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OpenMS
2.6.0
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73 void rip(std::map<
String, std::pair<std::vector<ProteinIdentification>, std::vector<PeptideIdentification> > > & ripped, std::vector<ProteinIdentification> & proteins, std::vector<PeptideIdentification> & peptides);
86 void getProteinHits_(std::vector<ProteinHit> & result,
const std::vector<ProteinHit> & protein_hits,
const std::vector<String> & protein_accessions);
88 void getProteinAccessions_(std::vector<String> & result,
const std::vector<PeptideHit> & peptide_hits);
static std::map< String, std::vector< std::vector< double > > > extractAndTransformScores(const std::vector< ProteinIdentification > &protein_ids, const std::vector< PeptideIdentification > &peptide_ids, const bool split_charge, const bool top_hits_only, const bool target_decoy_available, const double fdr_for_targets_smaller)
extract and transform score types to a range and score orientation that the PEP model can handle
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void store(const 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.
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
A more convenient string class.
Definition: String.h:59
Precondition failed exception.
Definition: Exception.h:166
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
String toString(bool full_precision=true) const
Conversion to String full_precision Controls number of fractional digits for all double types or list...
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
static bool writable(const String &file)
Return true if the file is writable.
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
Ripping protein/peptide identification according their file origin.
Definition: IDRipper.h:52
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool exists(const String &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
static void updateScores(const PosteriorErrorProbabilityModel &PEP_model, const String &search_engine, const Int charge, const bool prob_correct, const bool split_charge, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids, bool &unable_to_fit_data, bool &data_might_not_be_well_fit)
update score entries with PEP (or 1-PEP) estimates
bool split(const char splitter, std::vector< String > &substrings, bool quote_protect=false) const
Splits a string into substrings using splitter as delimiter.
void setParameters(const Param ¶m)
Sets the parameters.
QString toQString() const
Conversion to Qt QString.
const Param & getParameters() const
Non-mutable access to the parameters.
bool fit(std::vector< double > &search_engine_scores, const String &outlier_handling)
fits the distributions to the data points(search_engine_scores). Estimated parameters for the distrib...
void rip(std::map< String, std::pair< std::vector< ProteinIdentification >, std::vector< PeptideIdentification > > > &ripped, std::vector< ProteinIdentification > &proteins, std::vector< PeptideIdentification > &peptides)
Ripping protein/peptide identification according their file origin.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void plotTargetDecoyEstimation(std::vector< double > &target, std::vector< double > &decoy)
plots the estimated distribution against target and decoy hits
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
Management and storage of parameters / INI files.
Definition: Param.h:73
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
Implements a mixture model of the inverse gumbel and the gauss distribution or a gaussian mixture.
Definition: PosteriorErrorProbabilityModel.h:73
Used to load and store idXML files.
Definition: IdXMLFile.h:63