OpenMS  2.8.0
IDMapper.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Marc Sturm, Hendrik Weisser, Chris Bielow $
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34 
35 #pragma once
36 
41 
43 
45 
46 #include <algorithm>
47 #include <limits>
48 
49 namespace OpenMS
50 {
64  class OPENMS_DLLAPI IDMapper :
65  public DefaultParamHandler
66  {
67 public:
68  enum Measure {MEASURE_PPM = 0, MEASURE_DA};
69 
72 
74  IDMapper(const IDMapper& cp);
75 
77  IDMapper& operator=(const IDMapper& rhs);
78 
94  void annotate(PeakMap& map, const std::vector<PeptideIdentification>& peptide_ids, const std::vector<ProteinIdentification>& protein_ids, const bool clear_ids = false, const bool map_ms1 = false);
95 
111  void annotate(PeakMap& map, FeatureMap fmap, const bool clear_ids = false, const bool map_ms1 = false);
112 
131  void annotate(FeatureMap& map, const std::vector<PeptideIdentification>& ids, const std::vector<ProteinIdentification>& protein_ids, bool use_centroid_rt = false, bool use_centroid_mz = false, const PeakMap& spectra = PeakMap());
132 
149  void annotate(ConsensusMap& map, const std::vector<PeptideIdentification>& ids,
150  const std::vector<ProteinIdentification>& protein_ids,
151  bool measure_from_subelements = false,
152  bool annotate_ids_with_subelements = false,
153  const PeakMap& spectra = PeakMap());
154 
155 
160  {
161  std::vector<Size> no_precursors;
162  std::vector<Size> identified;
163  std::vector<Size> unidentified;
164  };
165 
182  const std::vector<PeptideIdentification>& ids,
183  double mz_tol = 0.001,
184  double rt_tol = 0.001)
185  {
187  for (Size spectrum_index = 0; spectrum_index < spectra.size(); ++spectrum_index)
188  {
189  const MSSpectrum& spectrum = spectra[spectrum_index];
190  if (!spectrum.getPrecursors().empty())
191  {
192  bool identified(false);
193  const std::vector<Precursor>& precursors = spectrum.getPrecursors();
194 
195  // check if precursor has been identified
196  for (Size i_p = 0; i_p < precursors.size(); ++i_p)
197  {
198  // check by precursor mass and spectrum RT
199  double mz_p = precursors[i_p].getMZ();
200  double rt_s = spectrum.getRT();
201 
202  for (Size i_id = 0; i_id != ids.size(); ++i_id)
203  {
204  const PeptideIdentification& pid = ids[i_id];
205 
206  // do not count empty ids as identification of a spectrum
207  if (pid.getHits().empty()) continue;
208 
209  double mz_id = pid.getMZ();
210  double rt_id = pid.getRT();
211 
212  if ( fabs(mz_id - mz_p) < mz_tol && fabs(rt_s - rt_id) < rt_tol )
213  {
214  identified = true;
215  break;
216  }
217  }
218  }
219  if (!identified)
220  {
221  ret.unidentified.push_back(spectrum_index);
222  }
223  else
224  {
225  ret.identified.push_back(spectrum_index);
226  }
227  }
228  else
229  {
230  ret.no_precursors.push_back(spectrum_index);
231  }
232  }
233  return ret;
234  }
235 
236 
237 protected:
238  void updateMembers_() override;
239 
248 
252  double getAbsoluteMZTolerance_(const double mz) const;
253 
255  bool isMatch_(const double rt_distance, const double mz_theoretical, const double mz_observed) const;
256 
258  void checkHits_(const std::vector<PeptideIdentification>& ids) const;
259 
263  void getIDDetails_(const PeptideIdentification& id, double& rt_pep, DoubleList& mz_values, IntList& charges, bool use_avg_mass = false) const;
264 
267 
270  bool checkMassType_(const std::vector<DataProcessing>& processing) const;
271 
272  };
273 
274 } // namespace OpenMS
275 
A container for consensus elements.
Definition: ConsensusMap.h:90
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
A container for features.
Definition: FeatureMap.h:106
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
void getIDDetails_(const PeptideIdentification &id, double &rt_pep, DoubleList &mz_values, IntList &charges, bool use_avg_mass=false) const
std::vector< Size > unidentified
Definition: IDMapper.h:163
Measure measure_
Measure used for m/z.
Definition: IDMapper.h:245
void increaseBoundingBox_(DBoundingBox< 2 > &box)
increase a bounding box by the given RT and m/z tolerances
double getAbsoluteMZTolerance_(const double mz) const
void checkHits_(const std::vector< PeptideIdentification > &ids) const
helper function that checks if all peptide hits are annotated with RT and MZ meta values
bool isMatch_(const double rt_distance, const double mz_theoretical, const double mz_observed) const
check if distance constraint is fulfilled (using rt_tolerance_, mz_tolerance_ and measure_)
IDMapper & operator=(const IDMapper &rhs)
Assignment.
double mz_tolerance_
Allowed m/z deviation.
Definition: IDMapper.h:243
static SpectraIdentificationState mapPrecursorsToIdentifications(const PeakMap &spectra, const std::vector< PeptideIdentification > &ids, double mz_tol=0.001, double rt_tol=0.001)
Mapping of peptide identifications to spectra This helper function partitions all spectra into those ...
Definition: IDMapper.h:181
void annotate(ConsensusMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool measure_from_subelements=false, bool annotate_ids_with_subelements=false, const PeakMap &spectra=PeakMap())
Mapping method for consensus maps.
IDMapper()
Default constructor.
std::vector< Size > no_precursors
Definition: IDMapper.h:161
bool checkMassType_(const std::vector< DataProcessing > &processing) const
IDMapper(const IDMapper &cp)
Copy C'Tor.
void annotate(PeakMap &map, FeatureMap fmap, const bool clear_ids=false, const bool map_ms1=false)
Mapping method for peak maps.
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
void annotate(FeatureMap &map, const std::vector< PeptideIdentification > &ids, const std::vector< ProteinIdentification > &protein_ids, bool use_centroid_rt=false, bool use_centroid_mz=false, const PeakMap &spectra=PeakMap())
Mapping method for feature maps.
bool ignore_charge_
Ignore charge states during matching?
Definition: IDMapper.h:247
std::vector< Size > identified
Definition: IDMapper.h:162
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool map_ms1=false)
Mapping method for peak maps.
Measure
Definition: IDMapper.h:68
double rt_tolerance_
Allowed RT deviation.
Definition: IDMapper.h:241
Result of a partitioning by identification state with mapPrecursorsToIdentifications().
Definition: IDMapper.h:160
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
Size size() const
Definition: MSExperiment.h:120
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
double getRT() const
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
double getMZ() const
returns the MZ of the MS2 spectrum
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
std::vector< double > DoubleList
Vector of double precision real types.
Definition: ListUtils.h:62
MSExperiment PeakMap
Two-dimensional map of raw data points or peaks.
Definition: StandardTypes.h:61
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47