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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 ScanInfoScanInfoMap
 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 PSMInfoExtractorextractors_
 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

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)


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:54:05 using doxygen 1.8.9.1