| OpenMS 2.5.0

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>`

## 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)