PeptideEvidence Class Reference

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 &source)
	copy constructor More...
	~PeptideEvidence ()
	destructor More...
PeptideEvidence &	operator= (const PeptideEvidence &source)
	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() [1/3]

PeptideEvidence

(

)

constructor

PeptideEvidence() [2/3]

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

constructor

PeptideEvidence() [3/3]

PeptideEvidence

(

const PeptideEvidence &

source

)

copy 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::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=()

PeptideEvidence& operator=

(

const PeptideEvidence &

source

)

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