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OpenMS
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77 void apply(std::vector<PeptideIdentification> & fwd_ids, std::vector<PeptideIdentification> & rev_ids)
const;
84 void apply(std::vector<PeptideIdentification> &
id)
const;
92 void apply(std::vector<ProteinIdentification> & fwd_ids, std::vector<ProteinIdentification> & rev_ids)
const;
100 void apply(std::vector<ProteinIdentification> & ids)
const;
110 void calculateFDRs_(
Map<double, double> & score_to_fdr, std::vector<double> & target_scores, std::vector<double> & decoy_scores,
bool q_value,
bool higher_score_better)
const;
Base class for TOPP applications.
Definition: TOPPBase.h:150
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void apply(std::vector< PeptideIdentification > &fwd_ids, std::vector< PeptideIdentification > &rev_ids) const
Calculates the FDR of two runs, a forward run and a decoy run on peptide level.
A more convenient string class.
Definition: String.h:57
static void updateProteinReferences(std::vector< PeptideIdentification > &peptides, const std::vector< ProteinIdentification > &proteins, bool remove_peptides_without_reference=false)
Removes references to missing proteins.
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
static bool updateProteinGroups(std::vector< ProteinIdentification::ProteinGroup > &groups, const std::vector< ProteinHit > &hits)
Update protein groups after protein hits were filtered.
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
static void removeUnreferencedProteins(std::vector< ProteinIdentification > &proteins, const std::vector< PeptideIdentification > &peptides)
Removes protein hits from proteins that are not referenced by a peptide in peptides.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
#define LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:450
#define LOG_FATAL_ERROR
Macro to be used if fatal error are reported (processing stops)
Definition: LogStream.h:442
static void updateHitRanks(std::vector< IdentificationType > &ids)
Updates the hit ranks on all peptide or protein IDs.
Definition: IDFilter.h:636
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
static Size countHits(const std::vector< IdentificationType > &ids)
Returns the total number of peptide/protein hits in a vector of peptide/protein identifications.
Definition: IDFilter.h:514
Calculates an FDR from identifications.
Definition: FalseDiscoveryRate.h:64
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void store(String filename, const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const String &document_id="")
Stores the data in an idXML file.
static void removeEmptyIdentifications(std::vector< IdentificationType > &ids)
Removes peptide or protein identifications that have no hits in them.
Definition: IDFilter.h:682
Management and storage of parameters / INI files.
Definition: Param.h:74
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
static void filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)
Filters peptide or protein identifications according to the score of the hits.
Definition: IDFilter.h:694
Used to load and store idXML files.
Definition: IdXMLFile.h:63