43 #include <boost/unordered_map.hpp> 46 #include <unordered_set> 51 struct ScoreToTgtDecLabelPairs;
90 void apply(std::vector<PeptideIdentification>& fwd_ids, std::vector<PeptideIdentification>& rev_ids)
const;
97 void apply(std::vector<PeptideIdentification>&
id)
const;
105 void apply(std::vector<ProteinIdentification>& fwd_ids, std::vector<ProteinIdentification>& rev_ids)
const;
112 void apply(std::vector<ProteinIdentification>& ids)
const;
119 void applyEstimated(std::vector<ProteinIdentification>& ids)
const;
130 double applyEvaluateProteinIDs(
const std::vector<ProteinIdentification>& ids,
double pepCutoff = 1.0,
UInt fpCutoff = 50,
double diffWeight = 0.2);
131 double applyEvaluateProteinIDs(
const ProteinIdentification& ids,
double pepCutoff = 1.0,
UInt fpCutoff = 50,
double diffWeight = 0.2);
134 void applyBasic(std::vector<PeptideIdentification> & ids);
136 void applyBasic(
ConsensusMap & cmap,
bool use_unassigned_peptides =
true);
142 double rocN(
const std::vector<PeptideIdentification>& ids,
Size fp_cutoff)
const;
146 double rocN(
const std::vector<PeptideIdentification>& ids,
Size fp_cutoff,
const String& identifier)
const;
176 void calculateFDRs_(std::map<double, double>& score_to_fdr, std::vector<double>& target_scores, std::vector<double>& decoy_scores,
bool q_value,
bool higher_score_better)
const;
179 void handleQueryMatch_(
182 std::vector<double>& target_scores,
183 std::vector<double>& decoy_scores,
184 std::map<IdentificationData::IdentifiedMoleculeRef, bool>& molecule_to_decoy,
185 std::map<IdentificationData::QueryMatchRef, double>& match_to_score)
const;
189 void calculateEstimatedQVal_(std::map<double, double> &scores_to_FDR,
191 bool higher_score_better)
const;
198 void calculateFDRBasic_(std::map<double,double>& scores_to_FDR,
ScoreToTgtDecLabelPairs& scores_labels,
bool qvalue,
bool higher_score_better)
const;
211 double trapezoidal_area_xEqy(
double exp1,
double exp2,
double act1,
double act2)
const;
214 double trapezoidal_area(
double x1,
double x2,
double y1,
double y2)
const;
A more convenient string class.
Definition: String.h:58
Calculates false discovery rates (FDR) from identifications.
Definition: FalseDiscoveryRate.h:77
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:43
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
A container for consensus elements.
Definition: ConsensusMap.h:79
Definition: IDScoreGetterSetter.h:53
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:89
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127