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, 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. 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 Int	getScanNumber_ (const String &scan_identifier)
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

getScanNumber_()

static Int getScanNumber_ ( const String &  scan_identifier )

staticprotected

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, 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.

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