libpappsomspp
Library for mass spectrometry
peptideisotopespectrummatch.cpp
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1 /*
2  * *******************************************************************************
3  * * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
4  * *
5  * * This file is part of MassChroqPRM.
6  * *
7  * * MassChroqPRM is free software: you can redistribute it and/or modify
8  * * it under the terms of the GNU General Public License as published by
9  * * the Free Software Foundation, either version 3 of the License, or
10  * * (at your option) any later version.
11  * *
12  * * MassChroqPRM is distributed in the hope that it will be useful,
13  * * but WITHOUT ANY WARRANTY; without even the implied warranty of
14  * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15  * * GNU General Public License for more details.
16  * *
17  * * You should have received a copy of the GNU General Public License
18  * * along with MassChroqPRM. If not, see <http://www.gnu.org/licenses/>.
19  * *
20  * * Contributors:
21  * * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
22  * implementation
23  * ******************************************************************************/
24 
25 
27 
28 namespace pappso
29 {
31  const MassSpectrum &spectrum,
32  const PeptideSp &peptideSp,
33  unsigned int parent_charge,
34  PrecisionPtr precision,
35  const std::list<PeptideIon> &ion_type_list,
36  unsigned int max_isotope_number,
37  [[maybe_unused]] unsigned int max_isotope_rank)
38  : _precision(precision)
39 {
40 
41  try
42  {
43  _peak_ion_match_list.clear();
44  qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
45  "begin max_isotope_number="
46  << max_isotope_number;
47  PeptideFragmentIonListBase fragmentIonList(peptideSp, ion_type_list);
48  qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
49  "peak_list spectrum.size="
50  << spectrum.size();
51  std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
52  for(auto ion_type : ion_type_list)
53  {
54  auto ion_list = fragmentIonList.getPeptideFragmentIonSp(ion_type);
55 
56  for(unsigned int charge = 1; charge <= parent_charge; charge++)
57  {
58  for(auto &&ion : ion_list)
59  {
60  for(unsigned int isotope_number = 0;
61  isotope_number <= max_isotope_number;
62  isotope_number++)
63  {
64  PeptideNaturalIsotopeAverage isotopeIon(
65  ion, isotope_number, charge, precision);
66 
67  qDebug()
68  << isotope_number << " " << isotopeIon.toString();
69 
70  std::vector<DataPoint>::iterator it_peak =
71  getBestPeakIterator(peak_list, isotopeIon);
72  if(it_peak != peak_list.end())
73  {
74  _peak_ion_match_list.push_back(PeakIonIsotopeMatch(
75  *it_peak,
76  isotopeIon.makePeptideNaturalIsotopeAverageSp(),
77  ion));
78  peak_list.erase(it_peak);
79 
80  qDebug() << isotope_number << " "
81  << _peak_ion_match_list.back().toString();
82  }
83  }
84  }
85  }
86  }
87  }
88  catch(PappsoException &exception_pappso)
89  {
90  QString errorStr =
91  QObject::tr(
92  "ERROR building PeptideIsotopeSpectrumMatch, PAPPSO exception:\n%1")
93  .arg(exception_pappso.qwhat());
94  qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
95  "PappsoException :\n"
96  << errorStr;
97  throw PappsoException(errorStr);
98  }
99  catch(std::exception &exception_std)
100  {
101  QString errorStr =
102  QObject::tr(
103  "ERROR building PeptideIsotopeSpectrumMatch, std exception:\n%1")
104  .arg(exception_std.what());
105  qDebug() << "PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch "
106  "std::exception :\n"
107  << errorStr;
108  throw PappsoException(errorStr);
109  }
110 }
111 
112 PeptideIsotopeSpectrumMatch::PeptideIsotopeSpectrumMatch(
113  const MassSpectrum &spectrum,
114  std::vector<PeptideNaturalIsotopeAverageSp> v_peptideIsotopeList,
115  std::vector<PeptideFragmentIonSp> v_peptideIonList,
116  PrecisionPtr precision)
117  : _precision(precision)
118 {
119  qDebug() << " begin";
120  if(v_peptideIsotopeList.size() != v_peptideIonList.size())
121  {
122  throw PappsoException(
123  QObject::tr(
124  "v_peptideIsotopeList.size() %1 != v_peptideIonList.size() %2")
125  .arg(v_peptideIsotopeList.size())
126  .arg(v_peptideIonList.size()));
127  }
128 
129  auto isotopeIt = v_peptideIsotopeList.begin();
130  auto ionIt = v_peptideIonList.begin();
131  std::vector<DataPoint> peak_list(spectrum.begin(), spectrum.end());
132 
133  while(isotopeIt != v_peptideIsotopeList.end())
134  {
135  std::vector<DataPoint>::iterator it_peak =
136  getBestPeakIterator(peak_list, *(isotopeIt->get()));
137  if(it_peak != peak_list.end())
138  {
139  _peak_ion_match_list.push_back(
140  PeakIonIsotopeMatch(*it_peak, *isotopeIt, *ionIt));
141  peak_list.erase(it_peak);
142  }
143  isotopeIt++;
144  ionIt++;
145  }
146  qDebug() << " end";
147 }
148 
149 
151  const PeptideIsotopeSpectrumMatch &other)
152  : _precision(other._precision),
153  _peak_ion_match_list(other._peak_ion_match_list)
154 {
155  qDebug();
156 }
157 
159 {
160 }
161 
162 
163 std::vector<DataPoint>::iterator
165  std::vector<DataPoint> &peak_list,
166  const PeptideNaturalIsotopeAverage &ion) const
167 {
168  // qDebug();
169  std::vector<DataPoint>::iterator itpeak = peak_list.begin();
170  std::vector<DataPoint>::iterator itend = peak_list.end();
171  std::vector<DataPoint>::iterator itselect = peak_list.end();
172 
173  pappso_double best_intensity = 0;
174 
175  while(itpeak != itend)
176  {
177  if(ion.matchPeak(itpeak->x))
178  {
179  if(itpeak->y > best_intensity)
180  {
181  best_intensity = itpeak->y;
182  itselect = itpeak;
183  }
184  }
185  itpeak++;
186  }
187  // qDebug();
188  return (itselect);
189 }
190 
191 const std::list<PeakIonIsotopeMatch> &
193 {
194  return _peak_ion_match_list;
195 }
196 
197 std::size_t
199 {
200  return _peak_ion_match_list.size();
201 }
204 {
205  return _peak_ion_match_list.begin();
206 }
209 {
210  return _peak_ion_match_list.end();
211 }
212 
213 void
215 {
216  qDebug();
218  [](const PeakIonIsotopeMatch &a, const PeakIonIsotopeMatch &b) {
219  if(a.getPeptideIonType() < b.getPeptideIonType())
220  return true;
221  if(a.getPeptideFragmentIonSp().get()->size() <
222  b.getPeptideFragmentIonSp().get()->size())
223  return true;
224  if(a.getCharge() < b.getCharge())
225  return true;
226  if(a.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber() <
227  b.getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
228  return true;
229  return false;
230  });
231  PeptideIon ion_type = PeptideIon::b;
232  std::size_t nserie = 0;
233  std::size_t isotopeserie = 0;
234  unsigned int charge = 0;
235  for(std::list<PeakIonIsotopeMatch>::iterator it =
236  _peak_ion_match_list.begin();
237  it != _peak_ion_match_list.end();
238  it++)
239  {
240  if((nserie != it->getPeptideFragmentIonSp().get()->size()) ||
241  (ion_type != it->getPeptideIonType()) || (charge != it->getCharge()))
242  {
243  ion_type = it->getPeptideIonType();
244  isotopeserie = 0;
245  nserie = it->getPeptideFragmentIonSp().get()->size();
246  charge = it->getCharge();
247  }
248  if(isotopeserie <=
249  it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber())
250  {
251  isotopeserie =
252  it->getPeptideNaturalIsotopeAverageSp().get()->getIsotopeNumber();
253  }
254  else
255  {
256  it = _peak_ion_match_list.erase(it);
257  }
258  }
259  qDebug();
260 }
261 } // namespace pappso
Class to represent a mass spectrum.
Definition: massspectrum.h:71
std::list< PeakIonIsotopeMatch >::const_iterator const_iterator
std::list< PeakIonIsotopeMatch > _peak_ion_match_list
PeptideIsotopeSpectrumMatch(const MassSpectrum &spectrum, const PeptideSp &peptide_sp, unsigned int parent_charge, PrecisionPtr precision, const std::list< PeptideIon > &ion_type_list, unsigned int max_isotope_number, unsigned int max_isotope_rank)
annotate spectrum with peptide ions and isotopes
const std::list< PeakIonIsotopeMatch > & getPeakIonIsotopeMatchList() const
virtual std::vector< DataPoint >::iterator getBestPeakIterator(std::vector< DataPoint > &peak_list, const PeptideNaturalIsotopeAverage &ion) const
virtual bool matchPeak(pappso_double peak_mz) const final
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:386
@ b
Nter acylium ions.
std::shared_ptr< const Peptide > PeptideSp
double pappso_double
A type definition for doubles.
Definition: types.h:49
const PrecisionBase * PrecisionPtr
Definition: precision.h:122