| OpenMS 2.5.0

Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
PeptideEvidence Class Reference
Metadata

Representation of a peptide evidence. More...

`#include <OpenMS/METADATA/PeptideEvidence.h>`

## Public Member Functions

| PeptideEvidence ()
| Constructor. More...
| PeptideEvidence (const String &accession, Int start, Int end, char aa_before, char aa_after)
| Constructor. More...
| PeptideEvidence (const PeptideEvidence &)=default
| Copy constructor. More...
| PeptideEvidence (PeptideEvidence &&) noexcept=default
| Move constructor. More...
| ~PeptideEvidence ()
| Destructor. More...
PeptideEvidence & | operator= (const PeptideEvidence &)=default
| Assignment operator. More...
PeptideEvidence & | operator= (PeptideEvidence &&)=default
| Move assignment operator. More...
bool | operator== (const PeptideEvidence &rhs) const
| Equality operator. More...
bool | operator< (const PeptideEvidence &rhs) const
| Less operator. More...
bool | operator!= (const PeptideEvidence &rhs) const
| not equal More...
bool | hasValidLimits () const
| start and end numbers in evidence represent actual numeric indices More...
const String & | getProteinAccession () const
| get the protein accession the peptide matches to. If not available the empty string is returned. More...
void | setProteinAccession (const String &s)
| set the protein accession the peptide matches to. If not available set to empty string. More...
void | setStart (const Int a)
| set the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available, set to UNKNOWN_POSITION. N-terminal positions must be marked with N_TERMINAL_AA More...
Int | getStart () const
| get the position in the protein (starting at 0 for the N-terminus). If not available UNKNOWN_POSITION constant is returned. More...
void | setEnd (const Int a)
| set the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available, set UNKNOWN_POSITION. C-terminal positions must be marked with C_TERMINAL_AA More...
Int | getEnd () const
| get the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available UNKNOWN_POSITION constant is returned. More...
void | setAABefore (const char acid)
| sets the amino acid single letter code before the sequence (preceding amino acid in the protein). If not available, set to UNKNOWN_AA. If N-terminal set to N_TERMINAL_AA More...
char | getAABefore () const
| returns the amino acid single letter code before the sequence (preceding amino acid in the protein). If not available, UNKNOWN_AA is returned. If N-terminal, N_TERMINAL_AA is returned. More...
void | setAAAfter (const char acid)
| sets the amino acid single letter code after the sequence (subsequent amino acid in the protein). If not available, set to UNKNOWN_AA. If C-terminal set to C_TERMINAL_AA More...
char | getAAAfter () const
| returns the amino acid single letter code after the sequence (subsequent amino acid in the protein). If not available, UNKNOWN_AA is returned. If C-terminal, C_TERMINAL_AA is returned. More...

## Static Public Attributes

static const int | UNKNOWN_POSITION
static const int | N_TERMINAL_POSITION
static const char | UNKNOWN_AA
static const char | N_TERMINAL_AA
static const char | C_TERMINAL_AA

## Protected Attributes

String | accession_
Int | start_
Int | end_
char | aa_before_
char | aa_after_

## Detailed Description

Representation of a peptide evidence.

A peptide evidence object describes a single peptide to protein match.

## Constructor & Destructor Documentation

## ◆ PeptideEvidence() [1/4]

PeptideEvidence | ( |  | ) |

Constructor.

## ◆ PeptideEvidence() [2/4]

PeptideEvidence | ( | const String & | accession,
|  | Int | start,
|  | Int | end,
|  | char | aa_before,
|  | char | aa_after
| ) |  |

Constructor.

## ◆ PeptideEvidence() [3/4]

PeptideEvidence | ( | const PeptideEvidence & |  | ) |

default

Copy constructor.

## ◆ PeptideEvidence() [4/4]

PeptideEvidence | ( | PeptideEvidence && |  | ) |

default noexcept

Move constructor.

## ◆ ~PeptideEvidence()

~PeptideEvidence | ( |  | ) |

inline

Destructor.

## Member Function Documentation

## ◆ getAAAfter()

char getAAAfter | ( |  | ) | const

returns the amino acid single letter code after the sequence (subsequent amino acid in the protein). If not available, UNKNOWN_AA is returned. If C-terminal, C_TERMINAL_AA is returned.

## ◆ getAABefore()

char getAABefore | ( |  | ) | const

returns the amino acid single letter code before the sequence (preceding amino acid in the protein). If not available, UNKNOWN_AA is returned. If N-terminal, N_TERMINAL_AA is returned.

## ◆ getEnd()

Int getEnd | ( |  | ) | const

get the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available UNKNOWN_POSITION constant is returned.

Referenced by IDFilter::DigestionFilter::operator()().

## ◆ getProteinAccession()

const String& getProteinAccession | ( |  | ) | const

get the protein accession the peptide matches to. If not available the empty string is returned.

Referenced by IDFilter::GetMatchingItems< OpenMS::PeptideEvidence, OpenMS::FASTAFile::FASTAEntry >::getHitKey(), PercolatorFeatureSetHelper::lq_PeptideEvidence::operator()(), IDFilter::HasMatchingAccessionUnordered< HitType >::operator()(), IDFilter::HasMatchingAccession< HitType >::operator()(), and IDFilter::DigestionFilter::operator()().

## ◆ getStart()

Int getStart | ( |  | ) | const

get the position in the protein (starting at 0 for the N-terminus). If not available UNKNOWN_POSITION constant is returned.

Referenced by IDFilter::DigestionFilter::operator()().

## ◆ hasValidLimits()

bool hasValidLimits | ( |  | ) | const

start and end numbers in evidence represent actual numeric indices

Referenced by IDFilter::DigestionFilter::operator()().

## ◆ operator!=()

bool operator!= | ( | const PeptideEvidence & | rhs | ) | const

not equal

## ◆ operator<()

bool operator< | ( | const PeptideEvidence & | rhs | ) | const

Less operator.

## ◆ operator=() [1/2]

PeptideEvidence& operator= | ( | const PeptideEvidence & |  | ) |

default

Assignment operator.

## ◆ operator=() [2/2]

PeptideEvidence& operator= | ( | PeptideEvidence && |  | ) |

default

Move assignment operator.

## ◆ operator==()

bool operator== | ( | const PeptideEvidence & | rhs | ) | const

Equality operator.

## ◆ setAAAfter()

void setAAAfter | ( | const char | acid | ) |

sets the amino acid single letter code after the sequence (subsequent amino acid in the protein). If not available, set to UNKNOWN_AA. If C-terminal set to C_TERMINAL_AA

## ◆ setAABefore()

void setAABefore | ( | const char | acid | ) |

sets the amino acid single letter code before the sequence (preceding amino acid in the protein). If not available, set to UNKNOWN_AA. If N-terminal set to N_TERMINAL_AA

## ◆ setEnd()

void setEnd | ( | const Int | a | ) |

set the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available, set UNKNOWN_POSITION. C-terminal positions must be marked with C_TERMINAL_AA

## ◆ setProteinAccession()

void setProteinAccession | ( | const String & | s | ) |

set the protein accession the peptide matches to. If not available set to empty string.

## ◆ setStart()

void setStart | ( | const Int | a | ) |

set the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-terminus). If not available, set to UNKNOWN_POSITION. N-terminal positions must be marked with N_TERMINAL_AA

## Member Data Documentation

## ◆ aa_after_

char aa_after_

protected

## ◆ aa_before_

char aa_before_

protected

## ◆ accession_

String accession_

protected

## ◆ C_TERMINAL_AA

const char C_TERMINAL_AA

static

Referenced by PeptideIndexing::FoundProteinFunctor::addHit().

## ◆ end_

Int end_

protected

## ◆ N_TERMINAL_AA

const char N_TERMINAL_AA

static

Referenced by PeptideIndexing::FoundProteinFunctor::addHit().

## ◆ N_TERMINAL_POSITION

const int N_TERMINAL_POSITION

static

## ◆ start_

Int start_

protected

## ◆ UNKNOWN_AA

const char UNKNOWN_AA

static

## ◆ UNKNOWN_POSITION

const int UNKNOWN_POSITION

static