OpenMS
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< PeptideIdentificationload (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