100 void updateMembers_()
override;
111 void initDataStructures_(std::vector<PeptideIdentification>& peptide_ids,
ProteinIdentification& protein_id);
127 std::vector< double >& fdr,
bool mono);
134 static void calc_qfdr_(
const std::vector< double >& fdr, std::vector< double >& qfdr);
136 void findTopUniqueHits_(std::vector<PeptideIdentification>& peptide_ids);
138 void writeArgumentsLog_()
const;
146 return std::min(alpha_ions, beta_ions);
165 const String &decoy_string)
171 return prot1 == prot2;
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
static const String param_decoy_string_
Definition: XFDRAlgorithm.h:197
String decoy_string_
Definition: XFDRAlgorithm.h:186
static const String crosslink_class_monolinks_
Definition: XFDRAlgorithm.h:215
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
Int min_score_
Definition: XFDRAlgorithm.h:175
double arg_mindeltas_
Definition: XFDRAlgorithm.h:187
std::vector< double > unique_id_scores_
Definition: XFDRAlgorithm.h:180
static bool isSameProtein_(String prot1, String prot2, const String &decoy_string)
Determines whether the Petide Evidences belong to the same protein, modulo decoy. ...
Definition: XFDRAlgorithm.h:162
ExitCodes
Exit codes.
Definition: XFDRAlgorithm.h:72
double arg_minscore_
Definition: XFDRAlgorithm.h:191
static const String param_mindeltas_
Definition: XFDRAlgorithm.h:200
double arg_binsize_
Definition: XFDRAlgorithm.h:194
static const String crosslink_class_interdecoys_
Definition: XFDRAlgorithm.h:210
static const String crosslink_class_fulldecoysintralinks_
Definition: XFDRAlgorithm.h:209
static Size getMinIonsMatched_(const PeptideHit &ph)
Definition: XFDRAlgorithm.h:142
bool arg_uniquex_
Definition: XFDRAlgorithm.h:192
static void setIntraProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:149
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double arg_minborder_
Definition: XFDRAlgorithm.h:188
static const String param_no_qvalues_
Definition: XFDRAlgorithm.h:203
static const String param_uniquexl_
Definition: XFDRAlgorithm.h:202
Definition: XFDRAlgorithm.h:75
bool arg_no_qvalues_
Definition: XFDRAlgorithm.h:193
static const String param_minborder_
Definition: XFDRAlgorithm.h:198
static const String crosslink_class_hybriddecoysintralinks_
Definition: XFDRAlgorithm.h:218
static void setInterProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:154
static const String crosslink_class_targets_
Definition: XFDRAlgorithm.h:217
static const String crosslink_class_interlinks_
Definition: XFDRAlgorithm.h:214
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
Int max_score_
Definition: XFDRAlgorithm.h:176
static const String crosslink_class_intradecoys_
Definition: XFDRAlgorithm.h:208
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...
static const String crosslink_class_intralinks_
Definition: XFDRAlgorithm.h:213
static const String crosslink_class_monodecoys_
Definition: XFDRAlgorithm.h:212
static const String crosslink_class_decoys_
Definition: XFDRAlgorithm.h:216
static const String param_minscore_
Definition: XFDRAlgorithm.h:204
Int arg_minionsmatched_
Definition: XFDRAlgorithm.h:190
static const String crosslink_class_fulldecoysinterlinks_
Definition: XFDRAlgorithm.h:211
Representation of a peptide hit.
Definition: PeptideHit.h:54
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
static const String param_binsize_
Definition: XFDRAlgorithm.h:205
double arg_maxborder_
Definition: XFDRAlgorithm.h:189
A more convenient string class.
Definition: String.h:58
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
std::map< String, std::vector< String > > cross_link_classes_
Definition: XFDRAlgorithm.h:183
static const String param_minionsmatched_
Definition: XFDRAlgorithm.h:201
static const String crosslink_class_hybriddecoysinterlinks_
Definition: XFDRAlgorithm.h:219
std::vector< String > unique_ids_
Definition: XFDRAlgorithm.h:179
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
Representation of a histogram.
Definition: Histogram.h:63
static const String param_maxborder_
Definition: XFDRAlgorithm.h:199
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Definition: XFDRAlgorithm.h:74
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Calculates false discovery rate estimates on crosslink identifications.
Definition: XFDRAlgorithm.h:65