37 #include <OpenMS/config.h> 92 virtual void generateScores(
94 std::vector<std::pair<Size,double>>& scores,
99 const std::vector<MSSpectrum>& library,
100 const std::map<String,DataValue>& options
118 std::vector<std::pair<Size,double>>& scores,
123 const BinnedSpectrum in_bs(spec, bin_size_,
false, peak_spread_, bin_offset_);
124 for (
Size i = 0; i < bs_library_.size(); ++i)
126 const double cmp_score = cmp_bs_(in_bs, bs_library_[i]);
127 if (cmp_score >= min_score)
129 scores.emplace_back(i, cmp_score);
134 void init(
const std::vector<MSSpectrum>& library,
const std::map<String,DataValue>& options)
override 136 if (options.count(
"bin_size"))
138 bin_size_ = options.at(
"bin_size");
140 if (options.count(
"peak_spread"))
142 peak_spread_ = options.at(
"peak_spread");
144 if (options.count(
"bin_offset"))
146 bin_offset_ = options.at(
"bin_offset");
152 bs_library_.emplace_back(s, bin_size_,
false, peak_spread_, bin_offset_);
154 OPENMS_LOG_INFO <<
"The library contains " << bs_library_.size() <<
" spectra." << std::endl;
159 double bin_size_ = 1.0;
161 double bin_offset_ = 0.4;
164 void getDefaultParameters(
Param& params)
const;
182 void annotateSpectra(
183 const std::vector<MSSpectrum>& spectra,
185 std::vector<MSSpectrum>& annotated_spectra,
187 bool compute_features =
true 204 void annotateSpectra(
205 const std::vector<MSSpectrum>& spectra,
207 std::vector<MSSpectrum>& annotated_spectra
248 const std::vector<MSSpectrum>& annotated_spectra,
249 const std::vector<MSSpectrum>& picked_spectra,
251 std::vector<MSSpectrum>& scored_spectra,
252 bool compute_features =
true 269 const std::vector<MSSpectrum>& annotated_spectra,
270 const std::vector<MSSpectrum>& picked_spectra,
271 std::vector<MSSpectrum>& scored_spectra
287 const std::vector<MSSpectrum>& scored_spectra,
289 std::vector<MSSpectrum>& selected_spectra,
291 bool compute_features =
true 302 const std::vector<MSSpectrum>& scored_spectra,
303 std::vector<MSSpectrum>& selected_spectra
325 std::vector<MSSpectrum>& extracted_spectra,
327 bool compute_features =
true 346 std::vector<MSSpectrum>& extracted_spectra
360 std::vector<Match>& matches
385 void targetedMatching(
386 const std::vector<MSSpectrum>& spectra,
412 void untargetedMatching(
413 const std::vector<MSSpectrum>& spectra,
420 void updateMembers_()
override;
const std::vector< MSSpectrum > & getLibrary() const
Definition: TargetedSpectraExtractor.h:103
Definition: TargetedSpectraExtractor.h:112
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double peak_height_max_
Definition: TargetedSpectraExtractor.h:456
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
A container for features.
Definition: FeatureMap.h:95
This class filters, annotates, picks, and scores spectra (e.g., taken from a DDA experiment) based on...
Definition: TargetedSpectraExtractor.h:69
void init(const std::vector< MSSpectrum > &library, const std::map< String, DataValue > &options) override
Definition: TargetedSpectraExtractor.h:134
Definition: TargetedSpectraExtractor.h:88
Match(MSSpectrum a, double b)
Definition: TargetedSpectraExtractor.h:83
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
BinnedSpectralContrastAngle cmp_bs_
Definition: TargetedSpectraExtractor.h:157
std::vector< BinnedSpectrum > bs_library_
Definition: TargetedSpectraExtractor.h:158
bool mz_unit_is_Da_
Definition: TargetedSpectraExtractor.h:426
MSSpectrum spectrum
Definition: TargetedSpectraExtractor.h:84
Compare functor scoring the spectral contrast angle for similarity measurement.
Definition: BinnedSpectralContrastAngle.h:57
double peak_height_min_
Definition: TargetedSpectraExtractor.h:450
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Definition: TargetedSpectraExtractor.h:80
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
double min_select_score_
Definition: TargetedSpectraExtractor.h:474
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Management and storage of parameters / INI files.
Definition: Param.h:73
Size top_matches_to_report_
Definition: TargetedSpectraExtractor.h:487
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75
double fwhm_threshold_
Definition: TargetedSpectraExtractor.h:462
bool use_gauss_
Definition: TargetedSpectraExtractor.h:481
std::vector< MSSpectrum > library_
Definition: TargetedSpectraExtractor.h:109
double mz_tolerance_
Definition: TargetedSpectraExtractor.h:444
double min_match_score_
Minimum score for a match to be considered valid in `matchSpectrum()`.
Definition: TargetedSpectraExtractor.h:490
double snr_weight_
Definition: TargetedSpectraExtractor.h:466
double fwhm_weight_
Definition: TargetedSpectraExtractor.h:465
double tic_weight_
Definition: TargetedSpectraExtractor.h:464
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
void generateScores(const MSSpectrum &spec, std::vector< std::pair< Size, double >> &scores, double min_score) const override
Definition: TargetedSpectraExtractor.h:116
double rt_window_
Definition: TargetedSpectraExtractor.h:435