OpenMS  3.0.0
FeatureFinderIdentificationAlgorithm.h
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34 
35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
37 
45 
46 #include <vector>
47 #include <fstream>
48 #include <map>
49 
50 namespace OpenMS
51 {
52  class IsotopeDistribution;
53 
54 
55 
57  public DefaultParamHandler
58 {
59 public:
62 
75  void run(
76  std::vector<PeptideIdentification> peptides,
77  const std::vector<ProteinIdentification>& proteins,
78  std::vector<PeptideIdentification> peptides_ext,
79  std::vector<ProteinIdentification> proteins_ext,
80  FeatureMap& features,
81  const FeatureMap& seeds = FeatureMap(),
82  const String spectra_file = ""
83  );
84 
85  void runOnCandidates(FeatureMap& features);
86 
87  PeakMap& getMSData();
88  const PeakMap& getMSData() const;
89 
91  void setMSData(const PeakMap& ms_data); // for pyOpenMS
92  void setMSData(PeakMap&& ms_data); // moves peak data and saves the copy. Note that getMSData() will give back a processed/modified version.
93 
94  PeakMap& getChromatograms();
95  const PeakMap& getChromatograms() const;
96 
97  ProgressLogger& getProgressLogger();
98  const ProgressLogger& getProgressLogger() const;
99 
100  TargetedExperiment& getLibrary();
101  const TargetedExperiment& getLibrary() const;
102 
103 protected:
106 
108  typedef std::multimap<double, PeptideIdentification*> RTMap;
110  typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap;
112  typedef std::map<AASequence, ChargeMap> PeptideMap;
114  typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap;
115 
117 
120 
122  double rt_window_;
123  double mz_window_;
125 
127 
128  double isotope_pmin_;
130 
131  double rt_quantile_;
132 
133  double peak_width_;
136 
138 
139  // SVM related parameters
146 
147  // output file (before filtering)
149 
151 
152  void updateMembers_() override;
153 
155  struct RTRegion
156  {
157  double start, end;
159  };
160 
163  {
164  bool operator()(const Feature& feature)
165  {
166  return feature.getOverallQuality() == 0.0;
167  }
168  } feature_filter_quality_;
169 
172  {
173  bool operator()(const Feature& feature)
174  {
175  return feature.getPeptideIdentifications().empty();
176  }
177  } feature_filter_peptides_;
178 
181  {
183  const PeptideIdentification& p2)
184  {
185  const String& seq1 = p1.getHits()[0].getSequence().toString();
186  const String& seq2 = p2.getHits()[0].getSequence().toString();
187  if (seq1 == seq2)
188  {
189  Int charge1 = p1.getHits()[0].getCharge();
190  Int charge2 = p2.getHits()[0].getCharge();
191  if (charge1 == charge2)
192  {
193  return p1.getRT() < p2.getRT();
194  }
195  return charge1 < charge2;
196  }
197  return seq1 < seq2;
198  }
199  } peptide_compare_;
200 
203  {
204  bool operator()(const Feature& f1, const Feature& f2)
205  {
206  const String& ref1 = f1.getMetaValue("PeptideRef");
207  const String& ref2 = f2.getMetaValue("PeptideRef");
208  if (ref1 == ref2)
209  {
210  return f1.getRT() < f2.getRT();
211  }
212  return ref1 < ref2;
213  }
214  } feature_compare_;
215 
219 
221 
222  const double seed_rt_window_ = 60.0;
223 
225  std::map<double, std::pair<Size, Size> > svm_probs_internal_;
227  std::multiset<double> svm_probs_external_;
230  TransformationDescription trafo_external_;
232  std::map<String, double> isotope_probs_;
234 
236 
238  void generateTransitions_(const String& peptide_id, double mz, Int charge,
239  const IsotopeDistribution& iso_dist);
240 
241  void addPeptideRT_(TargetedExperiment::Peptide& peptide, double rt) const;
242 
244  void getRTRegions_(ChargeMap& peptide_data, std::vector<RTRegion>& rt_regions, bool clear_IDs = true) const;
245 
246  void annotateFeaturesFinalizeAssay_(
247  FeatureMap& features,
248  std::map<Size, std::vector<PeptideIdentification*> >& feat_ids,
249  RTMap& rt_internal);
250 
252  void annotateFeatures_(FeatureMap& features, PeptideRefRTMap& ref_rt_map);
253 
254  void ensureConvexHulls_(Feature& feature) const;
255 
256  void postProcess_(FeatureMap& features, bool with_external_ids);
257 
259  void statistics_(const FeatureMap& features) const;
260 
264  void createAssayLibrary_(const PeptideMap::iterator& begin, const PeptideMap::iterator& end, PeptideRefRTMap& ref_rt_map, bool clear_IDs = true);
265 
269  void addPeptideToMap_(PeptideIdentification& peptide,
270  PeptideMap& peptide_map,
271  bool external = false) const;
272 
273  void checkNumObservations_(Size n_pos, Size n_neg, const String& note = "") const;
274 
275  void getUnbiasedSample_(const std::multimap<double, std::pair<Size, bool> >& valid_obs,
276  std::map<Size, Int>& training_labels);
277 
278  void getRandomSample_(std::map<Size, Int>& training_labels) const;
279 
280  void classifyFeatures_(FeatureMap& features);
281 
282  void filterFeaturesFinalizeAssay_(Feature& best_feature, double best_quality,
283  const double quality_cutoff);
284 
285  void filterFeatures_(FeatureMap& features, bool classified);
286 
287  void calculateFDR_(FeatureMap& features);
288 
291  template <typename It>
292  std::vector<std::pair<It,It>>
293  chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)
294  {
295  /* Aliases, to make the rest of the code more readable. */
296  using std::vector;
297  using std::pair;
298  using std::make_pair;
299  using std::distance;
300  using diff_t = std::ptrdiff_t;
301 
302  /* Total item number and batch_size size. */
303  const diff_t total {distance(range_from, range_to)};
304  const diff_t num {total / batch_size};
305 
306  vector<pair<It,It>> chunks(num);
307 
308  It batch_end {range_from};
309 
310  /* Use the 'generate' algorithm to create batches. */
311  std::generate(begin(chunks), end(chunks), [&batch_end, batch_size]()
312  {
313  It batch_start {batch_end };
314 
315  std::advance(batch_end, batch_size);
316  return make_pair(batch_start, batch_end);
317  });
318 
319  /* The last batch_size's end must always be 'range_to'. */
320  if (chunks.empty())
321  {
322  chunks.emplace_back(range_from, range_to);
323  }
324  else
325  {
326  chunks.back().second = range_to;
327  }
328 
329  return chunks;
330  }
331 };
332 
333 } // namespace OpenMS
334 
335 #endif
336 
DefaultParamHandler.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare::operator()
bool operator()(const Feature &f1, const Feature &f2)
Definition: FeatureFinderIdentificationAlgorithm.h:204
OpenMS::FeatureFinderIdentificationAlgorithm::batch_size_
Size batch_size_
nr of peptides to use at the same time during chromatogram extraction
Definition: FeatureFinderIdentificationAlgorithm.h:121
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
TargetedExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideMap
std::map< AASequence, ChargeMap > PeptideMap
mapping: sequence -> charge -> internal/external ID information
Definition: FeatureFinderIdentificationAlgorithm.h:112
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:173
OpenMS::TraMLFile::store
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
OpenMS::FeatureFinderIdentificationAlgorithm::ms_data_
PeakMap ms_data_
input LC-MS data
Definition: FeatureFinderIdentificationAlgorithm.h:216
OpenMS::FeatureFinderIdentificationAlgorithm::feat_finder_
MRMFeatureFinderScoring feat_finder_
OpenSWATH feature finder.
Definition: FeatureFinderIdentificationAlgorithm.h:233
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
PeakMap & getChromatograms()
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_parts_
Size svm_n_parts_
number of partitions for SVM cross-validation
Definition: FeatureFinderIdentificationAlgorithm.h:144
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_pmin_
double isotope_pmin_
min. isotope probability for peptide assay
Definition: FeatureFinderIdentificationAlgorithm.h:128
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::start
double start
Definition: FeatureFinderIdentificationAlgorithm.h:157
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
OpenMS::FeatureFinderIdentificationAlgorithm::peptide_map_
PeptideMap peptide_map_
Definition: FeatureFinderIdentificationAlgorithm.h:116
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
PeakMap & getMSData()
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:358
TransformationModel.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::ids
ChargeMap ids
internal/external peptide IDs (per charge) in this region
Definition: FeatureFinderIdentificationAlgorithm.h:158
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:89
OpenMS::Feature::getOverallQuality
QualityType getOverallQuality() const
Non-mutable access to the overall quality.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MetaInfoInterface::getMetaValue
const DataValue & getMetaValue(const String &name, const DataValue &default_value=DataValue::EMPTY) const
Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not fo...
OpenMS::FeatureFinderIdentificationAlgorithm::peak_width_
double peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:133
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
ProgressLogger & getProgressLogger()
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_probs_
std::map< String, double > isotope_probs_
isotope probabilities of transitions
Definition: FeatureFinderIdentificationAlgorithm.h:232
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTrace
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:79
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare
comparison functor for features
Definition: FeatureFinderIdentificationAlgorithm.h:202
OpenMS::PeakFileOptions::addMSLevel
void addMSLevel(int level)
adds a desired MS level for peaks to load
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
FeatureXMLFile.h
OpenMS::FeatureFinderIdentificationAlgorithm::quantify_decoys_
bool quantify_decoys_
Definition: FeatureFinderIdentificationAlgorithm.h:220
OpenMS::FeatureFinderIdentificationAlgorithm::signal_to_noise_
double signal_to_noise_
Definition: FeatureFinderIdentificationAlgorithm.h:135
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()
bool operator()(const PeptideIdentification &p1, const PeptideIdentification &p2)
Definition: FeatureFinderIdentificationAlgorithm.h:182
FeatureFinderAlgorithmPickedHelperStructs.h
TransformationDescription.h
OpenMS::FeatureFinderIdentificationAlgorithm::candidates_out_
String candidates_out_
Definition: FeatureFinderIdentificationAlgorithm.h:148
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_external_
std::multiset< double > svm_probs_external_
SVM probabilities for "external" features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:227
OpenMS::FeatureFinderIdentificationAlgorithm::library_
TargetedExperiment library_
accumulated assays for peptides
Definition: FeatureFinderIdentificationAlgorithm.h:218
OpenMS::FeatureFinderIdentificationAlgorithm::MassTrace
FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
Definition: FeatureFinderIdentificationAlgorithm.h:104
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
TargetedExperiment & getLibrary()
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::PeptideIdentification::getHits
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
OpenMS::FeatureFinderIdentificationAlgorithm
Definition: FeatureFinderIdentificationAlgorithm.h:56
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_peps_
Size n_external_peps_
number of external peptides
Definition: FeatureFinderIdentificationAlgorithm.h:119
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality
predicate for filtering features by overall quality:
Definition: FeatureFinderIdentificationAlgorithm.h:162
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::FeatureFinderIdentificationAlgorithm::run
void run(std::vector< PeptideIdentification > peptides, const std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features, const FeatureMap &seeds=FeatureMap(), const String spectra_file="")
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_samples_
Size svm_n_samples_
number of samples for SVM training
Definition: FeatureFinderIdentificationAlgorithm.h:145
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FeatureFinderIdentificationAlgorithm::ChargeMap
std::map< Int, std::pair< RTMap, RTMap > > ChargeMap
mapping: charge -> internal/external: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:110
OpenMS::TraMLFile
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
IsotopeDistribution.h
ProgressLogger.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides
predicate for filtering features by assigned peptides:
Definition: FeatureFinderIdentificationAlgorithm.h:171
OpenMS::FeatureFinderIdentificationAlgorithm::svm_min_prob_
double svm_min_prob_
Definition: FeatureFinderIdentificationAlgorithm.h:140
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
MRMFeatureFinderScoring.h
TransformationXMLFile.h
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_
double mz_window_
m/z window width
Definition: FeatureFinderIdentificationAlgorithm.h:123
CoarseIsotopePatternGenerator.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_quality_cutoff
double svm_quality_cutoff
Definition: FeatureFinderIdentificationAlgorithm.h:143
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::FeatureFinderIdentificationAlgorithm::debug_level_
Size debug_level_
Definition: FeatureFinderIdentificationAlgorithm.h:150
MapAlignmentAlgorithmIdentification.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideRefRTMap
std::map< String, std::pair< RTMap, RTMap > > PeptideRefRTMap
mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:114
OpenMS::FeatureFinderIdentificationAlgorithm::mapping_tolerance_
double mapping_tolerance_
RT tolerance for mapping IDs to features.
Definition: FeatureFinderIdentificationAlgorithm.h:126
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::FeatureFinderIdentificationAlgorithm::svm_predictor_names_
StringList svm_predictor_names_
Definition: FeatureFinderIdentificationAlgorithm.h:141
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:164
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion
region in RT in which a peptide elutes:
Definition: FeatureFinderIdentificationAlgorithm.h:155
MSExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTMap
std::multimap< double, PeptideIdentification * > RTMap
mapping: RT (not necessarily unique) -> pointer to peptide
Definition: FeatureFinderIdentificationAlgorithm.h:108
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::FeatureFinderIdentificationAlgorithm::n_isotopes_
Size n_isotopes_
number of isotopes for peptide assay
Definition: FeatureFinderIdentificationAlgorithm.h:129
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare
comparison functor for (unassigned) peptide IDs
Definition: FeatureFinderIdentificationAlgorithm.h:180
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_features_
Size n_internal_features_
internal feature counter (for FDR calculation)
Definition: FeatureFinderIdentificationAlgorithm.h:228
OpenMS::FeatureFinderIdentificationAlgorithm::rt_quantile_
double rt_quantile_
Definition: FeatureFinderIdentificationAlgorithm.h:131
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::FeatureFinderIdentificationAlgorithm::MassTraces
FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
Definition: FeatureFinderIdentificationAlgorithm.h:105
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::FeatureFinderIdentificationAlgorithm::min_peak_width_
double min_peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:134
OpenMS::MSExperiment::clear
void clear(bool clear_meta_data)
Clears all data and meta data.
OpenMS::FeatureFinderIdentificationAlgorithm::rt_window_
double rt_window_
RT window width.
Definition: FeatureFinderIdentificationAlgorithm.h:122
OpenMS::FeatureFinderAlgorithmPickedHelperStructs::MassTraces
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:109
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_ppm_
bool mz_window_ppm_
m/z window width is given in PPM (not Da)?
Definition: FeatureFinderIdentificationAlgorithm.h:124
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_features_
Size n_external_features_
Definition: FeatureFinderIdentificationAlgorithm.h:229
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_internal_
std::map< double, std::pair< Size, Size > > svm_probs_internal_
SVM probability -> number of pos./neg. features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:225
OpenMS::FeatureFinderIdentificationAlgorithm::chrom_data_
PeakMap chrom_data_
accumulated chromatograms (XICs)
Definition: FeatureFinderIdentificationAlgorithm.h:217
OpenMS::FeatureFinderIdentificationAlgorithm::runOnCandidates
void runOnCandidates(FeatureMap &features)
OpenMS::DataProcessing::FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
TraMLFile.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
OpenMS::Param::remove
void remove(const std::string &key)
Remove the entry key or a section key (when suffix is ':')
FeatureFinderIdentificationAlgorithm.h
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_peps_
Size n_internal_peps_
number of internal peptide
Definition: FeatureFinderIdentificationAlgorithm.h:118
OpenMS::MzMLFile::getOptions
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::FeatureFinderIdentificationAlgorithm::prog_log_
ProgressLogger prog_log_
Definition: FeatureFinderIdentificationAlgorithm.h:235
OpenMS::FeatureFinderIdentificationAlgorithm::elution_model_
String elution_model_
Definition: FeatureFinderIdentificationAlgorithm.h:137
MSSpectrum.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_xval_out_
String svm_xval_out_
Definition: FeatureFinderIdentificationAlgorithm.h:142
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::PeptideIdentification::getRT
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred
OpenMS::FeatureFinderIdentificationAlgorithm::chunk_
std::vector< std::pair< It, It > > chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)
Definition: FeatureFinderIdentificationAlgorithm.h:293