PeptideHit Class Reference

Representation of a peptide hit. More...

#include <OpenMS/METADATA/PeptideHit.h>

Inheritance diagram for PeptideHit:

Classes
struct	PeakAnnotation
	Contains annotations of a peak. More...
class	PepXMLAnalysisResult
	Analysis Result (containing search engine / prophet results) More...
class	RankLess
	Lesser predicate for scores of hits. More...
class	ScoreLess
	Lesser predicate for scores of hits. More...
class	ScoreMore
	Greater predicate for scores of hits. More...
class	SequenceLessComparator
	Lesser predicate for (modified) sequence of hits. More...

Public Member Functions
PeptideHit &	operator= (const PeptideHit &source)
	assignment operator More...
bool	operator== (const PeptideHit &rhs) const
	Equality operator. More...
bool	operator!= (const PeptideHit &rhs) const
	Inequality operator. More...
std::set< String >	extractProteinAccessionsSet () const
	extracts the set of non-empty protein accessions from peptide evidences More...
Constructors and Destructor
	PeptideHit ()
	default constructor More...
	PeptideHit (double score, UInt rank, Int charge, const AASequence &sequence)
	values constructor More...
	PeptideHit (const PeptideHit &source)
	copy constructor More...
virtual	~PeptideHit ()
	destructor More...
Accessors
const AASequence &	getSequence () const
	returns the peptide sequence without trailing or following spaces More...
void	setSequence (const AASequence &sequence)
	sets the peptide sequence More...
Int	getCharge () const
	returns the charge of the peptide More...
void	setCharge (Int charge)
	sets the charge of the peptide More...
const std::vector< PeptideEvidence > &	getPeptideEvidences () const
	returns information on peptides (potentially) identified by this PSM More...
void	setPeptideEvidences (const std::vector< PeptideEvidence > &peptide_evidences)
	set information on peptides (potentially) identified by this PSM More...
void	addPeptideEvidence (const PeptideEvidence &peptide_evidence)
	adds information on a peptide that is (potentially) identified by this PSM More...
double	getScore () const
	returns the PSM score More...
void	setScore (double score)
	sets the PSM score More...
void	setAnalysisResults (std::vector< PepXMLAnalysisResult > aresult)
	set information on (search engine) sub scores associated with this PSM More...
void	addAnalysisResults (PepXMLAnalysisResult aresult)
	add information on (search engine) sub scores associated with this PSM More...
const std::vector< PepXMLAnalysisResult > &	getAnalysisResults () const
	returns information on (search engine) sub scores associated with this PSM More...
UInt	getRank () const
	returns the PSM rank More...
void	setRank (UInt newrank)
	sets the PSM rank More...
std::vector< PeptideHit::PeakAnnotation >	getPeakAnnotations () const
	returns the fragment annotations More...
void	setPeakAnnotations (std::vector< PeptideHit::PeakAnnotation > frag_annotations)
	sets the fragment annotations More...
Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...
	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...
	~MetaInfoInterface ()
	Destructor. More...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...
bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...
const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...
const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or DataValue::EMPTY if not found) More...
bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...
bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...
void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...
void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...
void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to name if it exists. More...
void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to index if it exists. More...
void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...
bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...
void	clearMetaInfo ()
	Removes all meta values. More...

Protected Attributes
AASequence	sequence_
double	score_
	the score of the peptide hit More...
std::vector< PepXMLAnalysisResult > *	analysis_results_
	additional scores attached to the original, aggregated score More...
UInt	rank_
	the position(rank) where the hit appeared in the hit list More...
Int	charge_
	the charge of the peptide More...
std::vector< PeptideEvidence >	peptide_evidences_
	information on the potential peptides observed through this PSM. More...
std::vector< PeptideHit::PeakAnnotation >	fragment_annotations_
	annotations of fragments in the corresponding spectrum More...
Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...
Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Detailed Description

Representation of a peptide hit.

It contains the fields score, score_type, rank, and sequence.

Constructor & Destructor Documentation

PeptideHit() [1/3]

PeptideHit

(

)

default constructor

PeptideHit() [2/3]

PeptideHit	(	double	score,
		UInt	rank,
		Int	charge,
		const AASequence &	sequence
	)

values constructor

PeptideHit() [3/3]

PeptideHit

(

const PeptideHit &

source

)

copy constructor

~PeptideHit()

virtual ~PeptideHit ( )

virtual

destructor

Member Function Documentation

addAnalysisResults()

void addAnalysisResults

(

PepXMLAnalysisResult

aresult

)

add information on (search engine) sub scores associated with this PSM

addPeptideEvidence()

void addPeptideEvidence

(

const PeptideEvidence &

peptide_evidence

)

adds information on a peptide that is (potentially) identified by this PSM

extractProteinAccessionsSet()

std::set<String> extractProteinAccessionsSet

(

)

const

extracts the set of non-empty protein accessions from peptide evidences

Referenced by TOPPMetaProSIP::main_(), and IDFilter::HasMatchingAccession< HitType >::operator()().

getAnalysisResults()

const std::vector<PepXMLAnalysisResult>& getAnalysisResults

(

)

const

returns information on (search engine) sub scores associated with this PSM

getCharge()

Int getCharge

(

)

const

returns the charge of the peptide

Referenced by TOPPMetaProSIP::main_().

getPeakAnnotations()

std::vector<PeptideHit::PeakAnnotation> getPeakAnnotations

(

)

const

returns the fragment annotations

getPeptideEvidences()

const std::vector<PeptideEvidence>& getPeptideEvidences

(

)

const

returns information on peptides (potentially) identified by this PSM

getRank()

UInt getRank

(

)

const

returns the PSM rank

getScore()

double getScore

(

)

const

returns the PSM score

Referenced by TOPPMetaProSIP::main_(), and RNPxlSearch::postProcessHits_().

getSequence()

const AASequence& getSequence

(

)

const

returns the peptide sequence without trailing or following spaces

Referenced by TOPPMetaProSIP::main_(), IDFilter::PeptideDigestionFilter::operator()(), and IDConflictResolverAlgorithm::resolveBetweenFeatures_().

operator!=()

bool operator!=

(

const PeptideHit &

rhs

)

const

Inequality operator.

operator=()

PeptideHit& operator=

(

const PeptideHit &

source

)

assignment operator

operator==()

bool operator==

(

const PeptideHit &

rhs

)

const

Equality operator.

setAnalysisResults()

void setAnalysisResults

(

std::vector< PepXMLAnalysisResult >

aresult

)

set information on (search engine) sub scores associated with this PSM

setCharge()

void setCharge

(

Int

charge

)

sets the charge of the peptide

Referenced by TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

setPeakAnnotations()

void setPeakAnnotations

(

std::vector< PeptideHit::PeakAnnotation >

frag_annotations

)

sets the fragment annotations

Referenced by RNPxlSearch::postProcessHits_().

setPeptideEvidences()

void setPeptideEvidences

(

const std::vector< PeptideEvidence > &

peptide_evidences

)

set information on peptides (potentially) identified by this PSM

setRank()

void setRank

(

UInt

newrank

)

sets the PSM rank

setScore()

void setScore

(

double

score

)

sets the PSM score

Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

setSequence()

void setSequence

(

const AASequence &

sequence

)

sets the peptide sequence

Referenced by TOPPMetaProSIP::main_(), SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().

Member Data Documentation

analysis_results_

std::vector<PepXMLAnalysisResult>* analysis_results_

protected

additional scores attached to the original, aggregated score

charge_

Int charge_

protected

the charge of the peptide

fragment_annotations_

std::vector<PeptideHit::PeakAnnotation> fragment_annotations_

protected

annotations of fragments in the corresponding spectrum

peptide_evidences_

std::vector<PeptideEvidence> peptide_evidences_

protected

information on the potential peptides observed through this PSM.

rank_

UInt rank_

protected

the position(rank) where the hit appeared in the hit list

score_

double score_

protected

the score of the peptide hit

sequence_

AASequence sequence_

protected