OpenMS  2.5.0
TargetedSpectraExtractor.h
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31 // $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
32 // $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h> // OPENMS_DLLAPI
44 
45 namespace OpenMS
46 {
69  class OPENMS_DLLAPI TargetedSpectraExtractor :
70  public DefaultParamHandler
71  {
72 public:
74  ~TargetedSpectraExtractor() override = default;
75 
80  struct Match
81  {
82  Match() = default;
83  Match(MSSpectrum a, double b) : spectrum(std::move(a)), score(b) {}
85  double score = 0.0;
86  };
87 
88  class Comparator
89  {
90  public:
91  virtual ~Comparator() = default;
92  virtual void generateScores(
93  const MSSpectrum& spec,
94  std::vector<std::pair<Size,double>>& scores,
95  double min_score
96  ) const = 0;
97 
98  virtual void init(
99  const std::vector<MSSpectrum>& library,
100  const std::map<String,DataValue>& options
101  ) = 0;
102 
103  const std::vector<MSSpectrum>& getLibrary() const
104  {
105  return library_;
106  }
107 
108  protected:
109  std::vector<MSSpectrum> library_;
110  };
111 
113  {
114  public:
115  ~BinnedSpectrumComparator() override = default;
117  const MSSpectrum& spec,
118  std::vector<std::pair<Size,double>>& scores,
119  double min_score
120  ) const override
121  {
122  scores.clear();
123  const BinnedSpectrum in_bs(spec, bin_size_, false, peak_spread_, bin_offset_);
124  for (Size i = 0; i < bs_library_.size(); ++i)
125  {
126  const double cmp_score = cmp_bs_(in_bs, bs_library_[i]);
127  if (cmp_score >= min_score)
128  {
129  scores.emplace_back(i, cmp_score);
130  }
131  }
132  }
133 
134  void init(const std::vector<MSSpectrum>& library, const std::map<String,DataValue>& options) override
135  {
136  if (options.count("bin_size"))
137  {
138  bin_size_ = options.at("bin_size");
139  }
140  if (options.count("peak_spread"))
141  {
142  peak_spread_ = options.at("peak_spread");
143  }
144  if (options.count("bin_offset"))
145  {
146  bin_offset_ = options.at("bin_offset");
147  }
148  library_ = library;
149  bs_library_.clear();
150  for (const MSSpectrum& s : library_)
151  {
152  bs_library_.emplace_back(s, bin_size_, false, peak_spread_, bin_offset_);
153  }
154  OPENMS_LOG_INFO << "The library contains " << bs_library_.size() << " spectra." << std::endl;
155  }
156  private:
158  std::vector<BinnedSpectrum> bs_library_;
159  double bin_size_ = 1.0;
160  UInt peak_spread_ = 0;
161  double bin_offset_ = 0.4;
162  };
163 
164  void getDefaultParameters(Param& params) const;
165 
182  void annotateSpectra(
183  const std::vector<MSSpectrum>& spectra,
184  const TargetedExperiment& targeted_exp,
185  std::vector<MSSpectrum>& annotated_spectra,
186  FeatureMap& features,
187  bool compute_features = true
188  ) const;
189 
204  void annotateSpectra(
205  const std::vector<MSSpectrum>& spectra,
206  const TargetedExperiment& targeted_exp,
207  std::vector<MSSpectrum>& annotated_spectra
208  ) const;
209 
227  void pickSpectrum(const MSSpectrum& spectrum, MSSpectrum& picked_spectrum) const;
228 
247  void scoreSpectra(
248  const std::vector<MSSpectrum>& annotated_spectra,
249  const std::vector<MSSpectrum>& picked_spectra,
250  FeatureMap& features,
251  std::vector<MSSpectrum>& scored_spectra,
252  bool compute_features = true
253  ) const;
254 
268  void scoreSpectra(
269  const std::vector<MSSpectrum>& annotated_spectra,
270  const std::vector<MSSpectrum>& picked_spectra,
271  std::vector<MSSpectrum>& scored_spectra
272  ) const;
273 
286  void selectSpectra(
287  const std::vector<MSSpectrum>& scored_spectra,
288  const FeatureMap& features,
289  std::vector<MSSpectrum>& selected_spectra,
290  FeatureMap& selected_features,
291  bool compute_features = true
292  ) const;
293 
301  void selectSpectra(
302  const std::vector<MSSpectrum>& scored_spectra,
303  std::vector<MSSpectrum>& selected_spectra
304  ) const;
305 
322  void extractSpectra(
323  const MSExperiment& experiment,
324  const TargetedExperiment& targeted_exp,
325  std::vector<MSSpectrum>& extracted_spectra,
326  FeatureMap& extracted_features,
327  bool compute_features = true
328  ) const;
329 
343  void extractSpectra(
344  const MSExperiment& experiment,
345  const TargetedExperiment& targeted_exp,
346  std::vector<MSSpectrum>& extracted_spectra
347  ) const;
348 
357  void matchSpectrum(
358  const MSSpectrum& input_spectrum,
359  const Comparator& cmp,
360  std::vector<Match>& matches
361  );
362 
385  void targetedMatching(
386  const std::vector<MSSpectrum>& spectra,
387  const Comparator& cmp,
388  FeatureMap& features
389  );
390 
412  void untargetedMatching(
413  const std::vector<MSSpectrum>& spectra,
414  const Comparator& cmp,
415  FeatureMap& features
416  );
417 
418 protected:
420  void updateMembers_() override;
421 
422 private:
427 
435  double rt_window_;
436 
445 
451 
457 
463 
464  double tic_weight_;
465  double fwhm_weight_;
466  double snr_weight_;
475 
482 
488 
491  };
492 }
Match(MSSpectrum a, double b)
Definition: TargetedSpectraExtractor.h:83
Size top_matches_to_report_
Definition: TargetedSpectraExtractor.h:487
std::vector< MSSpectrum > library_
Definition: TargetedSpectraExtractor.h:109
double min_match_score_
Minimum score for a match to be considered valid in `matchSpectrum()`.
Definition: TargetedSpectraExtractor.h:490
double min_select_score_
Definition: TargetedSpectraExtractor.h:474
void init(const std::vector< MSSpectrum > &library, const std::map< String, DataValue > &options) override
Definition: TargetedSpectraExtractor.h:134
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
bool mz_unit_is_Da_
Definition: TargetedSpectraExtractor.h:426
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Management and storage of parameters / INI files.
Definition: Param.h:73
This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on...
Definition: TargetedSpectraExtractor.h:69
double peak_height_max_
Definition: TargetedSpectraExtractor.h:456
double fwhm_weight_
Definition: TargetedSpectraExtractor.h:465
bool use_gauss_
Definition: TargetedSpectraExtractor.h:481
Definition: TargetedSpectraExtractor.h:88
A container for features.
Definition: FeatureMap.h:95
double peak_height_min_
Definition: TargetedSpectraExtractor.h:450
std::vector< BinnedSpectrum > bs_library_
Definition: TargetedSpectraExtractor.h:158
STL namespace.
double mz_tolerance_
Definition: TargetedSpectraExtractor.h:444
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Compare functor scoring the spectral contrast angle for similarity measurement.
Definition: BinnedSpectralContrastAngle.h:57
double rt_window_
Definition: TargetedSpectraExtractor.h:435
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
void generateScores(const MSSpectrum &spec, std::vector< std::pair< Size, double >> &scores, double min_score) const override
Definition: TargetedSpectraExtractor.h:116
double snr_weight_
Definition: TargetedSpectraExtractor.h:466
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
Definition: TargetedSpectraExtractor.h:80
double fwhm_threshold_
Definition: TargetedSpectraExtractor.h:462
Definition: TargetedSpectraExtractor.h:112
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
MSSpectrum spectrum
Definition: TargetedSpectraExtractor.h:84
BinnedSpectralContrastAngle cmp_bs_
Definition: TargetedSpectraExtractor.h:157
const std::vector< MSSpectrum > & getLibrary() const
Definition: TargetedSpectraExtractor.h:103
double tic_weight_
Definition: TargetedSpectraExtractor.h:464
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75