ProteinHit Class Reference

Representation of a protein hit. More...

#include <OpenMS/METADATA/ProteinHit.h>

Inheritance diagram for ProteinHit:

Classes
class	ScoreLess
	Lesser predicate for scores of hits. More...
class	ScoreMore
	Greater predicate for scores of hits. More...

Public Member Functions
ProteinHit &	operator= (const ProteinHit &source)
	assignment operator More...
ProteinHit &	operator= (const MetaInfoInterface &source)
	assignment for MetaInfo More...
bool	operator== (const ProteinHit &rhs) const
	Equality operator. More...
bool	operator!= (const ProteinHit &rhs) const
	Inequality operator. More...
Constructors and Destructor
	ProteinHit ()
	default constructor More...
	ProteinHit (double score, UInt rank, String accession, String sequence)
	values constructor More...
	ProteinHit (const ProteinHit &source)
	copy constructor More...
virtual	~ProteinHit ()
	destructor More...
Accessors
float	getScore () const
	returns the score of the protein hit More...
UInt	getRank () const
	returns the rank of the protein hit More...
const String &	getSequence () const
	returns the protein sequence More...
const String &	getAccession () const
	returns the accession of the protein More...
String	getDescription () const
	returns the description of the protein More...
double	getCoverage () const
	returns the coverage (in percent) of the protein hit based upon matched peptides More...
void	setScore (const double score)
	sets the score of the protein hit More...
void	setRank (UInt newrank)
	sets the rank More...
void	setSequence (const String &sequence)
	sets the protein sequence More...
void	setAccession (const String &accession)
	sets the accession of the protein More...
void	setDescription (const String &description)
	sets the description of the protein More...
void	setCoverage (const double coverage)
	sets the coverage (in percent) of the protein hit based upon matched peptides 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...

Static Public Attributes
static const double	COVERAGE_UNKNOWN

Protected Attributes
float	score_
	the score of the protein hit More...
UInt	rank_
	the position(rank) where the hit appeared in the hit list More...
String	accession_
	the protein identifier More...
String	sequence_
	the amino acid sequence of the protein hit More...
double	coverage_
	coverage of the protein based upon the matched peptide sequences 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 protein hit.

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

Constructor & Destructor Documentation

ProteinHit() [1/3]

ProteinHit

(

)

default constructor

ProteinHit() [2/3]

ProteinHit	(	double	score,
		UInt	rank,
		String	accession,
		String	sequence
	)

values constructor

ProteinHit() [3/3]

ProteinHit

(

const ProteinHit &

source

)

copy constructor

~ProteinHit()

virtual ~ProteinHit ( )

virtual

destructor

Member Function Documentation

getAccession()

const String& getAccession

(

)

const

returns the accession of the protein

Referenced by PercolatorFeatureSetHelper::lq_ProteinHit::operator()(), and IDFilter::HasMatchingAccession< HitType >::operator()().

getCoverage()

double getCoverage

(

)

const

returns the coverage (in percent) of the protein hit based upon matched peptides

getDescription()

String getDescription

(

)

const

returns the description of the protein

getRank()

UInt getRank

(

)

const

returns the rank of the protein hit

getScore()

float getScore

(

)

const

returns the score of the protein hit

getSequence()

const String& getSequence

(

)

const

returns the protein sequence

operator!=()

bool operator!=

(

const ProteinHit &

rhs

)

const

Inequality operator.

operator=() [1/2]

ProteinHit& operator=

(

const ProteinHit &

source

)

assignment operator

operator=() [2/2]

ProteinHit& operator=

(

const MetaInfoInterface &

source

)

assignment for MetaInfo

operator==()

bool operator==

(

const ProteinHit &

rhs

)

const

Equality operator.

setAccession()

void setAccession

(

const String &

accession

)

sets the accession of the protein

Referenced by PeptideIndexing::run().

setCoverage()

void setCoverage

(

const double

coverage

)

sets the coverage (in percent) of the protein hit based upon matched peptides

setDescription()

void setDescription

(

const String &

description

)

sets the description of the protein

Referenced by PeptideIndexing::run().

setRank()

void setRank

(

UInt

newrank

)

sets the rank

setScore()

void setScore

(

const double

score

)

sets the score of the protein hit

setSequence()

void setSequence

(

const String &

sequence

)

sets the protein sequence

Referenced by PeptideIndexing::run().

Member Data Documentation

accession_

String accession_

protected

the protein identifier

coverage_

double coverage_

protected

coverage of the protein based upon the matched peptide sequences

COVERAGE_UNKNOWN

const double COVERAGE_UNKNOWN

static

rank_

UInt rank_

protected

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

score_

float score_

protected

the score of the protein hit

sequence_

String sequence_

protected

the amino acid sequence of the protein hit