OpenMS  2.6.0
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 
66  void run(
67  std::vector<PeptideIdentification> peptides,
68  const std::vector<ProteinIdentification>& proteins,
69  std::vector<PeptideIdentification> peptides_ext,
70  std::vector<ProteinIdentification> proteins_ext,
71  FeatureMap& features,
72  const FeatureMap& seeds = FeatureMap()
73  );
74 
75  void runOnCandidates(FeatureMap& features);
76 
77  PeakMap& getMSData() { return ms_data_; }
78  const PeakMap& getMSData() const { return ms_data_; }
79 
80  PeakMap& getChromatograms() { return chrom_data_; }
81  const PeakMap& getChromatograms() const { return chrom_data_; }
82 
83  ProgressLogger& getProgressLogger() { return prog_log_; }
84  const ProgressLogger& getProgressLogger() const { return prog_log_; }
85 
86  TargetedExperiment& getLibrary() { return library_; }
87  const TargetedExperiment& getLibrary() const { return library_; }
88 
89 protected:
92 
94  typedef std::multimap<double, PeptideIdentification*> RTMap;
96  typedef std::map<Int, std::pair<RTMap, RTMap> > ChargeMap;
98  typedef std::map<AASequence, ChargeMap> PeptideMap;
100  typedef std::map<String, std::pair<RTMap, RTMap> > PeptideRefRTMap;
101 
103 
106 
108  double rt_window_;
109  double mz_window_;
111 
113 
114  double isotope_pmin_;
116 
117  double rt_quantile_;
118 
119  double peak_width_;
122 
124 
125  // SVM related parameters
132 
133  // output file (before filtering)
135 
137 
138  void updateMembers_() override;
139 
141  struct RTRegion
142  {
143  double start, end;
145  };
146 
149  {
150  bool operator()(const Feature& feature)
151  {
152  return feature.getOverallQuality() == 0.0;
153  }
154  } feature_filter_quality_;
155 
158  {
159  bool operator()(const Feature& feature)
160  {
161  return feature.getPeptideIdentifications().empty();
162  }
163  } feature_filter_peptides_;
164 
167  {
169  const PeptideIdentification& p2)
170  {
171  const String& seq1 = p1.getHits()[0].getSequence().toString();
172  const String& seq2 = p2.getHits()[0].getSequence().toString();
173  if (seq1 == seq2)
174  {
175  Int charge1 = p1.getHits()[0].getCharge();
176  Int charge2 = p2.getHits()[0].getCharge();
177  if (charge1 == charge2)
178  {
179  return p1.getRT() < p2.getRT();
180  }
181  return charge1 < charge2;
182  }
183  return seq1 < seq2;
184  }
185  } peptide_compare_;
186 
189  {
190  bool operator()(const Feature& f1, const Feature& f2)
191  {
192  const String& ref1 = f1.getMetaValue("PeptideRef");
193  const String& ref2 = f2.getMetaValue("PeptideRef");
194  if (ref1 == ref2)
195  {
196  return f1.getRT() < f2.getRT();
197  }
198  return ref1 < ref2;
199  }
200  } feature_compare_;
201 
205 
207  std::map<double, std::pair<Size, Size> > svm_probs_internal_;
209  std::multiset<double> svm_probs_external_;
212  TransformationDescription trafo_external_;
214  std::map<String, double> isotope_probs_;
216 
218 
220  void generateTransitions_(const String& peptide_id, double mz, Int charge,
221  const IsotopeDistribution& iso_dist);
222 
223  void addPeptideRT_(TargetedExperiment::Peptide& peptide, double rt) const;
224 
226  void getRTRegions_(ChargeMap& peptide_data, std::vector<RTRegion>& rt_regions) const;
227 
228  void annotateFeaturesFinalizeAssay_(
229  FeatureMap& features,
230  std::map<Size, std::vector<PeptideIdentification*> >& feat_ids,
231  RTMap& rt_internal);
232 
234  void annotateFeatures_(FeatureMap& features, PeptideRefRTMap& ref_rt_map);
235 
236  void ensureConvexHulls_(Feature& feature);
237 
238  void postProcess_(FeatureMap& features, bool with_external_ids);
239 
241  void statistics_(const FeatureMap& features) const;
242 
245  void createAssayLibrary_(const PeptideMap::iterator& begin, const PeptideMap::iterator& end, PeptideRefRTMap& ref_rt_map);
246 
247  void addPeptideToMap_(PeptideIdentification& peptide,
248  PeptideMap& peptide_map,
249  bool external = false) const;
250 
251  void checkNumObservations_(Size n_pos, Size n_neg, const String& note = "") const;
252 
253  void getUnbiasedSample_(const std::multimap<double, std::pair<Size, bool> >& valid_obs,
254  std::map<Size, Int>& training_labels);
255 
256  void getRandomSample_(std::map<Size, Int>& training_labels);
257 
258  void classifyFeatures_(FeatureMap& features);
259 
260  void filterFeaturesFinalizeAssay_(Feature& best_feature, double best_quality,
261  const double quality_cutoff);
262 
263  void filterFeatures_(FeatureMap& features, bool classified);
264 
265  void calculateFDR_(FeatureMap& features);
266 
269  template <typename It>
270  std::vector<std::pair<It,It>>
271  chunk_(It range_from, It range_to, const std::ptrdiff_t batch_size)
272  {
273  /* Aliases, to make the rest of the code more readable. */
274  using std::vector;
275  using std::pair;
276  using std::make_pair;
277  using std::distance;
278  using diff_t = std::ptrdiff_t;
279 
280  /* Total item number and batch_size size. */
281  const diff_t total {distance(range_from, range_to)};
282  const diff_t num {total / batch_size};
283 
284  vector<pair<It,It>> chunks(num);
285 
286  It batch_end {range_from};
287 
288  /* Use the 'generate' algorithm to create batches. */
289  std::generate(begin(chunks), end(chunks), [&batch_end, batch_size]()
290  {
291  It batch_start {batch_end };
292 
293  std::advance(batch_end, batch_size);
294  return make_pair(batch_start, batch_end);
295  });
296 
297  /* The last batch_size's end must always be 'range_to'. */
298  if (chunks.empty())
299  {
300  chunks.emplace_back(range_from, range_to);
301  }
302  else
303  {
304  chunks.back().second = range_to;
305  }
306 
307  return chunks;
308  }
309 };
310 
311 } // namespace OpenMS
312 
313 #endif
314 
DefaultParamHandler.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureCompare::operator()
bool operator()(const Feature &f1, const Feature &f2)
Definition: FeatureFinderIdentificationAlgorithm.h:190
OpenMS::FeatureFinderIdentificationAlgorithm::batch_size_
Size batch_size_
nr of peptides to use at the same time during chromatogram extraction
Definition: FeatureFinderIdentificationAlgorithm.h:107
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
TargetedExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideMap
std::map< AASequence, ChargeMap > PeptideMap
mapping: sequence -> charge -> internal/external ID information
Definition: FeatureFinderIdentificationAlgorithm.h:98
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides::operator()
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:159
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:202
OpenMS::FeatureFinderIdentificationAlgorithm::feat_finder_
MRMFeatureFinderScoring feat_finder_
OpenSWATH feature finder.
Definition: FeatureFinderIdentificationAlgorithm.h:215
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
PeakMap & getChromatograms()
Definition: FeatureFinderIdentificationAlgorithm.h:80
OpenMS::FeatureFinderIdentificationAlgorithm::svm_n_parts_
Size svm_n_parts_
number of partitions for SVM cross-validation
Definition: FeatureFinderIdentificationAlgorithm.h:130
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
const TargetedExperiment & getLibrary() const
Definition: FeatureFinderIdentificationAlgorithm.h:87
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_pmin_
double isotope_pmin_
min. isotope probability for peptide assay
Definition: FeatureFinderIdentificationAlgorithm.h:114
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::start
double start
Definition: FeatureFinderIdentificationAlgorithm.h:143
OpenMS::FeatureFinderIdentificationAlgorithm::peptide_map_
PeptideMap peptide_map_
Definition: FeatureFinderIdentificationAlgorithm.h:102
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
PeakMap & getMSData()
Definition: FeatureFinderIdentificationAlgorithm.h:77
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
TransformationModel.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion::ids
ChargeMap ids
internal/external peptide IDs (per charge) in this region
Definition: FeatureFinderIdentificationAlgorithm.h:144
OpenMS::MRMFeatureFinderScoring
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
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:119
OpenMS::FeatureFinderIdentificationAlgorithm::getProgressLogger
ProgressLogger & getProgressLogger()
Definition: FeatureFinderIdentificationAlgorithm.h:83
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:59
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureFinderIdentificationAlgorithm::isotope_probs_
std::map< String, double > isotope_probs_
isotope probabilities of transitions
Definition: FeatureFinderIdentificationAlgorithm.h:214
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:188
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::getProgressLogger
const ProgressLogger & getProgressLogger() const
Definition: FeatureFinderIdentificationAlgorithm.h:84
OpenMS::FeatureFinderIdentificationAlgorithm::signal_to_noise_
double signal_to_noise_
Definition: FeatureFinderIdentificationAlgorithm.h:121
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare::operator()
bool operator()(const PeptideIdentification &p1, const PeptideIdentification &p2)
Definition: FeatureFinderIdentificationAlgorithm.h:168
OpenMS::FeatureMap::setPrimaryMSRunPath
void setPrimaryMSRunPath(const StringList &s)
set the file path to the primary MS run (usually the mzML file obtained after data conversion from ra...
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())
FeatureFinderAlgorithmPickedHelperStructs.h
TransformationDescription.h
OpenMS::FeatureFinderIdentificationAlgorithm::candidates_out_
String candidates_out_
Definition: FeatureFinderIdentificationAlgorithm.h:134
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::FeatureFinderIdentificationAlgorithm::svm_probs_external_
std::multiset< double > svm_probs_external_
SVM probabilities for "external" features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:209
OpenMS::FeatureFinderIdentificationAlgorithm::library_
TargetedExperiment library_
accumulated assays for peptides
Definition: FeatureFinderIdentificationAlgorithm.h:204
OpenMS::FeatureFinderIdentificationAlgorithm::MassTrace
FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
Definition: FeatureFinderIdentificationAlgorithm.h:90
OpenMS::FeatureFinderIdentificationAlgorithm::getLibrary
TargetedExperiment & getLibrary()
Definition: FeatureFinderIdentificationAlgorithm.h:86
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:105
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterQuality
predicate for filtering features by overall quality:
Definition: FeatureFinderIdentificationAlgorithm.h:148
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::svm_n_samples_
Size svm_n_samples_
number of samples for SVM training
Definition: FeatureFinderIdentificationAlgorithm.h:131
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FeatureFinderIdentificationAlgorithm::ChargeMap
std::map< Int, std::pair< RTMap, RTMap > > ChargeMap
mapping: charge -> internal/external: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:96
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:54
IsotopeDistribution.h
ProgressLogger.h
OpenMS::FeatureFinderIdentificationAlgorithm::FeatureFilterPeptides
predicate for filtering features by assigned peptides:
Definition: FeatureFinderIdentificationAlgorithm.h:157
OpenMS::FeatureFinderIdentificationAlgorithm::svm_min_prob_
double svm_min_prob_
Definition: FeatureFinderIdentificationAlgorithm.h:126
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
int
OpenMS::FeatureFinderIdentificationAlgorithm::mz_window_
double mz_window_
m/z window width
Definition: FeatureFinderIdentificationAlgorithm.h:109
CoarseIsotopePatternGenerator.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_quality_cutoff
double svm_quality_cutoff
Definition: FeatureFinderIdentificationAlgorithm.h:129
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:136
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:100
OpenMS::FeatureFinderIdentificationAlgorithm::mapping_tolerance_
double mapping_tolerance_
RT tolerance for mapping IDs to features.
Definition: FeatureFinderIdentificationAlgorithm.h:112
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::FeatureFinderIdentificationAlgorithm::svm_predictor_names_
StringList svm_predictor_names_
Definition: FeatureFinderIdentificationAlgorithm.h:127
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:150
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
OpenMS::FeatureFinderIdentificationAlgorithm::getChromatograms
const PeakMap & getChromatograms() const
Definition: FeatureFinderIdentificationAlgorithm.h:81
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::FeatureFinderIdentificationAlgorithm::RTRegion
region in RT in which a peptide elutes:
Definition: FeatureFinderIdentificationAlgorithm.h:141
MSExperiment.h
OpenMS::FeatureFinderIdentificationAlgorithm::RTMap
std::multimap< double, PeptideIdentification * > RTMap
mapping: RT (not necessarily unique) -> pointer to peptide
Definition: FeatureFinderIdentificationAlgorithm.h:94
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:97
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::Param::remove
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
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:115
OpenMS::FeatureFinderIdentificationAlgorithm::PeptideCompare
comparison functor for (unassigned) peptide IDs
Definition: FeatureFinderIdentificationAlgorithm.h:166
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_features_
Size n_internal_features_
internal feature counter (for FDR calculation)
Definition: FeatureFinderIdentificationAlgorithm.h:210
OpenMS::FeatureFinderIdentificationAlgorithm::rt_quantile_
double rt_quantile_
Definition: FeatureFinderIdentificationAlgorithm.h:117
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::DataProcessing::QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
OpenMS::FeatureFinderIdentificationAlgorithm::MassTraces
FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
Definition: FeatureFinderIdentificationAlgorithm.h:91
OpenMS::FeatureFinderIdentificationAlgorithm::getMSData
const PeakMap & getMSData() const
Definition: FeatureFinderIdentificationAlgorithm.h:78
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::FeatureFinderIdentificationAlgorithm::min_peak_width_
double min_peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:120
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:108
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:110
OpenMS::FeatureFinderIdentificationAlgorithm::n_external_features_
Size n_external_features_
Definition: FeatureFinderIdentificationAlgorithm.h:211
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:207
OpenMS::FeatureFinderIdentificationAlgorithm::chrom_data_
PeakMap chrom_data_
accumulated chromatograms (XICs)
Definition: FeatureFinderIdentificationAlgorithm.h:203
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:61
OpenMS::Param::insert
void insert(const String &prefix, const Param &param)
FeatureFinderIdentificationAlgorithm.h
OpenMS::FeatureFinderIdentificationAlgorithm::n_internal_peps_
Size n_internal_peps_
number of internal peptide
Definition: FeatureFinderIdentificationAlgorithm.h:104
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:217
OpenMS::FeatureFinderIdentificationAlgorithm::elution_model_
String elution_model_
Definition: FeatureFinderIdentificationAlgorithm.h:123
MSSpectrum.h
OpenMS::FeatureFinderIdentificationAlgorithm::svm_xval_out_
String svm_xval_out_
Definition: FeatureFinderIdentificationAlgorithm.h:128
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63
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:271