)
492  {
493  data_point.y = (data_point.x - data_point.y);
494  }
495 
496  qDebug();
497  // Here, the correction parameter is the slope of old rt points curve
498  // (divided by 4 to get a finer correction).
499  double correction_parameter =
500  (m_ms1RetentionTimeVector.back().retentionTime -
501  m_ms1RetentionTimeVector.front().retentionTime) /
502  (ms1_aligned_points.size());
503  // set_correction_parameter(correction_parameter / 4);
504  correction_parameter = correction_parameter / (double)4;
505  correctNewTimeValues(ms1_aligned_points, correction_parameter);
506 
507  m_alignedRetentionTimeVector = ms1_aligned_points.yValues();
508 
509  qDebug();
510  return ms1_aligned_points;
511 }

References pappso::Trace::filter(), pappso::MsRunRetentionTime< T >::getBackRetentionTimeReference(), pappso::MsRunRetentionTime< T >::getFrontRetentionTimeReference(), pappso::MsRunRetentionTime< T >::getSeamarks(), pappso::MsRunRetentionTime< T >::getSeamarksReferences(), pappso::MsRunRetentionTime< T >::isAligned(), pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ computePeptideRetentionTimes()

template<class T >
void MsRunRetentionTime::computePeptideRetentionTimes

convert Peptide seamarks into PeptideMs2Point this is required before computing alignment

Definition at line 206 of file msrunretentiontime.cpp.

207 {
208 
209  qDebug();
210  if(msp_msrunReader == nullptr)
211  {
212  throw ExceptionNotPossible(
213  QObject::tr("ERROR : msp_msrunReader == nullptr"));
214  }
215  m_seamarks.clear();
218  {
219 
220 
221  std::sort(m_allMs2Points.begin(),
222  m_allMs2Points.end(),
223  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
224  if(a.entityHash == b.entityHash)
225  {
226  return (a.precursorIntensity > b.precursorIntensity);
227  }
228  return (a.entityHash < b.entityHash);
229  });
230 
231  auto itend =
232  std::unique(m_allMs2Points.begin(),
233  m_allMs2Points.end(),
234  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
235  return (a.entityHash == b.entityHash);
236  });
237 
238  auto it = m_allMs2Points.begin();
239  while(it != itend)
240  {
241  m_seamarks.push_back(
242  {it->entityHash, it->retentionTime, it->precursorIntensity});
243  it++;
244  }
245  }
246  msp_msrunReader = nullptr;
247  m_allMs2Points.clear();
248 
249  std::sort(m_seamarks.begin(),
250  m_seamarks.end(),
253  return (a.entityHash < b.entityHash);
254  });
255  qDebug();
256 }

References pappso::MsRunRetentionTime< T >::PeptideMs2Point::entityHash.

◆ correctNewTimeValues()

template<class T >
void MsRunRetentionTime::correctNewTimeValues ( Trace ms1_aligned_points,
double  correction_parameter 
)
private

Definition at line 569 of file msrunretentiontime.cpp.

571 {
572 
573  m_valuesCorrected = 0;
574  auto new_it(ms1_aligned_points.begin());
575  auto new_nextit(ms1_aligned_points.begin());
576  new_nextit++;
577  for(; new_nextit != ms1_aligned_points.end(); ++new_nextit, ++new_it)
578  {
579  if(new_nextit->y < new_it->y)
580  {
582  new_nextit->y = new_it->y + correction_parameter;
583  }
584  }
585 }

◆ getAlignedRetentionTimeVector()

template<class T >
const std::vector< double > & MsRunRetentionTime::getAlignedRetentionTimeVector

Definition at line 154 of file msrunretentiontime.cpp.

155 {
157 }

◆ getBackRetentionTimeReference()

template<class T >
double MsRunRetentionTime::getBackRetentionTimeReference
protected

Definition at line 327 of file msrunretentiontime.cpp.

328 {
329  if(isAligned())
330  {
331  return m_alignedRetentionTimeVector.back();
332  }
333  return m_ms1RetentionTimeVector.back().retentionTime;
334 }

Referenced by pappso::MsRunRetentionTime< T >::align().

◆ getCommonDeltaRt() [1/2]

template<class T >
Trace MsRunRetentionTime::getCommonDeltaRt ( const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &  other_seamarks) const

Definition at line 174 of file msrunretentiontime.cpp.

176 {
177  Trace common_points;
178  getCommonDeltaRt(common_points, other_seamarks);
179  return common_points;
180 }

◆ getCommonDeltaRt() [2/2]

template<class T >
void MsRunRetentionTime::getCommonDeltaRt ( Trace delta_rt,
const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &  other_seamarks 
) const
private

Definition at line 260 of file msrunretentiontime.cpp.

263 {
264 
265  qDebug();
266  auto it = other_seamarks.begin();
267 
268  for(const MsRunRetentionTimeSeamarkPoint<T> &seamark : m_seamarks)
269  {
270  while((it != other_seamarks.end()) &&
271  (it->entityHash < seamark.entityHash))
272  {
273  it++;
274  }
275  if(it == other_seamarks.end())
276  break;
277  if(it->entityHash == seamark.entityHash)
278  {
279  delta_rt.push_back(DataPoint(
280  seamark.retentionTime, seamark.retentionTime - it->retentionTime));
281  }
282  }
283 
284  qDebug();
285  if((m_ms2MedianFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
286  {
287  throw ExceptionNotPossible(
288  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
289  "\ntoo few MS2 points (%3) in common")
290  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
291  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
292  .arg(delta_rt.size()));
293  }
294 
295  qDebug();
296  if((m_ms2MeanFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
297  {
298  throw ExceptionNotPossible(
299  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
300  "\ntoo few MS2 points (%3) in common")
301  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
302  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
303  .arg(delta_rt.size()));
304  }
305  delta_rt.sortX();
306 
307  // there can be multiple entities (peptides) at one retention time
308  // in this case, avoid retention time redundancy by applying unique on trace :
309  delta_rt.unique();
310 
311  qDebug();
312 }

References pappso::Trace::sortX(), and pappso::Trace::unique().

◆ getFrontRetentionTimeReference()

template<class T >
double MsRunRetentionTime::getFrontRetentionTimeReference
protected

Definition at line 317 of file msrunretentiontime.cpp.

318 {
319  if(isAligned())
320  {
321  return m_alignedRetentionTimeVector.front();
322  }
323  return m_ms1RetentionTimeVector.front().retentionTime;
324 }

Referenced by pappso::MsRunRetentionTime< T >::align().

◆ getMs1RetentionTimeVector()

template<class T >
const std::vector< RtPoint > & MsRunRetentionTime::getMs1RetentionTimeVector

Definition at line 167 of file msrunretentiontime.cpp.

168 {
170 }

◆ getMsRunReaderSPtr()

template<typename T >
pappso::MsRunReaderSPtr pappso::MsRunRetentionTime< T >::getMsRunReaderSPtr

Definition at line 590 of file msrunretentiontime.cpp.

591 {
592  return msp_msrunReader;
593 }

◆ getNumberOfCorrectedValues()

template<class T >
std::size_t MsRunRetentionTime::getNumberOfCorrectedValues

Definition at line 161 of file msrunretentiontime.cpp.

162 {
163  return m_valuesCorrected;
164 }

◆ getSeamarks()

template<class T >
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & MsRunRetentionTime::getSeamarks

Definition at line 146 of file msrunretentiontime.cpp.

147 {
148  qDebug();
149  return m_seamarks;
150 }

Referenced by pappso::MsRunRetentionTime< T >::align().

◆ getSeamarksReferences()

template<class T >
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > MsRunRetentionTime::getSeamarksReferences
protected

Definition at line 391 of file msrunretentiontime.cpp.

392 {
393  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks = m_seamarks;
394  for(auto &seamark : other_seamarks)
395  {
396  seamark.retentionTime =
397  translateOriginal2AlignedRetentionTime(seamark.retentionTime);
398  }
399  return other_seamarks;
400 }

Referenced by pappso::MsRunRetentionTime< T >::align().

◆ isAligned()

template<class T >
bool MsRunRetentionTime::isAligned

Definition at line 404 of file msrunretentiontime.cpp.

405 {
406  return (m_alignedRetentionTimeVector.size() > 0);
407 }

Referenced by pappso::MsRunRetentionTime< T >::align().

◆ linearRegressionMs2toMs1()

template<class T >
void MsRunRetentionTime::linearRegressionMs2toMs1 ( Trace ms1_aligned_points,
const Trace common_points 
)
private

Definition at line 516 of file msrunretentiontime.cpp.

518 {
519 
520  // first slope :
521  std::vector<DataPoint>::const_iterator itms2 = common_points.begin();
522  std::vector<DataPoint>::const_iterator itms2next = itms2 + 1;
523  if(itms2next == common_points.end())
524  {
525  // error
526  throw ExceptionNotPossible(
527  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
528  "\ntoo few common points (%3)")
529  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
530  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
531  .arg(common_points.size()));
532  }
533  qDebug() << "() itms2->x=" << itms2->x << " itms2->y=" << itms2->y;
534 
535  for(RtPoint &original_rt_point : m_ms1RetentionTimeVector)
536  {
537  DataPoint ms1_point;
538  ms1_point.x = original_rt_point.retentionTime;
539 
540  while(ms1_point.x > itms2next->x)
541  {
542  itms2++;
543  itms2next++;
544  }
545 
546  double ratio = (itms2next->x - itms2->x);
547  if(ratio != 0)
548  {
549  ratio = (ms1_point.x - itms2->x) / ratio;
550  }
551  else
552  {
553  // avoid division by zero
554  ratio = 1;
555  }
556  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " <<
557  // ratio;
558 
559  ms1_point.y = itms2->y + ((itms2next->y - itms2->y) * ratio);
560 
561  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "
562  // << ms1_point.y;
563  ms1_aligned_points.push_back(ms1_point);
564  }
565 }

References pappso::DataPoint::x, and pappso::DataPoint::y.

◆ setMs1MeanFilter()

template<class T >
void MsRunRetentionTime::setMs1MeanFilter ( const FilterMorphoMean ms1MeanFilter)

Definition at line 139 of file msrunretentiontime.cpp.

140 {
141  m_ms1MeanFilter = ms1MeanFilter;
142 }

◆ setMs2MeanFilter()

template<class T >
void MsRunRetentionTime::setMs2MeanFilter ( const FilterMorphoMean ms2MeanFilter)

Definition at line 132 of file msrunretentiontime.cpp.

133 {
134  m_ms2MeanFilter = ms2MeanFilter;
135 }

◆ setMs2MedianFilter()

template<class T >
void MsRunRetentionTime::setMs2MedianFilter ( const FilterMorphoMedian ms2MedianFilter)

Definition at line 124 of file msrunretentiontime.cpp.

126 {
127  m_ms2MedianFilter = ms2MedianFilter;
128 }

◆ translateOriginal2AlignedRetentionTime()

template<class T >
double MsRunRetentionTime::translateOriginal2AlignedRetentionTime ( double  original_retention_time) const

Definition at line 339 of file msrunretentiontime.cpp.

341 {
342  if(m_alignedRetentionTimeVector.size() < 3)
343  {
344  throw ExceptionNotPossible(
345  QObject::tr("ERROR : too few aligned points to compute aligned "
346  "retention time (%1)")
347  .arg(m_ms1RetentionTimeVector.size()));
348  }
350  {
351  throw ExceptionNotPossible(
352  QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 "
353  "m_ms1RetentionTimeVector.size()")
354  .arg(m_alignedRetentionTimeVector.size())
355  .arg(m_ms1RetentionTimeVector.size()));
356  }
357  auto it_plus =
358  std::find_if(m_ms1RetentionTimeVector.begin(),
360  [original_retention_time](const RtPoint &rt_point) {
361  return original_retention_time < rt_point.retentionTime;
362  });
363  double rt1_a, rt2_a, rt1_b, rt2_b;
364  if(it_plus == m_ms1RetentionTimeVector.end())
365  {
366  it_plus--;
367  }
368  if(it_plus == m_ms1RetentionTimeVector.begin())
369  {
370  it_plus++;
371  }
372  auto it_minus = it_plus - 1;
373 
374  rt1_a = it_minus->retentionTime;
375  rt2_a = it_plus->retentionTime;
376 
377  double ratio = (original_retention_time - rt1_a) / (rt2_a - rt1_a);
378 
379  auto itref = m_alignedRetentionTimeVector.begin() +
380  std::distance(m_ms1RetentionTimeVector.begin(), it_minus);
381 
382  rt1_b = *itref;
383  itref++;
384  rt2_b = *itref;
385 
386  return (((rt2_b - rt1_b) * ratio) + rt1_b);
387 }

Member Data Documentation

◆ m_alignedRetentionTimeVector

template<class T >
std::vector<double> pappso::MsRunRetentionTime< T >::m_alignedRetentionTimeVector
private

◆ m_allMs2Points

template<class T >
std::vector<PeptideMs2Point> pappso::MsRunRetentionTime< T >::m_allMs2Points
private

◆ m_ms1MeanFilter

template<class T >
FilterMorphoMean pappso::MsRunRetentionTime< T >::m_ms1MeanFilter
private

Definition at line 124 of file msrunretentiontime.h.

◆ m_ms1RetentionTimeVector

template<class T >
std::vector<RtPoint> pappso::MsRunRetentionTime< T >::m_ms1RetentionTimeVector
private

◆ m_ms2MeanFilter

template<class T >
FilterMorphoMean pappso::MsRunRetentionTime< T >::m_ms2MeanFilter
private

Definition at line 123 of file msrunretentiontime.h.

◆ m_ms2MedianFilter

template<class T >
FilterMorphoMedian pappso::MsRunRetentionTime< T >::m_ms2MedianFilter
private

Definition at line 122 of file msrunretentiontime.h.

◆ m_retentionTimeReferenceMethod

template<class T >
ComputeRetentionTimeReference pappso::MsRunRetentionTime< T >::m_retentionTimeReferenceMethod
private

◆ m_seamarks

template<class T >
std::vector<MsRunRetentionTimeSeamarkPoint<T> > pappso::MsRunRetentionTime< T >::m_seamarks
private

◆ m_valuesCorrected

template<class T >
std::size_t pappso::MsRunRetentionTime< T >::m_valuesCorrected = 0
private

◆ mcsp_msrunId

template<class T >
pappso::MsRunIdCstSPtr pappso::MsRunRetentionTime< T >::mcsp_msrunId
private

◆ msp_msrunReader

template<class T >
pappso::MsRunReaderSPtr pappso::MsRunRetentionTime< T >::msp_msrunReader
private

The documentation for this class was generated from the following files:
pappso::MsRunRetentionTime::msp_msrunReader
pappso::MsRunReaderSPtr msp_msrunReader
Definition: msrunretentiontime.h:125
pappso::MsRunRetentionTime::m_valuesCorrected
std::size_t m_valuesCorrected
Definition: msrunretentiontime.h:131
pappso::DataPoint::y
pappso_double y
Definition: datapoint.h:23
pappso::MsRunRetentionTime::m_allMs2Points
std::vector< PeptideMs2Point > m_allMs2Points
Definition: msrunretentiontime.h:133
pappso::MsRunRetentionTime::correctNewTimeValues
void correctNewTimeValues(Trace &ms1_aligned_points, double correction_parameter)
Definition: msrunretentiontime.cpp:569
pappso::QualifiedMassSpectrum::getPrecursorIntensity
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
Definition: qualifiedmassspectrum.cpp:381
pappso::MsRunRetentionTime::getSeamarksReferences
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > getSeamarksReferences() const
Definition: msrunretentiontime.cpp:391
pappso::FilterMorphoWindowBase::filter
virtual Trace & filter(Trace &data_points) const override
Definition: filtermorpho.cpp:60
pappso::QualifiedMassSpectrumParameter::OneOverK0
@ OneOverK0
1/kO of a simple scan
pappso::MsRunRetentionTime::getCommonDeltaRt
Trace getCommonDeltaRt(const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
Definition: msrunretentiontime.cpp:174
pappso::DataPoint
Definition: datapoint.h:21
pappso::ExceptionNotPossible
Definition: exceptionnotpossible.h:32
pappso::MsRunRetentionTime::m_ms2MeanFilter
FilterMorphoMean m_ms2MeanFilter
Definition: msrunretentiontime.h:123
pappso::MsRunRetentionTime::m_ms1RetentionTimeVector
std::vector< RtPoint > m_ms1RetentionTimeVector
Definition: msrunretentiontime.h:127
pappso::MsRunRetentionTime::getBackRetentionTimeReference
double getBackRetentionTimeReference() const
Definition: msrunretentiontime.cpp:327
RetentionTimeReader
Definition: msrunretentiontime.cpp:55
pappso::MsRunRetentionTimeSeamarkPoint
Definition: msrunretentiontime.h:41
pappso::MsRunRetentionTime::m_ms2MedianFilter
FilterMorphoMedian m_ms2MedianFilter
Definition: msrunretentiontime.h:122
pappso::MsRunRetentionTime::ComputeRetentionTimeReference::maximum_intensity
@ maximum_intensity
pappso::Trace
A simple container of DataPoint instances.
Definition: trace.h:132
pappso::FilterMorphoWindowBase::getHalfWindowSize
virtual std::size_t getHalfWindowSize() const
Definition: filtermorpho.cpp:45
pappso::QualifiedMassSpectrum
Class representing a fully specified mass spectrum.
Definition: qualifiedmassspectrum.h:85
pappso::Trace::unique
void unique()
Definition: trace.cpp:806
pappso::DataPoint::x
pappso_double x
Definition: datapoint.h:22
pappso::Trace::sortX
void sortX()
Definition: trace.cpp:790
pappso::MsRunRetentionTime::linearRegressionMs2toMs1
void linearRegressionMs2toMs1(Trace &ms1_aligned_points, const Trace &common_points)
Definition: msrunretentiontime.cpp:516
pappso::RtPoint
Definition: msrunretentiontime.h:33
pappso::MsRunRetentionTime::m_ms1MeanFilter
FilterMorphoMean m_ms1MeanFilter
Definition: msrunretentiontime.h:124
pappso::MsRunRetentionTime::m_retentionTimeReferenceMethod
ComputeRetentionTimeReference m_retentionTimeReferenceMethod
Definition: msrunretentiontime.h:135
pappso::MsRunRetentionTime::isAligned
bool isAligned() const
Definition: msrunretentiontime.cpp:404
pappso::MsRunRetentionTime::m_alignedRetentionTimeVector
std::vector< double > m_alignedRetentionTimeVector
Definition: msrunretentiontime.h:128
pappso::MsRunRetentionTime::mcsp_msrunId
pappso::MsRunIdCstSPtr mcsp_msrunId
Definition: msrunretentiontime.h:126
pappso::MsRunRetentionTime::translateOriginal2AlignedRetentionTime
double translateOriginal2AlignedRetentionTime(double original_retention_time) const
Definition: msrunretentiontime.cpp:339
pappso::MsRunRetentionTime::m_seamarks
std::vector< MsRunRetentionTimeSeamarkPoint< T > > m_seamarks
Definition: msrunretentiontime.h:130
pappso::MsRunRetentionTime::getFrontRetentionTimeReference
double getFrontRetentionTimeReference() const
Definition: msrunretentiontime.cpp:317
pappso::MsRunRetentionTime::getSeamarks
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & getSeamarks() const
Definition: msrunretentiontime.cpp:146
pappso::QualifiedMassSpectrum::getRtInSeconds
pappso_double getRtInSeconds() const
Get the retention time in seconds.
Definition: qualifiedmassspectrum.cpp:203