OpenMS  2.8.0
Public Types | Public Member Functions | Static Public Member Functions | Static Public Attributes | Private Member Functions | List of all members
PercolatorOutfile Class Reference

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

#include <OpenMS/FORMAT/PercolatorOutfile.h>

Collaboration diagram for PercolatorOutfile:
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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()

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)