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 35 of file msrunretentiontime.cpp.

37 {
38  msp_msrunReader = msrun_reader_sp;
39  mcsp_msrunId = msp_msrunReader.get()->getMsRunId();
40  m_ms1RetentionTimeVector = msp_msrunReader.get()->getRetentionTimeLine();
41 
42 
43  std::sort(m_ms1RetentionTimeVector.begin(),
45  [](const double &a, const double &b) { return (a < b); });
46 }
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 49 of file msrunretentiontime.cpp.

53 {
55  mcsp_msrunId = other.mcsp_msrunId;
58 
59  m_seamarks = other.m_seamarks;
61 
63 
65 }
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 68 of file msrunretentiontime.cpp.

69 {
70 }

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 185 of file msrunretentiontime.cpp.

188 {
189  PeptideMs2Point ms2point;
190  ms2point.entityHash = peptide_id;
191  ms2point.precursorIntensity = precursorIntensity;
192  ms2point.retentionTime = retentionTime;
193  m_allMs2Points.push_back(ms2point);
194 }

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 163 of file msrunretentiontime.cpp.

165 {
166 
167  qDebug();
168  msp_msrunReader.get()->acquireDevice();
169  PeptideMs2Point ms2point;
170  ms2point.entityHash = peptide_id;
171  QualifiedMassSpectrum spectrum =
172  msp_msrunReader.get()->qualifiedMassSpectrum(ms2_spectrum_index, false);
173  ms2point.precursorIntensity = spectrum.getPrecursorIntensity();
174  ms2point.retentionTime = spectrum.getRtInSeconds();
175 
176  // addSeamark(m_hash_fn(peptide_str.toStdString()), retentionTime);
177 
178  m_allMs2Points.push_back(ms2point);
179 
180  qDebug();
181 }
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 454 of file msrunretentiontime.cpp.

456 {
457  computeSeamarks();
458  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks;
459  if(msrun_retention_time_reference.isAligned())
460  {
461  other_seamarks = msrun_retention_time_reference.getSeamarksReferences();
462  }
463  else
464  {
465  other_seamarks = msrun_retention_time_reference.getSeamarks();
466  }
467  qDebug();
468  if((m_ms1MeanFilter.getHalfWindowSize() * 2 + 1) >=
470  {
471  throw ExceptionNotPossible(
472  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
473  "\ntoo few MS1 points (%3)")
474  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
475  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
476  .arg(m_ms1RetentionTimeVector.size()));
477  }
478 
479  qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime
480  << " " << other_seamarks[0].entityHash
481  << other_seamarks[0].retentionTime << " ";
482  // both seamarks has to be ordered
483  Trace common_points;
484  getCommonDeltaRt(common_points, other_seamarks);
485 
486  // writeTrace("lib_ms2_delta_rt.ods", common_points);
487 
488  qDebug() << common_points.front().x << " " << common_points.front().y;
489  m_ms2MedianFilter.filter(common_points);
490  // writeTrace("lib_ms2_delta_rt_median.ods", common_points);
491  m_ms2MeanFilter.filter(common_points);
492  // writeTrace("lib_ms2_delta_rt_mean.ods", common_points);
493  // convert common delta rt to real retention times (for convenience)
494  qDebug() << common_points.front().x << " " << common_points.front().y;
495 
496 
497  // add a first point to ensure coherence:
498  DataPoint first_point;
499  first_point.x = m_ms1RetentionTimeVector.front() - (double)1;
500  if(first_point.x < 0)
501  {
502  first_point.x = 0;
503  }
504  first_point.y =
505  m_ms1RetentionTimeVector.front() -
506  msrun_retention_time_reference.getFrontRetentionTimeReference();
507 
508  common_points.push_back(first_point);
509  // add a last point to ensure coherence:
510  DataPoint last_point;
511  last_point.x = m_ms1RetentionTimeVector.back() + 1;
512  last_point.y = m_ms1RetentionTimeVector.back() -
513  msrun_retention_time_reference.getBackRetentionTimeReference();
514  common_points.push_back(last_point);
515  common_points.sortX();
516 
517  // now, it is possible for each time range to give a new MS1 time using a
518  // linear regression on MS2 corrected times
520 
521  qDebug() << common_points.front().x << " " << common_points.front().y;
522 
523  Trace ms1_aligned_points;
524 
525  linearRegressionMs2toMs1(ms1_aligned_points, common_points);
526 
527  // writeTrace("lib_ms1_map_rt.ods", ms1_aligned_points);
528  qDebug();
529  // smoothing on MS1 points
530  m_ms1MeanFilter.filter(ms1_aligned_points);
531 
532  // writeTrace("lib_ms1_map_rt_mean.ods", ms1_aligned_points);
533  // final aligned retentionTime vector
534 
535  for(DataPoint &data_point : ms1_aligned_points)
536  {
537  data_point.y = (data_point.x - data_point.y);
538  }
539 
540  qDebug();
541  // Here, the correction parameter is the slope of old rt points curve
542  // (divided by 4 to get a finer correction).
543  double correction_parameter =
545  (ms1_aligned_points.size());
546  // set_correction_parameter(correction_parameter / 4);
547  correction_parameter = correction_parameter / (double)4;
548  correctNewTimeValues(ms1_aligned_points, correction_parameter);
549 
550  m_alignedRetentionTimeVector = ms1_aligned_points.yValues();
551 
552  qDebug();
553  return ms1_aligned_points;
554 }
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:905
pappso_double x
Definition: datapoint.h:22
pappso_double y
Definition: datapoint.h:23

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 199 of file msrunretentiontime.cpp.

200 {
201 
202  qDebug();
203  if(m_allMs2Points.size() == 0)
204  {
205  // already computed
206  return;
207  }
208  m_seamarks.clear();
211  {
212 
213 
214  std::sort(m_allMs2Points.begin(),
215  m_allMs2Points.end(),
216  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
217  if(a.entityHash == b.entityHash)
218  {
219  return (a.precursorIntensity > b.precursorIntensity);
220  }
221  return (a.entityHash < b.entityHash);
222  });
223 
224  auto itend =
225  std::unique(m_allMs2Points.begin(),
226  m_allMs2Points.end(),
227  [](const PeptideMs2Point &a, const PeptideMs2Point &b) {
228  return (a.entityHash == b.entityHash);
229  });
230 
231  auto it = m_allMs2Points.begin();
232  while(it != itend)
233  {
234  m_seamarks.push_back(
235  {it->entityHash, it->retentionTime, it->precursorIntensity});
236  it++;
237  }
238  }
239  m_allMs2Points.clear();
240 
241  std::sort(m_seamarks.begin(),
242  m_seamarks.end(),
245  return (a.entityHash < b.entityHash);
246  });
247  qDebug();
248 }

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

◆ correctNewTimeValues()

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

Definition at line 612 of file msrunretentiontime.cpp.

614 {
615 
616  m_valuesCorrected = 0;
617  auto new_it(ms1_aligned_points.begin());
618  auto new_nextit(ms1_aligned_points.begin());
619  new_nextit++;
620  for(; new_nextit != ms1_aligned_points.end(); ++new_nextit, ++new_it)
621  {
622  if(new_nextit->y < new_it->y)
623  {
625  new_nextit->y = new_it->y + correction_parameter;
626  }
627  }
628 }

◆ getAlignedRetentionTimeVector()

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

get aligned retention time vector

Returns
vector of seconds (as double)

Definition at line 133 of file msrunretentiontime.cpp.

134 {
136 }

◆ getBackRetentionTimeReference()

template<class T >
double MsRunRetentionTime::getBackRetentionTimeReference
protected

Definition at line 319 of file msrunretentiontime.cpp.

320 {
321  if(isAligned())
322  {
323  return m_alignedRetentionTimeVector.back();
324  }
325  return m_ms1RetentionTimeVector.back();
326 }

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 153 of file msrunretentiontime.cpp.

155 {
156  Trace common_points;
157  getCommonDeltaRt(common_points, other_seamarks);
158  return common_points;
159 }

◆ 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 252 of file msrunretentiontime.cpp.

255 {
256 
257  qDebug();
258  auto it = other_seamarks.begin();
259 
260  for(const MsRunRetentionTimeSeamarkPoint<T> &seamark : m_seamarks)
261  {
262  while((it != other_seamarks.end()) &&
263  (it->entityHash < seamark.entityHash))
264  {
265  it++;
266  }
267  if(it == other_seamarks.end())
268  break;
269  if(it->entityHash == seamark.entityHash)
270  {
271  delta_rt.push_back(DataPoint(
272  seamark.retentionTime, seamark.retentionTime - it->retentionTime));
273  }
274  }
275 
276  qDebug();
277  if((m_ms2MedianFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
278  {
279  throw ExceptionNotPossible(
280  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
281  "\ntoo few MS2 points (%3) in common")
282  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
283  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
284  .arg(delta_rt.size()));
285  }
286 
287  qDebug();
288  if((m_ms2MeanFilter.getHalfWindowSize() * 2 + 1) >= delta_rt.size())
289  {
290  throw ExceptionNotPossible(
291  QObject::tr("ERROR : MS2 alignment of MS run '%1' (%2)' not possible : "
292  "\ntoo few MS2 points (%3) in common")
293  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
294  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
295  .arg(delta_rt.size()));
296  }
297  delta_rt.sortX();
298 
299  // there can be multiple entities (peptides) at one retention time
300  // in this case, avoid retention time redundancy by applying unique on trace :
301  delta_rt.unique();
302 
303  qDebug();
304 }
void unique()
Definition: trace.cpp:921

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 681 of file msrunretentiontime.cpp.

683 {
684  // computeSeamarks();
685  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks;
686  if(msrun_retention_time_reference.isAligned())
687  {
688  other_seamarks = msrun_retention_time_reference.getSeamarksReferences();
689  }
690  else
691  {
692  other_seamarks = msrun_retention_time_reference.getSeamarks();
693  }
694  qDebug();
695 
696  qDebug() << m_seamarks[0].entityHash << " " << m_seamarks[0].retentionTime
697  << " " << other_seamarks[0].entityHash
698  << other_seamarks[0].retentionTime << " ";
699  // both seamarks has to be ordered
700  Trace common_points;
701  getCommonDeltaRt(common_points, other_seamarks);
702  return common_points;
703 }

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 309 of file msrunretentiontime.cpp.

310 {
311  if(isAligned())
312  {
313  return m_alignedRetentionTimeVector.front();
314  }
315  return m_ms1RetentionTimeVector.front();
316 }

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

◆ getMs1MeanFilter()

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

Definition at line 111 of file msrunretentiontime.cpp.

112 {
113  return m_ms1MeanFilter;
114 }

◆ 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 146 of file msrunretentiontime.cpp.

147 {
149 }

◆ getMs2MeanFilter()

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

Definition at line 96 of file msrunretentiontime.cpp.

97 {
98  return m_ms2MeanFilter;
99 }

◆ getMs2MedianFilter()

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

Definition at line 81 of file msrunretentiontime.cpp.

82 {
83  return m_ms2MedianFilter;
84 }

◆ getMsRunId()

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

Definition at line 74 of file msrunretentiontime.cpp.

75 {
76  return *(mcsp_msrunId.get());
77 }

◆ getMsRunReaderSPtr()

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

Definition at line 633 of file msrunretentiontime.cpp.

634 {
635  return msp_msrunReader;
636 }

◆ getNumberOfCorrectedValues()

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

Definition at line 140 of file msrunretentiontime.cpp.

141 {
142  return m_valuesCorrected;
143 }

◆ getSeamarks()

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

Definition at line 125 of file msrunretentiontime.cpp.

126 {
127  qDebug();
128  return m_seamarks;
129 }

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 434 of file msrunretentiontime.cpp.

435 {
436  std::vector<MsRunRetentionTimeSeamarkPoint<T>> other_seamarks = m_seamarks;
437  for(auto &seamark : other_seamarks)
438  {
439  seamark.retentionTime =
440  translateOriginal2AlignedRetentionTime(seamark.retentionTime);
441  }
442  return other_seamarks;
443 }
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 559 of file msrunretentiontime.cpp.

561 {
562 
563  // first slope :
564  std::vector<DataPoint>::const_iterator itms2 = common_points.begin();
565  std::vector<DataPoint>::const_iterator itms2next = itms2 + 1;
566  if(itms2next == common_points.end())
567  {
568  // error
569  throw ExceptionNotPossible(
570  QObject::tr("ERROR : MS1 alignment of MS run '%1' (%2)' not possible : "
571  "\ntoo few common points (%3)")
572  .arg(msp_msrunReader.get()->getMsRunId().get()->getXmlId())
573  .arg(msp_msrunReader.get()->getMsRunId().get()->getFileName())
574  .arg(common_points.size()));
575  }
576  qDebug() << "() itms2->x=" << itms2->x << " itms2->y=" << itms2->y;
577 
578  for(double &original_rt_point : m_ms1RetentionTimeVector)
579  {
580  DataPoint ms1_point;
581  ms1_point.x = original_rt_point;
582 
583  while(ms1_point.x > itms2next->x)
584  {
585  itms2++;
586  itms2next++;
587  }
588 
589  double ratio = (itms2next->x - itms2->x);
590  if(ratio != 0)
591  {
592  ratio = (ms1_point.x - itms2->x) / ratio;
593  }
594  else
595  {
596  // avoid division by zero
597  ratio = 1;
598  }
599  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() " <<
600  // ratio;
601 
602  ms1_point.y = itms2->y + ((itms2next->y - itms2->y) * ratio);
603 
604  // qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "() "
605  // << ms1_point.y;
606  ms1_aligned_points.push_back(ms1_point);
607  }
608 }

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 640 of file msrunretentiontime.cpp.

642 {
643 
644  if(aligned_times.size() == m_ms1RetentionTimeVector.size())
645  {
646  m_alignedRetentionTimeVector = aligned_times;
647  }
648  else
649  {
650  if(aligned_times.size() == m_ms1RetentionTimeVector.size() * 2)
651  {
653  for(std::size_t i = 0; i < m_ms1RetentionTimeVector.size(); i++)
654  {
655  if(aligned_times[2 * i] != m_ms1RetentionTimeVector[i])
656  {
658  QObject::tr(
659  "ERROR : aligned_times (size=%1) vector does not have "
660  "required size (size=%2)")
661  .arg(aligned_times.size())
662  .arg(m_ms1RetentionTimeVector.size()));
663  }
664  m_alignedRetentionTimeVector[i] = aligned_times[(2 * i) + 1];
665  }
666  }
667  else
668  {
669  throw ExceptionNotPossible(
670  QObject::tr("ERROR : aligned_times (size=%1) vector does not have "
671  "required size (size=%2)")
672  .arg(aligned_times.size())
673  .arg(m_ms1RetentionTimeVector.size()));
674  }
675  }
676 }

◆ setMs1MeanFilter()

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

Definition at line 118 of file msrunretentiontime.cpp.

119 {
120  m_ms1MeanFilter = ms1MeanFilter;
121 }

◆ setMs2MeanFilter()

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

Definition at line 104 of file msrunretentiontime.cpp.

105 {
106  m_ms2MeanFilter = ms2MeanFilter;
107 }

◆ setMs2MedianFilter()

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

Definition at line 88 of file msrunretentiontime.cpp.

90 {
91  m_ms2MedianFilter = ms2MedianFilter;
92 }

◆ translateAligned2OriginalRetentionTime()

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

Definition at line 383 of file msrunretentiontime.cpp.

385 {
386  if(m_alignedRetentionTimeVector.size() < 3)
387  {
388  throw ExceptionNotPossible(
389  QObject::tr("ERROR : too few aligned points to compute aligned "
390  "retention time (%1)")
391  .arg(m_ms1RetentionTimeVector.size()));
392  }
394  {
395  throw ExceptionNotPossible(
396  QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 "
397  "m_ms1RetentionTimeVector.size()")
398  .arg(m_alignedRetentionTimeVector.size())
399  .arg(m_ms1RetentionTimeVector.size()));
400  }
401  auto it_plus = std::find_if(m_alignedRetentionTimeVector.begin(),
403  [aligned_retention_time](const double &rt_point) {
404  return aligned_retention_time < rt_point;
405  });
406  double rt1_a, rt2_a, rt1_b, rt2_b;
407  if(it_plus == m_alignedRetentionTimeVector.end())
408  {
409  it_plus--;
410  }
411  if(it_plus == m_alignedRetentionTimeVector.begin())
412  {
413  it_plus++;
414  }
415  auto it_minus = it_plus - 1;
416 
417  rt1_a = *it_minus;
418  rt2_a = *it_plus;
419 
420  double ratio = (aligned_retention_time - rt1_a) / (rt2_a - rt1_a);
421 
422  auto itref = m_ms1RetentionTimeVector.begin() +
423  std::distance(m_alignedRetentionTimeVector.begin(), it_minus);
424 
425  rt1_b = *itref;
426  itref++;
427  rt2_b = *itref;
428 
429  return (((rt2_b - rt1_b) * ratio) + rt1_b);
430 }

◆ translateOriginal2AlignedRetentionTime()

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

Definition at line 331 of file msrunretentiontime.cpp.

333 {
334  if(m_alignedRetentionTimeVector.size() < 3)
335  {
336  throw ExceptionNotPossible(
337  QObject::tr("ERROR : too few aligned points to compute aligned "
338  "retention time (%1)")
339  .arg(m_ms1RetentionTimeVector.size()));
340  }
342  {
343  throw ExceptionNotPossible(
344  QObject::tr("ERROR : m_alignedRetentionTimeVector.size() %1 != %2 "
345  "m_ms1RetentionTimeVector.size()")
346  .arg(m_alignedRetentionTimeVector.size())
347  .arg(m_ms1RetentionTimeVector.size()));
348  }
349  auto it_plus =
350  std::find_if(m_ms1RetentionTimeVector.begin(),
352  [original_retention_time](const double &rt_point) {
353  return original_retention_time < rt_point;
354  });
355  double rt1_a, rt2_a, rt1_b, rt2_b;
356  if(it_plus == m_ms1RetentionTimeVector.end())
357  {
358  it_plus--;
359  }
360  if(it_plus == m_ms1RetentionTimeVector.begin())
361  {
362  it_plus++;
363  }
364  auto it_minus = it_plus - 1;
365 
366  rt1_a = *it_minus;
367  rt2_a = *it_plus;
368 
369  double ratio = (original_retention_time - rt1_a) / (rt2_a - rt1_a);
370 
371  auto itref = m_alignedRetentionTimeVector.begin() +
372  std::distance(m_ms1RetentionTimeVector.begin(), it_minus);
373 
374  rt1_b = *itref;
375  itref++;
376  rt2_b = *itref;
377 
378  return (((rt2_b - rt1_b) * ratio) + rt1_b);
379 }

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: