PercolatorOutfile Class Reference

Class for reading Percolator tab-delimited output files. More...

#include <OpenMS/FORMAT/PercolatorOutfile.h>

Collaboration diagram for PercolatorOutfile:

Public Types
enum	ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE }
	Types of Percolator scores. More...

Public Member Functions
	PercolatorOutfile ()
	Constructor. More...
void	load (const String &filename, ProteinIdentification &proteins, std::vector< PeptideIdentification > &peptides, SpectrumMetaDataLookup &lookup, enum ScoreType output_score=QVALUE)
	Loads a Percolator output file. More...

Static Public Member Functions
static enum ScoreType	getScoreType (String score_type_name)
	Return a score type given its name. More...

Static Public Attributes
static const std::string	score_type_names [SIZE_OF_SCORETYPE]
	Names of Percolator scores (to match ScoreType) More...

Private Member Functions
void	getPeptideSequence_ (String peptide, AASequence &seq) const
	Converts the peptide string to an 'AASequence' instance. More...
void	resolveMisassignedNTermMods_ (String &peptide) const
	Resolve cases where N-terminal modifications may be misassigned to the first residue (for X! Tandem results) More...

Detailed Description

Class for reading Percolator tab-delimited output files.

For PSM-level output, the file extension should be ".psms".

Member Enumeration Documentation

ScoreType

enum ScoreType

Types of Percolator scores.

Enumerator
QVALUE
POSTERRPROB
SCORE
SIZE_OF_SCORETYPE

Constructor & Destructor Documentation

PercolatorOutfile()

PercolatorOutfile

(

)

Constructor.

Member Function Documentation

getPeptideSequence_()

void getPeptideSequence_ ( String  peptide, AASequence &  seq  ) const

private

Converts the peptide string to an 'AASequence' instance.

getScoreType()

static enum ScoreType getScoreType ( String  score_type_name )

static

Return a score type given its name.

load()

void load	(	const String &	filename,
		ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		SpectrumMetaDataLookup &	lookup,
		enum ScoreType	output_score = QVALUE
	)

Loads a Percolator output file.

resolveMisassignedNTermMods_()

void resolveMisassignedNTermMods_ ( String &  peptide ) const

private

Resolve cases where N-terminal modifications may be misassigned to the first residue (for X! Tandem results)

Member Data Documentation

score_type_names

const std::string score_type_names[SIZE_OF_SCORETYPE]

static

Names of Percolator scores (to match ScoreType)