PercolatorOutfile Class Reference

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

#include <OpenMS/FORMAT/PercolatorOutfile.h>

Classes
struct	PSMInfoExtractor
	Description of how to extract information from PSM IDs. More...
struct	ScanInfo
	Information about a single fragment spectrum. More...

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, enum ScoreType output_score=QVALUE, const String &psm_regex="", bool count_from_zero=false, const MSExperiment<> *experiment_p=0)
	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 Types
typedef std::map< Size, struct ScanInfo >	ScanInfoMap
	Mapping: spectrum index -> fragment spectrum details. More...

Private Member Functions
bool	getPSMInfo_ (const String &PSM_ID, const std::vector< struct PSMInfoExtractor > &extractors, Int &scan_number, Int &charge, double &rt, double &mz)
	Extract information from a Percolator PSM ID. More...
void	getPeptideSequence_ (String peptide, AASequence &seq) const
	Converts the peptide string to an 'AASequence' instance. More...
void	preprocessExperiment_ (const MSExperiment<> &experiment, ScanInfoMap &scan_map)
	Extracts information from the raw data. More...

Private Attributes
std::vector< struct PSMInfoExtractor >	extractors_
	List of data extractors to try by default. More...

Detailed Description

Class for reading Percolator tab-delimited output files.

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

Member Typedef Documentation

typedef std::map<Size, struct ScanInfo> ScanInfoMap

private

Mapping: spectrum index -> fragment spectrum details.

Member Enumeration Documentation

enum ScoreType

Types of Percolator scores.

Enumerator
QVALUE
POSTERRPROB
SCORE
SIZE_OF_SCORETYPE

Constructor & Destructor Documentation

PercolatorOutfile

(

)

Constructor.

Member Function Documentation

void getPeptideSequence_ ( String  peptide, AASequence &  seq  ) const

private

Converts the peptide string to an 'AASequence' instance.

bool getPSMInfo_ ( const String &  PSM_ID, const std::vector< struct PSMInfoExtractor > &  extractors, Int &  scan_number, Int &  charge, double &  rt, double &  mz  )

private

Extract information from a Percolator PSM ID.

Returns

Returns whether extraction was successful

static enum ScoreType getScoreType ( String  score_type_name )

static

Return a score type given its name.

void load	(	const String &	filename,
		ProteinIdentification &	proteins,
		std::vector< PeptideIdentification > &	peptides,
		enum ScoreType	output_score = QVALUE,
		const String &	psm_regex = "",
		bool	count_from_zero = false,
		const MSExperiment<> *	experiment_p = 0
	)

Loads a Percolator output file.

void preprocessExperiment_ ( const MSExperiment<> &  experiment, ScanInfoMap &  scan_map  )

private

Extracts information from the raw data.

Member Data Documentation

std::vector<struct PSMInfoExtractor> extractors_

private

List of data extractors to try by default.

const std::string score_type_names[SIZE_OF_SCORETYPE]

static

Names of Percolator scores (to match ScoreType)