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OpenMS
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35 #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
36 #define OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERIDENTIFICATIONALGORITHM_H
52 class IsotopeDistribution;
65 std::vector<PeptideIdentification> peptides,
66 std::vector<ProteinIdentification> proteins,
67 std::vector<PeptideIdentification> peptides_ext,
68 std::vector<ProteinIdentification> proteins_ext,
91 typedef std::multimap<double, PeptideIdentification*>
RTMap;
93 typedef std::map<Int, std::pair<RTMap, RTMap> >
ChargeMap;
134 void updateMembers_()
override;
150 } feature_filter_quality_;
159 } feature_filter_peptides_;
167 const String& seq1 = p1.
getHits()[0].getSequence().toString();
168 const String& seq2 = p2.
getHits()[0].getSequence().toString();
173 if (charge1 == charge2)
177 return charge1 < charge2;
216 void generateTransitions_(
const String& peptide_id,
double mz,
Int charge,
222 void getRTRegions_(
ChargeMap& peptide_data, std::vector<RTRegion>& rt_regions)
const;
224 void annotateFeaturesFinalizeAssay_(
226 std::map<
Size, std::vector<PeptideIdentification*> >& feat_ids,
232 void ensureConvexHulls_(
Feature& feature);
234 void postProcess_(
FeatureMap& features,
bool with_external_ids);
237 void statistics_(
const FeatureMap& features)
const;
243 bool external =
false)
const;
245 void checkNumObservations_(
Size n_pos,
Size n_neg,
const String& note =
"")
const;
247 void getUnbiasedSample_(
const std::multimap<
double, std::pair<Size, bool> >& valid_obs,
248 std::map<Size, Int>& training_labels);
250 void getRandomSample_(std::map<Size, Int>& training_labels);
254 void filterFeaturesFinalizeAssay_(
Feature& best_feature,
double best_quality,
255 const double quality_cutoff);
257 void filterFeatures_(
FeatureMap& features,
bool classified);
bool operator()(const Feature &f1, const Feature &f2)
Definition: FeatureFinderIdentificationAlgorithm.h:186
double start
Definition: FeatureFinderIdentificationAlgorithm.h:139
Base class for TOPP applications.
Definition: TOPPBase.h:150
std::map< AASequence, ChargeMap > PeptideMap
mapping: sequence -> charge -> internal/external ID information
Definition: FeatureFinderIdentificationAlgorithm.h:95
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:155
void store(const String &filename, const TargetedExperiment &id) const
Stores a map in a TraML file.
PeakMap ms_data_
Definition: FeatureFinderIdentificationAlgorithm.h:198
MRMFeatureFinderScoring feat_finder_
Definition: FeatureFinderIdentificationAlgorithm.h:211
PeakMap & getChromatograms()
Definition: FeatureFinderIdentificationAlgorithm.h:77
Size svm_n_parts_
Definition: FeatureFinderIdentificationAlgorithm.h:126
const TargetedExperiment & getLibrary() const
Definition: FeatureFinderIdentificationAlgorithm.h:84
double isotope_pmin_
Definition: FeatureFinderIdentificationAlgorithm.h:110
PeptideMap peptide_map_
Definition: FeatureFinderIdentificationAlgorithm.h:99
PeakMap & getMSData()
Definition: FeatureFinderIdentificationAlgorithm.h:74
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:451
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:93
QualityType getOverallQuality() const
Non-mutable access to the overall quality.
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
double peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:115
ProgressLogger & getProgressLogger()
Definition: FeatureFinderIdentificationAlgorithm.h:80
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
std::map< String, double > isotope_probs_
Definition: FeatureFinderIdentificationAlgorithm.h:210
Helper struct for mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:79
comparison functor for features
Definition: FeatureFinderIdentificationAlgorithm.h:184
void addMSLevel(int level)
adds a desired MS level for peaks to load
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
ChargeMap ids
Definition: FeatureFinderIdentificationAlgorithm.h:140
const ProgressLogger & getProgressLogger() const
Definition: FeatureFinderIdentificationAlgorithm.h:81
double signal_to_noise_
Definition: FeatureFinderIdentificationAlgorithm.h:117
bool operator()(const PeptideIdentification &p1, const PeptideIdentification &p2)
Definition: FeatureFinderIdentificationAlgorithm.h:164
String candidates_out_
Definition: FeatureFinderIdentificationAlgorithm.h:130
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
std::multiset< double > svm_probs_external_
SVM probabilities for "external" features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:205
TargetedExperiment library_
Definition: FeatureFinderIdentificationAlgorithm.h:200
FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
Definition: FeatureFinderIdentificationAlgorithm.h:87
TargetedExperiment & getLibrary()
Definition: FeatureFinderIdentificationAlgorithm.h:83
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
Definition: FeatureFinderIdentificationAlgorithm.h:54
Size n_external_peps_
Definition: FeatureFinderIdentificationAlgorithm.h:102
predicate for filtering features by overall quality:
Definition: FeatureFinderIdentificationAlgorithm.h:144
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
int Int
Signed integer type.
Definition: Types.h:102
Size svm_n_samples_
Definition: FeatureFinderIdentificationAlgorithm.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::map< Int, std::pair< RTMap, RTMap > > ChargeMap
mapping: charge -> internal/external: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:93
File adapter for HUPO PSI TraML files.
Definition: TraMLFile.h:63
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
predicate for filtering features by assigned peptides:
Definition: FeatureFinderIdentificationAlgorithm.h:153
double svm_min_prob_
Definition: FeatureFinderIdentificationAlgorithm.h:122
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...
double mz_window_
Definition: FeatureFinderIdentificationAlgorithm.h:105
double svm_quality_cutoff
Definition: FeatureFinderIdentificationAlgorithm.h:125
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
Size debug_level_
Definition: FeatureFinderIdentificationAlgorithm.h:132
std::map< String, std::pair< RTMap, RTMap > > PeptideRefRTMap
mapping: peptide ref. -> int./ext.: (RT -> pointer to peptide)
Definition: FeatureFinderIdentificationAlgorithm.h:97
double mapping_tolerance_
Definition: FeatureFinderIdentificationAlgorithm.h:108
void setParameters(const Param ¶m)
Sets the parameters.
StringList svm_predictor_names_
Definition: FeatureFinderIdentificationAlgorithm.h:123
region in RT in which a peptide elutes:
Definition: FeatureFinderIdentificationAlgorithm.h:137
bool operator()(const Feature &feature)
Definition: FeatureFinderIdentificationAlgorithm.h:146
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:73
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
const PeakMap & getChromatograms() const
Definition: FeatureFinderIdentificationAlgorithm.h:78
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
std::multimap< double, PeptideIdentification * > RTMap
mapping: RT (not necessarily unique) -> pointer to peptide
Definition: FeatureFinderIdentificationAlgorithm.h:91
A container for features.
Definition: FeatureMap.h:93
Definition: IsotopeDistribution.h:72
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
An LC-MS feature.
Definition: Feature.h:70
void run(std::vector< PeptideIdentification > peptides, std::vector< ProteinIdentification > proteins, std::vector< PeptideIdentification > peptides_ext, std::vector< ProteinIdentification > proteins_ext, FeatureMap &features)
Size n_isotopes_
Definition: FeatureFinderIdentificationAlgorithm.h:111
comparison functor for (unassigned) peptide IDs
Definition: FeatureFinderIdentificationAlgorithm.h:162
TransformationDescription trafo_external_
TransformationDescription trafo_; // RT transformation (to range 0-1)
Definition: FeatureFinderIdentificationAlgorithm.h:209
Size n_internal_features_
Definition: FeatureFinderIdentificationAlgorithm.h:206
double rt_quantile_
Definition: FeatureFinderIdentificationAlgorithm.h:113
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
@ QUANTITATION
Quantitation.
Definition: DataProcessing.h:72
FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
Definition: FeatureFinderIdentificationAlgorithm.h:88
const PeakMap & getMSData() const
Definition: FeatureFinderIdentificationAlgorithm.h:75
double min_peak_width_
Definition: FeatureFinderIdentificationAlgorithm.h:116
void clear(bool clear_meta_data)
Clears all data and meta data.
double rt_window_
Definition: FeatureFinderIdentificationAlgorithm.h:104
Helper struct for a collection of mass traces used in FeatureFinderAlgorithmPicked.
Definition: FeatureFinderAlgorithmPickedHelperStructs.h:109
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
bool mz_window_ppm_
Definition: FeatureFinderIdentificationAlgorithm.h:106
Size n_external_features_
Definition: FeatureFinderIdentificationAlgorithm.h:207
std::map< double, std::pair< Size, Size > > svm_probs_internal_
SVM probability -> number of pos./neg. features (for FDR calculation):
Definition: FeatureFinderIdentificationAlgorithm.h:203
PeakMap chrom_data_
Definition: FeatureFinderIdentificationAlgorithm.h:199
void runOnCandidates(FeatureMap &features)
@ FILTERING
Data filtering or extraction.
Definition: DataProcessing.h:71
Size n_internal_peps_
Definition: FeatureFinderIdentificationAlgorithm.h:101
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
ProgressLogger prog_log_
Definition: FeatureFinderIdentificationAlgorithm.h:213
String elution_model_
Definition: FeatureFinderIdentificationAlgorithm.h:119
String svm_xval_out_
Definition: FeatureFinderIdentificationAlgorithm.h:124
Used to load and store idXML files.
Definition: IdXMLFile.h:63
double getRT() const
returns the RT of the MS2 spectrum where the identification occurred