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
 
const MsRunIdgetMsRunId () const
 
void setMs2MedianFilter (const FilterMorphoMedian &ms2MedianFilter)
 
void setMs2MeanFilter (const FilterMorphoMean &ms2MeanFilter)
 
void setMs1MeanFilter (const FilterMorphoMean &ms1MeanFilter)
 
const FilterMorphoMediangetMs2MedianFilter () const
 
const FilterMorphoMeangetMs2MeanFilter () const
 
const FilterMorphoMeangetMs1MeanFilter () const
 
Trace getCommonDeltaRt (const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
 
void addPeptideAsSeamark (const T &peptide_id, 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 addPeptideAsSeamark (const T &peptide_id, double retentionTime, double precursorIntensity)
 collects all peptide evidences of a given MSrun seamarks has to be converted to peptide retention time using computePeptideRetentionTimes More...
 
std::size_t getNumberOfCorrectedValues () const
 
Trace align (const MsRunRetentionTime< T > &msrun_retention_time_reference)
 align the current msrunretentiontime object using the given reference More...
 
Trace getCommonSeamarksDeltaRt (const MsRunRetentionTime< T > &msrun_retention_time_reference) const
 get common seamarks between msrunretentiontime objects and their deltart More...
 
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & getSeamarks () const
 
const std::vector< double > & getAlignedRetentionTimeVector () const
 get aligned retention time vector More...
 
void setAlignedRetentionTimeVector (const std::vector< double > &aligned_times)
 
const std::vector< double > & getMs1RetentionTimeVector () const
 get orginal retention time vector (not aligned) More...
 
bool isAligned () const
 
double translateOriginal2AlignedRetentionTime (double original_retention_time) const
 
double translateAligned2OriginalRetentionTime (double aligned_retention_time) const
 
void computeSeamarks ()
 convert PeptideMs2Point into Peptide seamarks this is required before computing alignment More...
 

Protected Member Functions

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

Private Types

enum class  ComputeRetentionTimeReference { maximum_intensity , weighted_intensity , last }
 

Private Member Functions

void getCommonDeltaRt (Trace &delta_rt, const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
 get a trace of common MS2 retention times (x values) by their deltart (y values) More...
 
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< double > m_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 42 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 52 of file msrunretentiontime.h.

53  {
54  maximum_intensity,
55  weighted_intensity,
56  last
57  };

Constructor & Destructor Documentation

◆ MsRunRetentionTime() [1/2]

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

Definition at line 37 of file msrunretentiontime.cpp.

39 {
40  msp_msrunReader = msrun_reader_sp;
41  mcsp_msrunId = msp_msrunReader.get()->getMsRunId();
42  m_ms1RetentionTimeVector = msp_msrunReader.get()->getRetentionTimeLine();
43 
44 
45  std::sort(m_ms1RetentionTimeVector.begin(),
47  [](const double &a, const double &b) { return (a < b); });
48 }
pappso::MsRunReaderSPtr msp_msrunReader
std::vector< double > m_ms1RetentionTimeVector
FilterMorphoMedian m_ms2MedianFilter
pappso::MsRunIdCstSPtr mcsp_msrunId

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

◆ MsRunRetentionTime() [2/2]

template<class T >
MsRunRetentionTime::MsRunRetentionTime ( const MsRunRetentionTime< T > &  other)

Definition at line 51 of file msrunretentiontime.cpp.

55 {
57  mcsp_msrunId = other.mcsp_msrunId;
60 
61  m_seamarks = other.m_seamarks;
63 
65 
67 }
std::vector< double > m_alignedRetentionTimeVector
std::vector< PeptideMs2Point > m_allMs2Points
std::vector< MsRunRetentionTimeSeamarkPoint< T > > m_seamarks
ComputeRetentionTimeReference m_retentionTimeReferenceMethod

References pappso::MsRunRetentionTime< T >::m_alignedRetentionTimeVector, pappso::MsRunRetentionTime< T >::m_allMs2Points, pappso::MsRunRetentionTime< T >::m_ms1RetentionTimeVector, pappso::MsRunRetentionTime< T >::m_retentionTimeReferenceMethod, pappso::MsRunRetentionTime< T >::m_seamarks, pappso::MsRunRetentionTime< T >::m_valuesCorrected, pappso::MsRunRetentionTime< T >::mcsp_msrunId, and pappso::MsRunRetentionTime< T >::msp_msrunReader.

◆ ~MsRunRetentionTime()

template<class T >
MsRunRetentionTime::~MsRunRetentionTime

Definition at line 70 of file msrunretentiontime.cpp.

71 {
72 }

Member Function Documentation

◆ addPeptideAsSeamark() [1/2]

template<class T >
void MsRunRetentionTime::addPeptideAsSeamark ( const T &  peptide_id,
double  retentionTime,
double  precursorIntensity 
)

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

Parameters
peptide_idunique identifier (whichever type) of a peptide
retentionTimeretention time of this peptide observation
precursorIntensityMS2 precursorIntensity of this peptide

Definition at line 187 of file msrunretentiontime.cpp.

190 {
191  PeptideMs2Point ms2point;
192  ms2point.entityHash = peptide_id;
193  ms2point.precursorIntensity = precursorIntensity;
194  ms2point.retentionTime = retentionTime;
195  m_allMs2Points.push_back(ms2point);
196 }

References pappso::MsRunRetentionTime< T >::PeptideMs2Point::entityHash, pappso::MsRunRetentionTime< T >::PeptideMs2Point::precursorIntensity, and pappso::MsRunRetentionTime< T >::PeptideMs2Point::retentionTime.

◆ addPeptideAsSeamark() [2/2]

template<class T >
void MsRunRetentionTime::addPeptideAsSeamark ( const T &  peptide_id,
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

Parameters
peptide_idunique identifier (whichever type) of a peptide
ms2_spectrum_indexassociated MS2 spectrum index ot this peptide

Definition at line 165 of file msrunretentiontime.cpp.

167 {
168 
169  qDebug();
170  msp_msrunReader.get()->acquireDevice();
171  PeptideMs2Point ms2point;
172  ms2point.entityHash = peptide_id;
173  QualifiedMassSpectrum spectrum =
174  msp_msrunReader.get()->qualifiedMassSpectrum(ms2_spectrum_index, false);
175  ms2point.precursorIntensity = spectrum.getPrecursorIntensity();
176  ms2point.retentionTime = spectrum.getRtInSeconds();
177 
178  // addSeamark(m_hash_fn(peptide_str.toStdString()), retentionTime);
179 
180  m_allMs2Points.push_back(ms2point);
181 
182  qDebug();
183 }
Class representing a fully specified mass spectrum.
pappso_double getPrecursorIntensity(bool *ok=nullptr) const
Get the intensity of the precursor ion.
pappso_double getRtInSeconds() const
Get the retention time in seconds.

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)

align the current msrunretentiontime object using the given reference

Parameters
msrun_retention_time_referencethe reference
Returns
a trace containing aligned MS1 retention times

Definition at line 456 of file msrunretentiontime.cpp.

458 {
459  computeSeamarks();
460  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks;
461  if(msrun_retention_time_reference.isAligned())
462  {
463  other_seamarks = msrun_retention_time_reference.getSeamarksReferences();
464  }
465  else
466  {
467  other_seamarks = msrun_retention_time_reference.getSeamarks();
468  }
469  qDebug();
470  if((m_ms1MeanFilter.getHalfWindowSize() * 2 + 1) >=
472  {
473  throw ExceptionNotPossible(
474  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
475  "\ntoo few MS1 points (%3)")
476  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
477  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
478  .arg(m_ms1RetentionTimeVector.size()));
479  }
480 
481  qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime
482  << " " << other_seamarks[0].entityHash
483  << other_seamarks[0].retentionTime << " ";
484  // both seamarks has to be ordered
485  Trace common_points;
486  getCommonDeltaRt(common_points, other_seamarks);
487 
488  // writeTrace("lib_ms2_delta_rt.ods", common_points);
489 
490  qDebug() << common_points.front().x << " " << common_points.front().y;
491  m_ms2MedianFilter.filter(common_points);
492  // writeTrace("lib_ms2_delta_rt_median.ods", common_points);
493  m_ms2MeanFilter.filter(common_points);
494  // writeTrace("lib_ms2_delta_rt_mean.ods", common_points);
495  // convert common delta rt to real retention times (for convenience)
496  qDebug() << common_points.front().x << " " << common_points.front().y;
497 
498 
499  // add a first point to ensure coherence:
500  DataPoint first_point;
501  first_point.x = m_ms1RetentionTimeVector.front() - (double)1;
502  if(first_point.x < 0)
503  {
504  first_point.x = 0;
505  }
506  first_point.y =
507  m_ms1RetentionTimeVector.front() -
508  msrun_retention_time_reference.getFrontRetentionTimeReference();
509 
510  common_points.push_back(first_point);
511  // add a last point to ensure coherence:
512  DataPoint last_point;
513  last_point.x = m_ms1RetentionTimeVector.back() + 1;
514  last_point.y = m_ms1RetentionTimeVector.back() -
515  msrun_retention_time_reference.getBackRetentionTimeReference();
516  common_points.push_back(last_point);
517  common_points.sortX();
518 
519  // now, it is possible for each time range to give a new MS1 time using a
520  // linear regression on MS2 corrected times
522 
523  qDebug() << common_points.front().x << " " << common_points.front().y;
524 
525  Trace ms1_aligned_points;
526 
527  linearRegressionMs2toMs1(ms1_aligned_points, common_points);
528 
529  // writeTrace("lib_ms1_map_rt.ods", ms1_aligned_points);
530  qDebug();
531  // smoothing on MS1 points
532  m_ms1MeanFilter.filter(ms1_aligned_points);
533 
534  // writeTrace("lib_ms1_map_rt_mean.ods", ms1_aligned_points);
535  // final aligned retentionTime vector
536 
537  for(DataPoint &data_point : ms1_aligned_points)
538  {
539  data_point.y = (data_point.x - data_point.y);
540  }
541 
542  qDebug();
543  // Here, the correction parameter is the slope of old rt points curve
544  // (divided by 4 to get a finer correction).
545  double correction_parameter =
547  (ms1_aligned_points.size());
548  // set_correction_parameter(correction_parameter / 4);
549  correction_parameter = correction_parameter / (double)4;
550  correctNewTimeValues(ms1_aligned_points, correction_parameter);
551 
552  m_alignedRetentionTimeVector = ms1_aligned_points.yValues();
553 
554  qDebug();
555  return ms1_aligned_points;
556 }
virtual Trace & filter(Trace &data_points) const override
virtual std::size_t getHalfWindowSize() const
void computeSeamarks()
convert PeptideMs2Point into Peptide seamarks this is required before computing alignment
Trace getCommonDeltaRt(const std::vector< MsRunRetentionTimeSeamarkPoint< T >> &other_seamarks) const
void linearRegressionMs2toMs1(Trace &ms1_aligned_points, const Trace &common_points)
double getFrontRetentionTimeReference() const
void correctNewTimeValues(Trace &ms1_aligned_points, double correction_parameter)
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > & getSeamarks() const
const std::vector< MsRunRetentionTimeSeamarkPoint< T > > getSeamarksReferences() const
double getBackRetentionTimeReference() const
A simple container of DataPoint instances.
Definition: trace.h:148
void sortX()
Definition: trace.cpp:956
pappso_double x
Definition: datapoint.h:23
pappso_double y
Definition: datapoint.h:24

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, pappso::DataPoint::y, and pappso::Trace::yValues().

◆ computeSeamarks()

template<class T >
void MsRunRetentionTime::computeSeamarks

convert PeptideMs2Point into Peptide seamarks this is required before computing alignment

Definition at line 201 of file msrunretentiontime.cpp.

202 {
203 
204  qDebug();
205  if(m_allMs2Points.size() == 0)
206  {
207  // already computed
208  return;
209  }
210  m_seamarks.clear();
213  {
214 
215 
216  std::sort(m_allMs2Points.begin(),
217  m_allMs2Points.end(),
218  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
219  if(a.entityHash == b.entityHash)
220  {
221  return (a.precursorIntensity > b.precursorIntensity);
222  }
223  return (a.entityHash < b.entityHash);
224  });
225 
226  auto itend =
227  std::unique(m_allMs2Points.begin(),
228  m_allMs2Points.end(),
229  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
230  return (a.entityHash == b.entityHash);
231  });
232 
233  auto it = m_allMs2Points.begin();
234  while(it != itend)
235  {
236  m_seamarks.push_back(
237  {it->entityHash, it->retentionTime, it->precursorIntensity});
238  it++;
239  }
240  }
241  m_allMs2Points.clear();
242 
243  std::sort(m_seamarks.begin(),
244  m_seamarks.end(),
247  return (a.entityHash < b.entityHash);
248  });
249  qDebug();
250 }

References pappso::a, and pappso::b.

◆ correctNewTimeValues()

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

Definition at line 614 of file msrunretentiontime.cpp.

616 {
617 
618  m_valuesCorrected = 0;
619  auto new_it(ms1_aligned_points.begin());
620  auto new_nextit(ms1_aligned_points.begin());
621  new_nextit++;
622  for(; new_nextit != ms1_aligned_points.end(); ++new_nextit, ++new_it)
623  {
624  if(new_nextit->y < new_it->y)
625  {
627  new_nextit->y = new_it->y + correction_parameter;
628  }
629  }
630 }

◆ getAlignedRetentionTimeVector()

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

get aligned retention time vector

Returns
vector of seconds (as double)

Definition at line 135 of file msrunretentiontime.cpp.

136 {
138 }

◆ getBackRetentionTimeReference()

template<class T >
double MsRunRetentionTime::getBackRetentionTimeReference
protected

Definition at line 321 of file msrunretentiontime.cpp.

322 {
323  if(isAligned())
324  {
325  return m_alignedRetentionTimeVector.back();
326  }
327  return m_ms1RetentionTimeVector.back();
328 }

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 155 of file msrunretentiontime.cpp.

157 {
158  Trace common_points;
159  getCommonDeltaRt(common_points, other_seamarks);
160  return common_points;
161 }

◆ getCommonDeltaRt() [2/2]

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

get a trace of common MS2 retention times (x values) by their deltart (y values)

Parameters
delta_rtthe trace result (common MS2 retention times vs counter part deltart)
other_seamarksseamarks of the counter part (reference)

Definition at line 254 of file msrunretentiontime.cpp.

257 {
258 
259  qDebug();
260  auto it = other_seamarks.begin();
261 
262  for(const MsRunRetentionTimeSeamarkPoint<T> &seamark : m_seamarks)
263  {
264  while((it != other_seamarks.end()) &&
265  (it->entityHash < seamark.entityHash))
266  {
267  it++;
268  }
269  if(it == other_seamarks.end())
270  break;
271  if(it->entityHash == seamark.entityHash)
272  {
273  delta_rt.push_back(DataPoint(
274  seamark.retentionTime, seamark.retentionTime - it->retentionTime));
275  }
276  }
277 
278  qDebug();
279  if((m_ms2MedianFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
280  {
281  throw ExceptionNotPossible(
282  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
283  "\ntoo few MS2 points (%3) in common")
284  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
285  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
286  .arg(delta_rt.size()));
287  }
288 
289  qDebug();
290  if((m_ms2MeanFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
291  {
292  throw ExceptionNotPossible(
293  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
294  "\ntoo few MS2 points (%3) in common")
295  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
296  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
297  .arg(delta_rt.size()));
298  }
299  delta_rt.sortX();
300 
301  // there can be multiple entities (peptides) at one retention time
302  // in this case, avoid retention time redundancy by applying unique on trace :
303  delta_rt.unique();
304 
305  qDebug();
306 }
void unique()
Definition: trace.cpp:972

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

◆ getCommonSeamarksDeltaRt()

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

get common seamarks between msrunretentiontime objects and their deltart

Parameters
msrun_retention_time_referencethe reference
Returns
a trace containing MS2 common points and their deltart

Definition at line 683 of file msrunretentiontime.cpp.

685 {
686  // computeSeamarks();
687  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks;
688  if(msrun_retention_time_reference.isAligned())
689  {
690  other_seamarks = msrun_retention_time_reference.getSeamarksReferences();
691  }
692  else
693  {
694  other_seamarks = msrun_retention_time_reference.getSeamarks();
695  }
696  qDebug();
697 
698  qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime
699  << " " << other_seamarks[0].entityHash
700  << other_seamarks[0].retentionTime << " ";
701  // both seamarks has to be ordered
702  Trace common_points;
703  getCommonDeltaRt(common_points, other_seamarks);
704  return common_points;
705 }

References pappso::MsRunRetentionTime< T >::getSeamarks(), pappso::MsRunRetentionTime< T >::getSeamarksReferences(), and pappso::MsRunRetentionTime< T >::isAligned().

◆ getFrontRetentionTimeReference()

template<class T >
double MsRunRetentionTime::getFrontRetentionTimeReference
protected

Definition at line 311 of file msrunretentiontime.cpp.

312 {
313  if(isAligned())
314  {
315  return m_alignedRetentionTimeVector.front();
316  }
317  return m_ms1RetentionTimeVector.front();
318 }

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

◆ getMs1MeanFilter()

template<typename T >
const pappso::FilterMorphoMean & pappso::MsRunRetentionTime< T >::getMs1MeanFilter

Definition at line 113 of file msrunretentiontime.cpp.

114 {
115  return m_ms1MeanFilter;
116 }

◆ getMs1RetentionTimeVector()

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

get orginal retention time vector (not aligned)

Returns
vector of seconds (as double)

Definition at line 148 of file msrunretentiontime.cpp.

149 {
151 }

◆ getMs2MeanFilter()

template<typename T >
const pappso::FilterMorphoMean & pappso::MsRunRetentionTime< T >::getMs2MeanFilter

Definition at line 98 of file msrunretentiontime.cpp.

99 {
100  return m_ms2MeanFilter;
101 }

◆ getMs2MedianFilter()

template<typename T >
const pappso::FilterMorphoMedian & pappso::MsRunRetentionTime< T >::getMs2MedianFilter

Definition at line 83 of file msrunretentiontime.cpp.

84 {
85  return m_ms2MedianFilter;
86 }

◆ getMsRunId()

template<class T >
const MsRunId & MsRunRetentionTime::getMsRunId

Definition at line 76 of file msrunretentiontime.cpp.

77 {
78  return *(mcsp_msrunId.get());
79 }

◆ getMsRunReaderSPtr()

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

Definition at line 635 of file msrunretentiontime.cpp.

636 {
637  return msp_msrunReader;
638 }

◆ getNumberOfCorrectedValues()

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

Definition at line 142 of file msrunretentiontime.cpp.

143 {
144  return m_valuesCorrected;
145 }

◆ getSeamarks()

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

Definition at line 127 of file msrunretentiontime.cpp.

128 {
129  qDebug();
130  return m_seamarks;
131 }

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

◆ getSeamarksReferences()

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

Definition at line 436 of file msrunretentiontime.cpp.

437 {
438  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks = m_seamarks;
439  for(auto &seamark : other_seamarks)
440  {
441  seamark.retentionTime =
442  translateOriginal2AlignedRetentionTime(seamark.retentionTime);
443  }
444  return other_seamarks;
445 }
double translateOriginal2AlignedRetentionTime(double original_retention_time) const

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

◆ isAligned()

template<class T >
bool MsRunRetentionTime::isAligned

◆ linearRegressionMs2toMs1()

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

Definition at line 561 of file msrunretentiontime.cpp.

563 {
564 
565  // first slope :
566  std::vector<DataPoint>::const_iterator itms2 = common_points.begin();
567  std::vector<DataPoint>::const_iterator itms2next = itms2 + 1;
568  if(itms2next == common_points.end())
569  {
570  // error
571  throw ExceptionNotPossible(
572  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
573  "\ntoo few common points (%3)")
574  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
575  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
576  .arg(common_points.size()));
577  }
578  qDebug() << "() itms2->x=" << itms2->x << " itms2->y=" << itms2->y;
579 
580  for(double &original_rt_point : m_ms1RetentionTimeVector)
581  {
582  DataPoint ms1_point;
583  ms1_point.x = original_rt_point;
584 
585  while(ms1_point.x > itms2next->x)
586  {
587  itms2++;
588  itms2next++;
589  }
590 
591  double ratio = (itms2next->x - itms2->x);
592  if(ratio != 0)
593  {
594  ratio = (ms1_point.x - itms2->x) / ratio;
595  }
596  else
597  {
598  // avoid division by zero
599  ratio = 1;
600  }
601  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " <<
602  // ratio;
603 
604  ms1_point.y = itms2->y + ((itms2next->y - itms2->y) * ratio);
605 
606  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "
607  // << ms1_point.y;
608  ms1_aligned_points.push_back(ms1_point);
609  }
610 }

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

◆ setAlignedRetentionTimeVector()

template<class T >
void pappso::MsRunRetentionTime< T >::setAlignedRetentionTimeVector ( const std::vector< double > &  aligned_times)

Definition at line 642 of file msrunretentiontime.cpp.

644 {
645 
646  if(aligned_times.size() == m_ms1RetentionTimeVector.size())
647  {
648  m_alignedRetentionTimeVector = aligned_times;
649  }
650  else
651  {
652  if(aligned_times.size() == m_ms1RetentionTimeVector.size() * 2)
653  {
655  for(std::size_t i = 0; i < m_ms1RetentionTimeVector.size(); i++)
656  {
657  if(aligned_times[2 * i] != m_ms1RetentionTimeVector[i])
658  {
660  QObject::tr(
661  "ERROR : aligned_times (size=%1) vector does not have "
662  "required size (size=%2)")
663  .arg(aligned_times.size())
664  .arg(m_ms1RetentionTimeVector.size()));
665  }
666  m_alignedRetentionTimeVector[i] = aligned_times[(2 * i) + 1];
667  }
668  }
669  else
670  {
671  throw ExceptionNotPossible(
672  QObject::tr("ERROR : aligned_times (size=%1) vector does not have "
673  "required size (size=%2)")
674  .arg(aligned_times.size())
675  .arg(m_ms1RetentionTimeVector.size()));
676  }
677  }
678 }

◆ setMs1MeanFilter()

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

Definition at line 120 of file msrunretentiontime.cpp.

121 {
122  m_ms1MeanFilter = ms1MeanFilter;
123 }

◆ setMs2MeanFilter()

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

Definition at line 106 of file msrunretentiontime.cpp.

107 {
108  m_ms2MeanFilter = ms2MeanFilter;
109 }

◆ setMs2MedianFilter()

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

Definition at line 90 of file msrunretentiontime.cpp.

92 {
93  m_ms2MedianFilter = ms2MedianFilter;
94 }

◆ translateAligned2OriginalRetentionTime()

template<class T >
double MsRunRetentionTime::translateAligned2OriginalRetentionTime ( double  aligned_retention_time) const

Definition at line 385 of file msrunretentiontime.cpp.

387 {
388  if(m_alignedRetentionTimeVector.size() < 3)
389  {
390  throw ExceptionNotPossible(
391  QObject::tr("ERROR : too few aligned points to compute aligned "
392  "retention time (%1)")
393  .arg(m_ms1RetentionTimeVector.size()));
394  }
396  {
397  throw ExceptionNotPossible(
398  QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 "
399  "m_ms1RetentionTimeVector.size()")
400  .arg(m_alignedRetentionTimeVector.size())
401  .arg(m_ms1RetentionTimeVector.size()));
402  }
403  auto it_plus = std::find_if(m_alignedRetentionTimeVector.begin(),
405  [aligned_retention_time](const double &rt_point) {
406  return aligned_retention_time < rt_point;
407  });
408  double rt1_a, rt2_a, rt1_b, rt2_b;
409  if(it_plus == m_alignedRetentionTimeVector.end())
410  {
411  it_plus--;
412  }
413  if(it_plus == m_alignedRetentionTimeVector.begin())
414  {
415  it_plus++;
416  }
417  auto it_minus = it_plus - 1;
418 
419  rt1_a = *it_minus;
420  rt2_a = *it_plus;
421 
422  double ratio = (aligned_retention_time - rt1_a) / (rt2_a - rt1_a);
423 
424  auto itref = m_ms1RetentionTimeVector.begin() +
425  std::distance(m_alignedRetentionTimeVector.begin(), it_minus);
426 
427  rt1_b = *itref;
428  itref++;
429  rt2_b = *itref;
430 
431  return (((rt2_b - rt1_b) * ratio) + rt1_b);
432 }

◆ translateOriginal2AlignedRetentionTime()

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

Definition at line 333 of file msrunretentiontime.cpp.

335 {
336  if(m_alignedRetentionTimeVector.size() < 3)
337  {
338  throw ExceptionNotPossible(
339  QObject::tr("ERROR : too few aligned points to compute aligned "
340  "retention time (%1)")
341  .arg(m_ms1RetentionTimeVector.size()));
342  }
344  {
345  throw ExceptionNotPossible(
346  QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 "
347  "m_ms1RetentionTimeVector.size()")
348  .arg(m_alignedRetentionTimeVector.size())
349  .arg(m_ms1RetentionTimeVector.size()));
350  }
351  auto it_plus =
352  std::find_if(m_ms1RetentionTimeVector.begin(),
354  [original_retention_time](const double &rt_point) {
355  return original_retention_time < rt_point;
356  });
357  double rt1_a, rt2_a, rt1_b, rt2_b;
358  if(it_plus == m_ms1RetentionTimeVector.end())
359  {
360  it_plus--;
361  }
362  if(it_plus == m_ms1RetentionTimeVector.begin())
363  {
364  it_plus++;
365  }
366  auto it_minus = it_plus - 1;
367 
368  rt1_a = *it_minus;
369  rt2_a = *it_plus;
370 
371  double ratio = (original_retention_time - rt1_a) / (rt2_a - rt1_a);
372 
373  auto itref = m_alignedRetentionTimeVector.begin() +
374  std::distance(m_ms1RetentionTimeVector.begin(), it_minus);
375 
376  rt1_b = *itref;
377  itref++;
378  rt2_b = *itref;
379 
380  return (((rt2_b - rt1_b) * ratio) + rt1_b);
381 }

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 171 of file msrunretentiontime.h.

◆ m_ms1RetentionTimeVector

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

◆ m_ms2MeanFilter

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

Definition at line 170 of file msrunretentiontime.h.

◆ m_ms2MedianFilter

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

Definition at line 169 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: