libpappsomspp
Library for mass spectrometry
pappso::PeptideSpectrumMatch Class Reference

#include <peptidespectrummatch.h>

Public Types

typedef std::list< PeakIonMatch >::const_iterator const_iterator
 

Public Member Functions

 PeptideSpectrumMatch (const MassSpectrum &spectrum, const pappso::PeptideSp &peptideSp, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list)
 
 PeptideSpectrumMatch (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &peptide_fragment_ion_list, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list)
 
 PeptideSpectrumMatch (const MassSpectrum &spectrum, std::vector< PeptideFragmentIonSp > &v_peptide_fragment_ion, std::vector< unsigned int > &v_peptide_fragment_ion_charge, PrecisionPtr precision)
 
 PeptideSpectrumMatch (const PeptideSpectrumMatch &other)
 
virtual ~PeptideSpectrumMatch ()
 
bool contains (const PeptideFragmentIon *peptideFragmentIonSp, unsigned int z) const
 
unsigned int size () const
 
const_iterator begin () const
 
const_iterator end () const
 
unsigned int countTotalMatchedIons () const
 
const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > & getIonTypeCountArray () const
 

Private Member Functions

void privMatchIonList (const MassSpectrum &spectrum, const PeptideFragmentIonListBase &fragmentIonList, unsigned int max_charge, const std::list< PeptideIon > &ion_type_list)
 
virtual std::list< DataPoint >::iterator getBestPeakIterator (std::list< DataPoint > &peak_list, const PeptideFragmentIonSp &ion, unsigned int charge) const
 

Private Attributes

PrecisionPtr _precision
 
std::list< PeakIonMatch_peak_ion_match_list
 
std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT_ion_type_count = {{0}}
 

Detailed Description

Definition at line 43 of file peptidespectrummatch.h.

Member Typedef Documentation

◆ const_iterator

Constructor & Destructor Documentation

◆ PeptideSpectrumMatch() [1/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch ( const MassSpectrum spectrum,
const pappso::PeptideSp peptideSp,
unsigned int  parent_charge,
PrecisionPtr  precision,
const std::list< PeptideIon > &  ion_type_list 
)

Definition at line 146 of file peptidespectrummatch.cpp.

152  : _precision(precision)
153 {
154  PeptideFragmentIonListBase fragmentIonList(peptideSp, ion_type_list);
155  privMatchIonList(spectrum, fragmentIonList, parent_charge, ion_type_list);
156  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
157  << " _ion_type_count[PeptideIon::y]="
158  << _ion_type_count[(std::int8_t)PeptideIon::y];
159 }
void privMatchIonList(const MassSpectrum &spectrum, const PeptideFragmentIonListBase &fragmentIonList, unsigned int max_charge, const std::list< PeptideIon > &ion_type_list)
std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > _ion_type_count
@ y
Cter amino ions.

References _ion_type_count, privMatchIonList(), and pappso::y.

◆ PeptideSpectrumMatch() [2/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch ( const MassSpectrum spectrum,
const PeptideFragmentIonListBase peptide_fragment_ion_list,
unsigned int  parent_charge,
PrecisionPtr  precision,
const std::list< PeptideIon > &  ion_type_list 
)

Definition at line 132 of file peptidespectrummatch.cpp.

138  : _precision(precision)
139 {
140  privMatchIonList(spectrum, fragmentIonList, max_charge, ion_type_list);
141  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
142  << " _ion_type_count[PeptideIon::y]="
143  << _ion_type_count[(std::int8_t)PeptideIon::y];
144 }

References _ion_type_count, privMatchIonList(), and pappso::y.

◆ PeptideSpectrumMatch() [3/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch ( const MassSpectrum spectrum,
std::vector< PeptideFragmentIonSp > &  v_peptide_fragment_ion,
std::vector< unsigned int > &  v_peptide_fragment_ion_charge,
PrecisionPtr  precision 
)

Definition at line 86 of file peptidespectrummatch.cpp.

91  : _precision(precision)
92 {
93  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
94  // throw PappsoException(QObject::tr("v_peptideIsotopeList.size() %1 !=
95  // v_peptideIonList.size()
96  // %2").arg(v_peptideIsotopeList.size()).arg(v_peptideIonList.size()));
97  if(v_peptide_fragment_ion.size() != v_peptide_fragment_ion_charge.size())
98  {
99  throw PappsoException(
100  QObject::tr("v_peptide_fragment_ion.size() != "
101  "v_peptide_fragment_ion_charge.size() %2")
102  .arg(v_peptide_fragment_ion.size())
103  .arg(v_peptide_fragment_ion_charge.size()));
104  }
105 
106 
107  auto ionIt = v_peptide_fragment_ion.begin();
108  auto chargeIt = v_peptide_fragment_ion_charge.begin();
109  std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
110 
111  while(ionIt != v_peptide_fragment_ion.end())
112  {
113  std::list<DataPoint>::iterator it_peak =
114  getBestPeakIterator(peak_list, *ionIt, *chargeIt);
115  if(it_peak != peak_list.end())
116  {
117  _peak_ion_match_list.push_back(
118  PeakIonMatch(*it_peak, *ionIt, *chargeIt));
119  _ion_type_count[(std::int8_t)ionIt->get()->getPeptideIonType()]++;
120  peak_list.erase(it_peak);
121  }
122 
123  ionIt++;
124  chargeIt++;
125  }
126  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
127  << " _ion_type_count[PeptideIon::y]="
128  << _ion_type_count[(std::int8_t)PeptideIon::y];
129 }
virtual std::list< DataPoint >::iterator getBestPeakIterator(std::list< DataPoint > &peak_list, const PeptideFragmentIonSp &ion, unsigned int charge) const
std::list< PeakIonMatch > _peak_ion_match_list

References _ion_type_count, _peak_ion_match_list, getBestPeakIterator(), and pappso::y.

◆ PeptideSpectrumMatch() [4/4]

pappso::PeptideSpectrumMatch::PeptideSpectrumMatch ( const PeptideSpectrumMatch other)

Definition at line 162 of file peptidespectrummatch.cpp.

163  : _precision(other._precision),
164  _peak_ion_match_list(other._peak_ion_match_list)
165 {
166 }

◆ ~PeptideSpectrumMatch()

pappso::PeptideSpectrumMatch::~PeptideSpectrumMatch ( )
virtual

Definition at line 202 of file peptidespectrummatch.cpp.

203 {
204 }

Member Function Documentation

◆ begin()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::begin ( ) const

Definition at line 214 of file peptidespectrummatch.cpp.

215 {
216  return _peak_ion_match_list.begin();
217 }

References _peak_ion_match_list.

◆ contains()

bool pappso::PeptideSpectrumMatch::contains ( const PeptideFragmentIon peptideFragmentIonSp,
unsigned int  z 
) const

Definition at line 237 of file peptidespectrummatch.cpp.

239 {
240  auto it = _peak_ion_match_list.begin();
241  while(it != _peak_ion_match_list.end())
242  {
243  const PeakIonMatch &ref = *it;
244  if((ref.getCharge() == z) &&
245  (ref.getPeptideFragmentIonSp().get() == peptideFragmentIonSp))
246  {
247  return true;
248  }
249  it++;
250  }
251  return false;
252 }

References _peak_ion_match_list, pappso::PeakIonMatch::getCharge(), pappso::PeakIonMatch::getPeptideFragmentIonSp(), and pappso::z.

◆ countTotalMatchedIons()

unsigned int pappso::PeptideSpectrumMatch::countTotalMatchedIons ( ) const

Definition at line 225 of file peptidespectrummatch.cpp.

226 {
227  return std::accumulate(_ion_type_count.begin(), _ion_type_count.end(), 0);
228 }

References _ion_type_count.

◆ end()

PeptideSpectrumMatch::const_iterator pappso::PeptideSpectrumMatch::end ( ) const

Definition at line 219 of file peptidespectrummatch.cpp.

220 {
221  return _peak_ion_match_list.end();
222 }

References _peak_ion_match_list.

◆ getBestPeakIterator()

std::list< DataPoint >::iterator pappso::PeptideSpectrumMatch::getBestPeakIterator ( std::list< DataPoint > &  peak_list,
const PeptideFragmentIonSp ion,
unsigned int  charge 
) const
privatevirtual

Definition at line 169 of file peptidespectrummatch.cpp.

172 {
173  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
174  // << " peak_list.size()=" << peak_list.size();
175  std::list<DataPoint>::iterator itpeak = peak_list.begin();
176  std::list<DataPoint>::iterator itend = peak_list.end();
177  std::list<DataPoint>::iterator itselect = peak_list.end();
178 
179  pappso_double best_intensity = 0;
180 
181  while(itpeak != itend)
182  {
183 
184  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
185  // << " itpeak->x=" << itpeak->x;
186  if(ion.get()->matchPeak(_precision, itpeak->x, charge))
187  {
188  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
189  // << " ion.get()->matchPeak";
190  if(itpeak->y > best_intensity)
191  {
192  best_intensity = itpeak->y;
193  itselect = itpeak;
194  }
195  }
196  itpeak++;
197  }
198 
199  return (itselect);
200 }
double pappso_double
A type definition for doubles.
Definition: types.h:49

References _precision.

Referenced by PeptideSpectrumMatch(), and privMatchIonList().

◆ getIonTypeCountArray()

const std::array< unsigned int, PEPTIDE_ION_TYPE_COUNT > & pappso::PeptideSpectrumMatch::getIonTypeCountArray ( ) const

Definition at line 231 of file peptidespectrummatch.cpp.

232 {
233  return _ion_type_count;
234 }

References _ion_type_count.

◆ privMatchIonList()

void pappso::PeptideSpectrumMatch::privMatchIonList ( const MassSpectrum spectrum,
const PeptideFragmentIonListBase fragmentIonList,
unsigned int  max_charge,
const std::list< PeptideIon > &  ion_type_list 
)
private

Definition at line 45 of file peptidespectrummatch.cpp.

50 {
51 
52  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
53  // << " ion_type_list.size()=" << ion_type_list.size();
54  std::list<DataPoint> peak_list(spectrum.begin(), spectrum.end());
55  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
56  // << " peak_list.size()=" << peak_list.size();
57 
58  for(auto ion_type : ion_type_list)
59  {
60  auto ion_list = fragmentIonList.getPeptideFragmentIonSp(ion_type);
61  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
62  // << " ion_list.size()=" << ion_list.size();
63  for(unsigned int charge = 1; charge <= max_charge; charge++)
64  {
65  for(auto &&ion : ion_list)
66  {
67  std::list<DataPoint>::iterator it_peak =
68  getBestPeakIterator(peak_list, ion, charge);
69 
70  if(it_peak != peak_list.end())
71  {
72 
73  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " <<
74  // __LINE__
75  // << " peak FOUND";
76  _peak_ion_match_list.push_back(
77  PeakIonMatch(*it_peak, ion, charge));
78  _ion_type_count[(std::int8_t)ion->getPeptideIonType()]++;
79  peak_list.erase(it_peak);
80  }
81  }
82  }
83  }
84 }

References _ion_type_count, _peak_ion_match_list, getBestPeakIterator(), and pappso::PeptideFragmentIonListBase::getPeptideFragmentIonSp().

Referenced by PeptideSpectrumMatch().

◆ size()

unsigned int pappso::PeptideSpectrumMatch::size ( ) const

Definition at line 208 of file peptidespectrummatch.cpp.

209 {
210  return _peak_ion_match_list.size();
211 }

References _peak_ion_match_list.

Member Data Documentation

◆ _ion_type_count

std::array<unsigned int, PEPTIDE_ION_TYPE_COUNT> pappso::PeptideSpectrumMatch::_ion_type_count = {{0}}
private

◆ _peak_ion_match_list

std::list<PeakIonMatch> pappso::PeptideSpectrumMatch::_peak_ion_match_list
private

◆ _precision

PrecisionPtr pappso::PeptideSpectrumMatch::_precision
private

Definition at line 92 of file peptidespectrummatch.h.

Referenced by getBestPeakIterator().


The documentation for this class was generated from the following files: