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OpenMS
2.6.0
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97 ExitCodes validateClassArguments()
const;
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;
static const String param_maxborder_
Definition: XFDRAlgorithm.h:199
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
static const String param_mindeltas_
Definition: XFDRAlgorithm.h:200
Base class for TOPP applications.
Definition: TOPPBase.h:144
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a MzIdentML file.
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.
double arg_minscore_
Definition: XFDRAlgorithm.h:191
bool arg_uniquex_
Definition: XFDRAlgorithm.h:192
String & substitute(char from, char to)
Replaces all occurrences of the character from by the character to.
static const String crosslink_class_intradecoys_
Definition: XFDRAlgorithm.h:208
void load(const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
Load the content of the xquest.xml file into the provided data structures.
static const String crosslink_class_monolinks_
Definition: XFDRAlgorithm.h:215
A more convenient string class.
Definition: String.h:59
std::vector< String > unique_ids_
Definition: XFDRAlgorithm.h:179
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static const String param_minborder_
Definition: XFDRAlgorithm.h:198
double arg_minborder_
Definition: XFDRAlgorithm.h:188
double arg_maxborder_
Definition: XFDRAlgorithm.h:189
double arg_binsize_
Definition: XFDRAlgorithm.h:194
double arg_mindeltas_
Definition: XFDRAlgorithm.h:187
Definition: XFDRAlgorithm.h:75
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:77
static Size getMinIonsMatched_(const PeptideHit &ph)
Definition: XFDRAlgorithm.h:142
Calculates false discovery rate estimates on crosslink identifications.
Definition: XFDRAlgorithm.h:65
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
bool arg_no_qvalues_
Definition: XFDRAlgorithm.h:193
ExitCodes run(std::vector< PeptideIdentification > &peptide_ids, ProteinIdentification &protein_id)
Performs the main function of this class, the FDR estimation for cross-linked peptide experiments.
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
Int max_score_
Definition: XFDRAlgorithm.h:176
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
ExitCodes
Exit codes.
Definition: XFDRAlgorithm.h:72
Int min_score_
Definition: XFDRAlgorithm.h:175
static const String param_decoy_string_
Definition: XFDRAlgorithm.h:197
File adapter for MzIdentML files.
Definition: MzIdentMLFile.h:67
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Representation of a histogram.
Definition: Histogram.h:63
ExitCodes validateClassArguments() const
Checks whether the parameters of the object are valid.
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
static const String crosslink_class_decoys_
Definition: XFDRAlgorithm.h:216
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
Int arg_minionsmatched_
Definition: XFDRAlgorithm.h:190
static const String crosslink_class_hybriddecoysintralinks_
Definition: XFDRAlgorithm.h:218
static const String crosslink_class_fulldecoysintralinks_
Definition: XFDRAlgorithm.h:209
static const String crosslink_class_interlinks_
Definition: XFDRAlgorithm.h:214
Type
Actual file types enum.
Definition: FileTypes.h:58
xQuest XML file format for protein-protein cross-link identifications (.xquest.xml)
Definition: FileTypes.h:112
static const String param_minionsmatched_
Definition: XFDRAlgorithm.h:201
std::vector< double > unique_id_scores_
Definition: XFDRAlgorithm.h:180
static const String crosslink_class_interdecoys_
Definition: XFDRAlgorithm.h:210
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
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
void setParameters(const Param ¶m)
Sets the parameters.
static const String crosslink_class_monodecoys_
Definition: XFDRAlgorithm.h:212
const Param & getParameters() const
Non-mutable access to the parameters.
Definition: XFDRAlgorithm.h:74
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void load(const String &filename, std::vector< ProteinIdentification > &poid, std::vector< PeptideIdentification > &peid)
Loads the identifications from a MzIdentML file.
static const String param_binsize_
Definition: XFDRAlgorithm.h:205
static const String param_minscore_
Definition: XFDRAlgorithm.h:204
static void setIntraProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:149
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
std::map< String, std::vector< String > > cross_link_classes_
Definition: XFDRAlgorithm.h:183
bool update(const Param &p_outdated, const bool add_unknown=false)
Rescue parameter values from p_outdated to current param.
static const String crosslink_class_hybriddecoysinterlinks_
Definition: XFDRAlgorithm.h:219
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
static const String crosslink_class_intralinks_
Definition: XFDRAlgorithm.h:213
static const String param_no_qvalues_
Definition: XFDRAlgorithm.h:203
static const String crosslink_class_fulldecoysinterlinks_
Definition: XFDRAlgorithm.h:211
static void setInterProtein_(PeptideHit &ph, const bool value)
Definition: XFDRAlgorithm.h:154
Management and storage of parameters / INI files.
Definition: Param.h:73
int getNumberOfHits() const
Returns the total number of hits in the file.
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:53
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
String decoy_string_
Definition: XFDRAlgorithm.h:186
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
static const String param_uniquexl_
Definition: XFDRAlgorithm.h:202
Used to load and store idXML files.
Definition: IdXMLFile.h:63
static const String crosslink_class_targets_
Definition: XFDRAlgorithm.h:217
Representation of a peptide hit.
Definition: PeptideHit.h:55