PercolatorOutfile Class Reference

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

#include <OpenMS/FORMAT/PercolatorOutfile.h>

Collaboration diagram for PercolatorOutfile:

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

Public Member Functions
	PercolatorOutfile ()
	Constructor.
void	load (const std::string &filename, ProteinIdentification &proteins, PeptideIdentificationList &peptides, SpectrumMetaDataLookup &lookup, ScoreType output_score=ScoreType::QVALUE)
	Loads a Percolator output file.

Static Public Member Functions
static ScoreType	getScoreType (std::string score_type_name)
	Return a score type given its name.

Static Public Attributes
static const std::string	score_type_names [static_cast< size_t >(ScoreType::SIZE_OF_SCORETYPE)]
	Names of Percolator scores (to match ScoreType)

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

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 class ScoreType

strong

Types of Percolator scores.

Enumerator
QVALUE
POSTERRPROB
SCORE
SIZE_OF_SCORETYPE

Constructor & Destructor Documentation

PercolatorOutfile()

PercolatorOutfile

(

)

Constructor.

Member Function Documentation

getPeptideSequence_()

void getPeptideSequence_ ( std::string  peptide, AASequence &  seq  ) const

private

Converts the peptide string to an 'AASequence' instance.

getScoreType()

static ScoreType getScoreType ( std::string  score_type_name )

static

Return a score type given its name.

load()

void load	(	const std::string &	filename,
		ProteinIdentification &	proteins,
		PeptideIdentificationList &	peptides,
		SpectrumMetaDataLookup &	lookup,
		ScoreType	output_score = ScoreType::QVALUE
	)

Loads a Percolator output file.

resolveMisassignedNTermMods_()

void resolveMisassignedNTermMods_ ( std::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[static_cast< size_t >(ScoreType::SIZE_OF_SCORETYPE)]

static

Names of Percolator scores (to match ScoreType)