PercolatorInfile Class Reference

Class for storing Percolator tab-delimited input files. More...

#include <OpenMS/FORMAT/PercolatorInfile.h>

Static Public Member Functions
static void	store (const String &pin_file, const std::vector< PeptideIdentification > &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)
static std::vector< PeptideIdentification >	load (const String &pin_file, bool higher_score_better, const String &score_name, const StringList &extra_scores, StringList &filenames, String decoy_prefix="")
	load pin file and convert to a vector of PeptideIdentification using the given score column score_name and orientation higher_score_better. If a decoy prefix is provided, the decoy status is set from the protein accessions. Otherwise, it assumes that the pin file already contains the correctly annotated decoy status. If extra_scores is not empty, the scores are added to the PeptideHit as MetaValues. If a filename column is encountered the set of filenames is filled in the order of appearance and PeptideIdentifications annotated with the id_merge_index meta value to link them to the filename (similar to a merged idXML file). TODO: implement something similar to PepXMLFile().setPreferredFixedModifications(getModifications_(fixed_modifications_names)); More...
static String	getScanIdentifier (const PeptideIdentification &pid, size_t index)

Static Protected Member Functions
static TextFile	preparePin_ (const std::vector< PeptideIdentification > &peptide_ids, const StringList &feature_set, const std::string &enz, int min_charge, int max_charge)
static bool	isEnz_ (const char &n, const char &c, const std::string &enz)
static Size	countEnzymatic_ (const String &peptide, const std::string &enz)

Detailed Description

Class for storing Percolator tab-delimited input files.

Member Function Documentation

countEnzymatic_()

static Size countEnzymatic_ ( const String &  peptide, const std::string &  enz  )

staticprotected

getScanIdentifier()

static String getScanIdentifier ( const PeptideIdentification &  pid, size_t  index  )

static

isEnz_()

static bool isEnz_ ( const char &  n, const char &  c, const std::string &  enz  )

staticprotected

load()

static std::vector<PeptideIdentification> load ( const String &  pin_file, bool  higher_score_better, const String &  score_name, const StringList &  extra_scores, StringList &  filenames, String  decoy_prefix = ""  )

static

load pin file and convert to a vector of PeptideIdentification using the given score column score_name and orientation higher_score_better. If a decoy prefix is provided, the decoy status is set from the protein accessions. Otherwise, it assumes that the pin file already contains the correctly annotated decoy status. If extra_scores is not empty, the scores are added to the PeptideHit as MetaValues. If a filename column is encountered the set of filenames is filled in the order of appearance and PeptideIdentifications annotated with the id_merge_index meta value to link them to the filename (similar to a merged idXML file). TODO: implement something similar to PepXMLFile().setPreferredFixedModifications(getModifications_(fixed_modifications_names));

preparePin_()

static TextFile preparePin_ ( const std::vector< PeptideIdentification > &  peptide_ids, const StringList &  feature_set, const std::string &  enz, int  min_charge, int  max_charge  )

staticprotected

store()

static void store ( const String &  pin_file, const std::vector< PeptideIdentification > &  peptide_ids, const StringList &  feature_set, const std::string &  enz, int  min_charge, int  max_charge  )

static